Starting phenix.real_space_refine on Sun Jul 21 15:10:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2t_40987/07_2024/8t2t_40987_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2t_40987/07_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_40987/07_2024/8t2t_40987.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2t_40987/07_2024/8t2t_40987.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2t_40987/07_2024/8t2t_40987_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2t_40987/07_2024/8t2t_40987_neut.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 Residue "D TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 33": "OD1" <-> "OD2" Residue "D PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 104": "OE1" <-> "OE2" Residue "D ASP 139": "OD1" <-> "OD2" Residue "D GLU 209": "OE1" <-> "OE2" Residue "D ASP 226": "OD1" <-> "OD2" Residue "D GLU 235": "OE1" <-> "OE2" Residue "D ASP 265": "OD1" <-> "OD2" Residue "D TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 376": "OD1" <-> "OD2" Residue "D TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 9.67, per 1000 atoms: 0.65 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 - 3.50 Amino acid : False - 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: 8.67 Conformation dependent library (CDL) restraints added in 651.6 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: 7.32 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: 6.95 Time building geometry restraints manager: 9.24 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: 97.25 - 105.34: 2686 105.34 - 113.43: 10139 113.43 - 121.53: 7899 121.53 - 129.62: 3688 129.62 - 137.72: 344 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 ========== 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: 2.780 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: 0.600 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 49.880 Find NCS groups from input model: 0.090 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: 0.010 Load rotamer database and sin/cos tables:10.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.410 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.677 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: 1.3382 time to fit residues: 111.3380 Evaluate side-chains 35 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.672 ------------------------------------------------------------------------------- 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: 3.9990 chunk 69 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 72 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 83 optimal weight: 0.0870 overall best weight: 4.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 96 GLN D 364 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2340 moved from start: 0.6874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.104 16327 Z= 0.414 Angle : 1.285 11.322 24756 Z= 0.617 Chirality : 0.059 0.398 3195 Planarity : 0.009 0.090 1089 Dihedral : 26.054 175.756 8809 Min Nonbonded Distance : 1.092 Molprobity Statistics. All-atom Clashscore : 36.81 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.20 % Favored : 95.28 % Rotamer: Outliers : 7.04 % Allowed : 29.03 % Favored : 63.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.53 % 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: -1.95 (0.38), residues: 381 helix: -0.89 (0.29), residues: 240 sheet: -0.03 (1.17), residues: 24 loop : -2.17 (0.49), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.005 TRP D 328 HIS 0.009 0.003 HIS D 107 PHE 0.029 0.005 PHE D 145 TYR 0.021 0.003 TYR D 20 ARG 0.036 0.003 ARG D 160 *********************** 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 66 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 42 time to evaluate : 0.679 Fit side-chains REVERT: D 7 MET cc_start: -0.0049 (OUTLIER) cc_final: -0.0356 (tmt) REVERT: D 27 LYS cc_start: 0.6224 (mttp) cc_final: 0.5742 (tttm) REVERT: D 106 PHE cc_start: 0.1689 (OUTLIER) cc_final: 0.1410 (m-80) REVERT: D 130 MET cc_start: 0.2668 (ptt) cc_final: 0.2466 (ptt) REVERT: D 236 MET cc_start: 0.3377 (mtt) cc_final: 0.1448 (ptm) REVERT: D 354 MET cc_start: -0.0776 (ptt) cc_final: -0.1030 (ptp) outliers start: 24 outliers final: 3 residues processed: 62 average time/residue: 1.0052 time to fit residues: 70.4115 Evaluate side-chains 37 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 32 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 7 MET Chi-restraints excluded: chain D residue 106 PHE Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain D residue 401 VAL 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: 0.9990 chunk 56 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 28 optimal weight: 10.0000 chunk 67 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 22 GLN D 314 ASN D 378 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1970 moved from start: 0.7004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16327 Z= 0.164 Angle : 0.692 8.061 24756 Z= 0.355 Chirality : 0.038 0.289 3195 Planarity : 0.006 0.087 1089 Dihedral : 25.361 175.307 8809 Min Nonbonded Distance : 1.053 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.41 % Favored : 96.06 % Rotamer: Outliers : 4.69 % Allowed : 33.14 % Favored : 62.17 % 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: -0.86 (0.40), residues: 381 helix: 0.15 (0.31), residues: 240 sheet: -0.16 (1.06), residues: 29 loop : -2.14 (0.52), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 328 HIS 0.005 0.001 HIS D 284 PHE 0.016 0.002 PHE D 286 TYR 0.010 0.001 TYR D 385 ARG 0.006 0.001 ARG D 326 *********************** 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 54 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 38 time to evaluate : 0.669 Fit side-chains REVERT: D 27 LYS cc_start: 0.6458 (mttp) cc_final: 0.5823 (tttm) REVERT: D 37 TYR cc_start: 0.4055 (p90) cc_final: 0.3455 (p90) REVERT: D 102 TYR cc_start: 0.2235 (OUTLIER) cc_final: 0.1380 (t80) REVERT: D 130 MET cc_start: 0.3068 (ptt) cc_final: 0.2782 (ptt) REVERT: D 231 MET cc_start: 0.3516 (mpt) cc_final: 0.3230 (tpp) REVERT: D 236 MET cc_start: 0.5000 (mtt) cc_final: 0.1097 (ptt) outliers start: 16 outliers final: 5 residues processed: 49 average time/residue: 0.9294 time to fit residues: 52.0989 Evaluate side-chains 38 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 32 time to evaluate : 0.617 ------------------------------------------------------------------------------- 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 118 CYS Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 155 MET Chi-restraints excluded: chain D residue 174 TYR 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: 0.1980 chunk 43 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 chunk 83 optimal weight: 0.5980 chunk 88 optimal weight: 9.9990 chunk 79 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 244 ASN ** D 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 ASN D 378 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2604 moved from start: 0.9854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 16327 Z= 0.248 Angle : 0.817 10.894 24756 Z= 0.416 Chirality : 0.042 0.294 3195 Planarity : 0.006 0.086 1089 Dihedral : 25.541 176.369 8809 Min Nonbonded Distance : 1.014 Molprobity Statistics. All-atom Clashscore : 28.22 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.51 % Favored : 94.23 % Rotamer: Outliers : 7.33 % Allowed : 32.84 % Favored : 59.82 % 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: -0.82 (0.41), residues: 381 helix: 0.26 (0.32), residues: 240 sheet: -0.44 (1.10), residues: 24 loop : -2.16 (0.52), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP D 328 HIS 0.008 0.003 HIS D 151 PHE 0.016 0.003 PHE D 106 TYR 0.036 0.003 TYR D 420 ARG 0.008 0.001 ARG D 56 *********************** 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 67 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 42 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 27 LYS cc_start: 0.6560 (mttp) cc_final: 0.6020 (mtpp) REVERT: D 89 PHE cc_start: 0.8525 (t80) cc_final: 0.8150 (t80) REVERT: D 130 MET cc_start: 0.4553 (ptt) cc_final: 0.4343 (ptt) REVERT: D 206 MET cc_start: 0.1144 (ttm) cc_final: -0.1037 (mmt) REVERT: D 236 MET cc_start: 0.5628 (mtt) cc_final: 0.0665 (ptt) REVERT: D 253 LEU cc_start: 0.2982 (OUTLIER) cc_final: 0.2699 (tp) REVERT: D 347 ARG cc_start: 0.2867 (OUTLIER) cc_final: 0.1697 (tpt170) outliers start: 25 outliers final: 7 residues processed: 62 average time/residue: 0.9649 time to fit residues: 67.7697 Evaluate side-chains 44 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 35 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 43 HIS Chi-restraints excluded: chain D residue 118 CYS Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 153 LYS Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 347 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 61 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 29 optimal weight: 7.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4019 moved from start: 1.5918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 16327 Z= 0.445 Angle : 1.436 16.013 24756 Z= 0.707 Chirality : 0.071 0.502 3195 Planarity : 0.010 0.099 1089 Dihedral : 27.132 166.829 8809 Min Nonbonded Distance : 1.276 Molprobity Statistics. All-atom Clashscore : 48.90 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.51 % Favored : 93.96 % Rotamer: Outliers : 12.02 % Allowed : 30.21 % Favored : 57.77 % 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: -2.47 (0.39), residues: 381 helix: -1.05 (0.30), residues: 236 sheet: -1.22 (1.12), residues: 24 loop : -2.71 (0.52), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.004 TRP D 328 HIS 0.071 0.009 HIS D 43 PHE 0.032 0.005 PHE D 298 TYR 0.037 0.005 TYR D 420 ARG 0.012 0.002 ARG D 160 *********************** 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 97 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 56 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 10 ILE cc_start: 0.5965 (OUTLIER) cc_final: 0.5668 (pp) REVERT: D 89 PHE cc_start: 0.8869 (t80) cc_final: 0.8476 (t80) REVERT: D 236 MET cc_start: 0.4442 (mtt) cc_final: 0.1317 (ptt) REVERT: D 253 LEU cc_start: 0.5189 (OUTLIER) cc_final: 0.4850 (tt) REVERT: D 289 LYS cc_start: 0.7652 (pttt) cc_final: 0.7413 (pttp) REVERT: D 347 ARG cc_start: 0.3546 (OUTLIER) cc_final: 0.1986 (tpp-160) outliers start: 41 outliers final: 13 residues processed: 86 average time/residue: 0.9668 time to fit residues: 93.8698 Evaluate side-chains 58 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 42 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 118 CYS Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 160 ARG 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 226 ASP Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 285 GLN Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 347 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 0.9980 chunk 17 optimal weight: 8.9990 chunk 52 optimal weight: 20.0000 chunk 21 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 41 optimal weight: 20.0000 chunk 7 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 chunk 85 optimal weight: 0.5980 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 128 ASN ** 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: 0.4363 moved from start: 1.8568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 16327 Z= 0.323 Angle : 1.099 12.255 24756 Z= 0.541 Chirality : 0.055 0.436 3195 Planarity : 0.008 0.096 1089 Dihedral : 26.739 173.140 8809 Min Nonbonded Distance : 1.734 Molprobity Statistics. All-atom Clashscore : 33.89 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.77 % Favored : 93.70 % Rotamer: Outliers : 7.33 % Allowed : 37.24 % Favored : 55.43 % 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: -1.86 (0.41), residues: 381 helix: -0.65 (0.32), residues: 238 sheet: -1.03 (1.06), residues: 24 loop : -2.26 (0.54), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP D 328 HIS 0.024 0.004 HIS D 43 PHE 0.023 0.003 PHE D 298 TYR 0.019 0.003 TYR D 111 ARG 0.005 0.001 ARG D 353 *********************** 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 78 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 53 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 10 ILE cc_start: 0.6305 (OUTLIER) cc_final: 0.6075 (pp) REVERT: D 39 GLU cc_start: 0.6543 (OUTLIER) cc_final: 0.6163 (pp20) REVERT: D 89 PHE cc_start: 0.8817 (t80) cc_final: 0.8426 (t80) REVERT: D 236 MET cc_start: 0.4282 (mtt) cc_final: 0.2037 (ptt) REVERT: D 289 LYS cc_start: 0.7934 (pttt) cc_final: 0.7702 (pttt) REVERT: D 347 ARG cc_start: 0.4188 (OUTLIER) cc_final: 0.2818 (tpp-160) outliers start: 25 outliers final: 9 residues processed: 67 average time/residue: 1.0961 time to fit residues: 82.0985 Evaluate side-chains 49 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 37 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 7 MET Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 337 MET Chi-restraints excluded: chain D residue 347 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 chunk 65 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 55 optimal weight: 8.9990 chunk 54 optimal weight: 0.9980 chunk 40 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 52 optimal weight: 20.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 5 ASN ** D 54 GLN ** 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: 0.4840 moved from start: 2.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 16327 Z= 0.290 Angle : 1.035 13.208 24756 Z= 0.512 Chirality : 0.051 0.347 3195 Planarity : 0.008 0.098 1089 Dihedral : 26.608 175.017 8809 Min Nonbonded Distance : 1.723 Molprobity Statistics. All-atom Clashscore : 32.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 8.50 % Allowed : 40.18 % Favored : 51.32 % 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: -1.77 (0.40), residues: 381 helix: -0.41 (0.32), residues: 239 sheet: None (None), residues: 0 loop : -2.46 (0.47), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.004 TRP D 328 HIS 0.004 0.002 HIS D 43 PHE 0.047 0.004 PHE D 221 TYR 0.022 0.004 TYR D 224 ARG 0.006 0.001 ARG D 282 *********************** 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 84 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 55 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 10 ILE cc_start: 0.6521 (OUTLIER) cc_final: 0.6172 (pp) REVERT: D 35 MET cc_start: -0.1133 (OUTLIER) cc_final: -0.4082 (mpp) REVERT: D 89 PHE cc_start: 0.8821 (t80) cc_final: 0.8460 (t80) REVERT: D 207 LEU cc_start: 0.9006 (tt) cc_final: 0.8740 (pt) REVERT: D 226 ASP cc_start: 0.8134 (OUTLIER) cc_final: 0.7566 (p0) REVERT: D 236 MET cc_start: 0.3739 (mtt) cc_final: 0.2811 (ptt) REVERT: D 302 MET cc_start: 0.5587 (OUTLIER) cc_final: 0.4997 (tmm) REVERT: D 337 MET cc_start: 0.4400 (pmt) cc_final: 0.4163 (tpp) outliers start: 29 outliers final: 9 residues processed: 76 average time/residue: 0.8530 time to fit residues: 74.2569 Evaluate side-chains 52 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 39 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 325 ILE 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: 10.0000 chunk 56 optimal weight: 7.9990 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4673 moved from start: 2.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 16327 Z= 0.188 Angle : 0.793 14.726 24756 Z= 0.389 Chirality : 0.040 0.331 3195 Planarity : 0.006 0.090 1089 Dihedral : 26.152 175.486 8809 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 23.51 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.99 % Favored : 94.75 % Rotamer: Outliers : 5.28 % Allowed : 44.57 % Favored : 50.15 % 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: -1.20 (0.40), residues: 381 helix: -0.05 (0.32), residues: 237 sheet: -0.23 (1.33), residues: 14 loop : -2.18 (0.50), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 328 HIS 0.002 0.000 HIS D 284 PHE 0.011 0.002 PHE D 145 TYR 0.015 0.002 TYR D 385 ARG 0.012 0.001 ARG D 326 *********************** 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 67 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 49 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 10 ILE cc_start: 0.6469 (OUTLIER) cc_final: 0.6144 (pp) REVERT: D 35 MET cc_start: -0.1490 (OUTLIER) cc_final: -0.3822 (mtp) REVERT: D 89 PHE cc_start: 0.8769 (t80) cc_final: 0.8443 (t80) REVERT: D 94 ILE cc_start: 0.8399 (tt) cc_final: 0.8140 (pp) REVERT: D 214 MET cc_start: 0.7419 (tpp) cc_final: 0.7077 (mmt) REVERT: D 226 ASP cc_start: 0.8086 (OUTLIER) cc_final: 0.7850 (p0) REVERT: D 236 MET cc_start: 0.3251 (mtt) cc_final: 0.2852 (ptt) REVERT: D 259 MET cc_start: 0.3939 (tpt) cc_final: 0.3654 (tpt) REVERT: D 320 LYS cc_start: 0.8341 (mmmm) cc_final: 0.8015 (mmmm) REVERT: D 337 MET cc_start: 0.4878 (pmt) cc_final: 0.4590 (tmm) outliers start: 18 outliers final: 4 residues processed: 61 average time/residue: 1.1285 time to fit residues: 76.6051 Evaluate side-chains 47 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 40 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 226 ASP 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: 7.9990 chunk 35 optimal weight: 9.9990 chunk 64 optimal weight: 0.8980 chunk 25 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 78 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 53 optimal weight: 9.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 120 GLN ** D 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 366 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4815 moved from start: 2.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 16327 Z= 0.185 Angle : 0.752 10.904 24756 Z= 0.370 Chirality : 0.038 0.334 3195 Planarity : 0.006 0.089 1089 Dihedral : 25.950 176.218 8809 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 21.51 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.77 % Favored : 93.70 % Rotamer: Outliers : 2.93 % Allowed : 46.33 % Favored : 50.73 % 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: -1.13 (0.42), residues: 381 helix: -0.01 (0.32), residues: 244 sheet: None (None), residues: 0 loop : -2.05 (0.52), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 328 HIS 0.019 0.002 HIS D 284 PHE 0.017 0.002 PHE D 286 TYR 0.017 0.002 TYR D 350 ARG 0.022 0.001 ARG D 282 *********************** 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 62 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 52 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 10 ILE cc_start: 0.6528 (OUTLIER) cc_final: 0.6185 (pp) REVERT: D 35 MET cc_start: -0.1604 (OUTLIER) cc_final: -0.4522 (mtp) REVERT: D 89 PHE cc_start: 0.8769 (t80) cc_final: 0.8376 (t80) REVERT: D 226 ASP cc_start: 0.8367 (p0) cc_final: 0.8149 (p0) REVERT: D 337 MET cc_start: 0.5066 (pmt) cc_final: 0.4480 (tmm) outliers start: 10 outliers final: 4 residues processed: 57 average time/residue: 1.1776 time to fit residues: 74.7695 Evaluate side-chains 46 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 40 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 265 ASP 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: 0.7980 chunk 91 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 72 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 56 optimal weight: 0.0270 chunk 44 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 chunk 77 optimal weight: 0.4980 chunk 22 optimal weight: 10.0000 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4751 moved from start: 2.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16327 Z= 0.154 Angle : 0.703 11.779 24756 Z= 0.345 Chirality : 0.035 0.313 3195 Planarity : 0.005 0.087 1089 Dihedral : 25.741 176.865 8809 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 19.26 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.46 % Favored : 95.01 % Rotamer: Outliers : 2.64 % Allowed : 46.04 % Favored : 51.32 % 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: -1.03 (0.42), residues: 381 helix: 0.06 (0.33), residues: 244 sheet: None (None), residues: 0 loop : -1.98 (0.52), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 328 HIS 0.004 0.001 HIS D 284 PHE 0.024 0.002 PHE D 106 TYR 0.021 0.002 TYR D 278 ARG 0.006 0.000 ARG D 326 ********************** 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 57 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 48 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 10 ILE cc_start: 0.6497 (OUTLIER) cc_final: 0.6180 (pp) REVERT: D 35 MET cc_start: -0.1752 (OUTLIER) cc_final: -0.4131 (mtt) REVERT: D 89 PHE cc_start: 0.8780 (t80) cc_final: 0.8337 (t80) REVERT: D 130 MET cc_start: 0.7305 (ptt) cc_final: 0.6975 (ptt) REVERT: D 214 MET cc_start: 0.7737 (tpp) cc_final: 0.7492 (mmt) REVERT: D 236 MET cc_start: 0.2798 (ptt) cc_final: 0.2544 (ppp) REVERT: D 337 MET cc_start: 0.4961 (pmt) cc_final: 0.3969 (tmt) outliers start: 9 outliers final: 3 residues processed: 54 average time/residue: 0.8952 time to fit residues: 55.6932 Evaluate side-chains 44 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 265 ASP 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: 10.0000 chunk 30 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 4 optimal weight: 8.9990 chunk 52 optimal weight: 20.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 322 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 = 0.4541 r_free = 0.4541 target = 0.139244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.120952 restraints weight = 54484.984| |-----------------------------------------------------------------------------| r_work (start): 0.4273 rms_B_bonded: 1.82 r_work: 0.4177 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.4177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6307 moved from start: 2.6272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 16327 Z= 0.418 Angle : 1.273 13.625 24756 Z= 0.607 Chirality : 0.059 0.358 3195 Planarity : 0.008 0.092 1089 Dihedral : 26.901 175.206 8809 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 40.65 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.30 % Favored : 93.18 % Rotamer: Outliers : 3.52 % Allowed : 46.04 % Favored : 50.44 % 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: -1.88 (0.39), residues: 381 helix: -0.68 (0.30), residues: 237 sheet: -0.71 (1.00), residues: 22 loop : -2.29 (0.55), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.004 TRP D 328 HIS 0.004 0.001 HIS D 291 PHE 0.025 0.004 PHE D 89 TYR 0.030 0.004 TYR D 102 ARG 0.011 0.001 ARG D 160 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3216.32 seconds wall clock time: 58 minutes 11.54 seconds (3491.54 seconds total)