Starting phenix.real_space_refine on Sat Mar 16 13:29:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2t_40987/03_2024/8t2t_40987_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2t_40987/03_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_40987/03_2024/8t2t_40987.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2t_40987/03_2024/8t2t_40987.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2t_40987/03_2024/8t2t_40987_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2t_40987/03_2024/8t2t_40987_updated.pdb" } 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-5265/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: 9.77, per 1000 atoms: 0.66 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: 9.07 Conformation dependent library (CDL) restraints added in 639.0 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... running ksdssp... Secondary structure from input PDB file: 22 helices and 2 sheets defined 60.7% alpha, 5.9% beta 172 base pairs and 301 stacking pairs defined. Time for finding SS restraints: 8.18 Creating SS restraints... Processing helix chain 'D' and resid 7 through 10 No H-bonds generated for 'chain 'D' and resid 7 through 10' Processing helix chain 'D' and resid 13 through 26 Processing helix chain 'D' and resid 37 through 45 removed outlier: 3.786A pdb=" N LEU D 40 " --> pdb=" O TYR D 37 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N LYS D 41 " --> pdb=" O THR D 38 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU D 42 " --> pdb=" O GLU D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 56 Processing helix chain 'D' and resid 85 through 98 Processing helix chain 'D' and resid 101 through 105 removed outlier: 3.661A pdb=" N GLN D 105 " --> pdb=" O TYR D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 132 Processing helix chain 'D' and resid 145 through 148 No H-bonds generated for 'chain 'D' and resid 145 through 148' Processing helix chain 'D' and resid 151 through 159 Processing helix chain 'D' and resid 165 through 176 Processing helix chain 'D' and resid 197 through 217 removed outlier: 4.440A pdb=" N GLU D 209 " --> pdb=" O ILE D 205 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N LEU D 210 " --> pdb=" O MET D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 251 Processing helix chain 'D' and resid 267 through 269 No H-bonds generated for 'chain 'D' and resid 267 through 269' Processing helix chain 'D' and resid 292 through 305 Processing helix chain 'D' and resid 314 through 331 Processing helix chain 'D' and resid 338 through 360 Processing helix chain 'D' and resid 363 through 373 Processing helix chain 'D' and resid 377 through 384 Processing helix chain 'D' and resid 390 through 395 Processing helix chain 'D' and resid 397 through 402 removed outlier: 3.526A pdb=" N ALA D 402 " --> pdb=" O VAL D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 411 Processing helix chain 'D' and resid 416 through 423 Processing sheet with id= A, first strand: chain 'D' and resid 264 through 266 removed outlier: 3.500A pdb=" N ASP D 265 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N CYS D 228 " --> pdb=" O ILE D 140 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASN D 220 " --> pdb=" O MET D 231 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 275 through 279 157 hydrogen bonds defined for protein. 450 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: 7.01 Time building geometry restraints manager: 9.52 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: 10150 3.15 - 3.73: 31219 3.73 - 4.32: 40587 4.32 - 4.90: 52343 Nonbonded interactions: 134441 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 134436 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: 4.080 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: 0.020 Extract box with map and model: 11.980 Check model and map are aligned: 0.190 Set scattering table: 0.140 Process input model: 51.660 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.390 ------------------------------------------------------------------------------- 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= 0.346 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 : 0.624 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: 1.3752 time to fit residues: 114.5978 Evaluate side-chains 35 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.687 ------------------------------------------------------------------------------- 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: 0.0170 chunk 69 optimal weight: 6.9990 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: 0.0570 overall best weight: 3.4142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 96 GLN ** D 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 364 GLN ** D 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2150 moved from start: 0.6258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 16327 Z= 0.353 Angle : 1.144 9.498 24756 Z= 0.558 Chirality : 0.054 0.368 3195 Planarity : 0.008 0.082 1089 Dihedral : 25.817 178.095 8809 Min Nonbonded Distance : 0.788 Molprobity Statistics. All-atom Clashscore : 32.31 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.99 % Favored : 94.49 % Rotamer: Outliers : 6.74 % Allowed : 28.15 % Favored : 65.10 % 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: -2.03 (0.37), residues: 381 helix: -0.96 (0.28), residues: 244 sheet: -0.02 (1.16), residues: 24 loop : -2.22 (0.50), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP D 328 HIS 0.010 0.003 HIS D 284 PHE 0.020 0.005 PHE D 145 TYR 0.017 0.003 TYR D 102 ARG 0.020 0.002 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 65 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 42 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 102 TYR cc_start: 0.2201 (OUTLIER) cc_final: 0.1017 (t80) REVERT: D 236 MET cc_start: 0.4035 (mtt) cc_final: 0.1220 (ptm) outliers start: 23 outliers final: 1 residues processed: 61 average time/residue: 0.9592 time to fit residues: 66.3976 Evaluate side-chains 37 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 35 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 265 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 8.9990 chunk 25 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 83 optimal weight: 0.9980 chunk 90 optimal weight: 0.0040 chunk 74 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.3998 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 ASN D 378 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2009 moved from start: 0.6962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 16327 Z= 0.191 Angle : 0.717 10.440 24756 Z= 0.364 Chirality : 0.038 0.287 3195 Planarity : 0.006 0.081 1089 Dihedral : 25.336 175.988 8809 Min Nonbonded Distance : 1.026 Molprobity Statistics. All-atom Clashscore : 19.93 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.41 % Favored : 96.06 % Rotamer: Outliers : 4.11 % Allowed : 33.43 % Favored : 62.46 % 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: -1.11 (0.39), residues: 381 helix: -0.00 (0.31), residues: 237 sheet: -0.10 (1.18), residues: 24 loop : -2.26 (0.49), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 328 HIS 0.003 0.001 HIS D 284 PHE 0.019 0.003 PHE D 275 TYR 0.009 0.002 TYR D 385 ARG 0.005 0.001 ARG D 347 *********************** 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 53 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 39 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 27 LYS cc_start: 0.6834 (mttp) cc_final: 0.6199 (mtpp) REVERT: D 236 MET cc_start: 0.5640 (mtt) cc_final: 0.0905 (ptt) outliers start: 14 outliers final: 4 residues processed: 48 average time/residue: 1.0460 time to fit residues: 56.9761 Evaluate side-chains 39 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 35 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 401 VAL 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: 2.9990 chunk 62 optimal weight: 0.4980 chunk 43 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 79 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- 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 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.2904 moved from start: 1.0926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 16327 Z= 0.285 Angle : 0.972 10.949 24756 Z= 0.491 Chirality : 0.050 0.434 3195 Planarity : 0.007 0.088 1089 Dihedral : 25.939 175.045 8809 Min Nonbonded Distance : 0.891 Molprobity Statistics. All-atom Clashscore : 34.69 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.46 % Favored : 95.28 % Rotamer: Outliers : 7.62 % Allowed : 31.38 % Favored : 61.00 % 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: -1.59 (0.39), residues: 381 helix: -0.39 (0.31), residues: 231 sheet: -0.82 (1.15), residues: 24 loop : -2.22 (0.51), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP D 328 HIS 0.006 0.003 HIS D 109 PHE 0.037 0.004 PHE D 106 TYR 0.024 0.003 TYR D 420 ARG 0.009 0.001 ARG D 217 *********************** 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 70 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 44 time to evaluate : 0.710 Fit side-chains revert: symmetry clash REVERT: D 27 LYS cc_start: 0.6954 (mttp) cc_final: 0.6325 (mtpp) REVERT: D 89 PHE cc_start: 0.8559 (t80) cc_final: 0.8265 (t80) REVERT: D 130 MET cc_start: 0.4679 (OUTLIER) cc_final: 0.4112 (ptt) REVERT: D 154 LEU cc_start: 0.4498 (OUTLIER) cc_final: 0.4274 (pp) REVERT: D 236 MET cc_start: 0.4629 (mtt) cc_final: 0.0733 (ptt) REVERT: D 242 MET cc_start: 0.5572 (mmm) cc_final: 0.5293 (mmp) REVERT: D 347 ARG cc_start: 0.3039 (OUTLIER) cc_final: 0.2284 (tpt170) outliers start: 26 outliers final: 7 residues processed: 61 average time/residue: 1.1798 time to fit residues: 80.1184 Evaluate side-chains 41 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 31 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 118 CYS Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 347 ARG Chi-restraints excluded: chain D residue 401 VAL 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: 1.9990 chunk 36 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 79 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- 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 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4399 moved from start: 1.8401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.117 16327 Z= 0.478 Angle : 1.531 13.837 24756 Z= 0.750 Chirality : 0.076 0.570 3195 Planarity : 0.010 0.099 1089 Dihedral : 27.639 164.621 8809 Min Nonbonded Distance : 1.691 Molprobity Statistics. All-atom Clashscore : 51.78 Ramachandran Plot: Outliers : 0.52 % Allowed : 7.09 % Favored : 92.39 % Rotamer: Outliers : 10.56 % Allowed : 31.67 % Favored : 57.77 % 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: -3.51 (0.34), residues: 381 helix: -1.80 (0.28), residues: 222 sheet: None (None), residues: 0 loop : -3.06 (0.41), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.007 TRP D 328 HIS 0.004 0.002 HIS D 151 PHE 0.037 0.006 PHE D 221 TYR 0.039 0.005 TYR D 419 ARG 0.020 0.002 ARG D 308 *********************** 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 87 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 51 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 89 PHE cc_start: 0.8835 (t80) cc_final: 0.8580 (t80) REVERT: D 102 TYR cc_start: 0.3880 (OUTLIER) cc_final: 0.3311 (t80) REVERT: D 208 ASN cc_start: 0.5935 (t0) cc_final: 0.5625 (p0) REVERT: D 236 MET cc_start: 0.3942 (OUTLIER) cc_final: 0.1109 (ptt) outliers start: 36 outliers final: 9 residues processed: 79 average time/residue: 0.9937 time to fit residues: 88.8570 Evaluate side-chains 44 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 33 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 236 MET Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 342 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 52 optimal weight: 20.0000 chunk 21 optimal weight: 9.9990 chunk 89 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 46 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 291 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5100 moved from start: 2.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.114 16327 Z= 0.439 Angle : 1.403 17.085 24756 Z= 0.681 Chirality : 0.066 0.510 3195 Planarity : 0.010 0.116 1089 Dihedral : 27.641 174.859 8809 Min Nonbonded Distance : 1.620 Molprobity Statistics. All-atom Clashscore : 44.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 10.26 % Allowed : 35.78 % 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: -2.72 (0.39), residues: 381 helix: -1.21 (0.31), residues: 227 sheet: -2.23 (0.89), residues: 24 loop : -2.58 (0.52), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.005 TRP D 328 HIS 0.005 0.002 HIS D 109 PHE 0.039 0.004 PHE D 298 TYR 0.024 0.004 TYR D 111 ARG 0.010 0.001 ARG D 266 *********************** 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 85 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 50 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 89 PHE cc_start: 0.8788 (t80) cc_final: 0.8495 (t80) REVERT: D 123 ILE cc_start: 0.9088 (OUTLIER) cc_final: 0.8817 (tp) REVERT: D 135 ASP cc_start: 0.7796 (m-30) cc_final: 0.7576 (p0) REVERT: D 137 ILE cc_start: 0.7356 (mm) cc_final: 0.6821 (mm) REVERT: D 206 MET cc_start: 0.7054 (ttt) cc_final: 0.6824 (ttt) REVERT: D 224 TYR cc_start: 0.7450 (OUTLIER) cc_final: 0.6317 (m-10) REVERT: D 236 MET cc_start: 0.3884 (mtt) cc_final: 0.3233 (ptt) REVERT: D 271 LYS cc_start: 0.8222 (tttt) cc_final: 0.7599 (tttt) REVERT: D 337 MET cc_start: 0.4577 (pmt) cc_final: 0.3071 (tmm) outliers start: 35 outliers final: 13 residues processed: 79 average time/residue: 0.9886 time to fit residues: 88.0508 Evaluate side-chains 54 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 39 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 224 TYR Chi-restraints excluded: chain D residue 228 CYS Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 291 HIS Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 415 SER Chi-restraints excluded: chain D residue 418 ASP Chi-restraints excluded: chain D residue 421 ILE 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: 0.9980 chunk 74 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 52 optimal weight: 20.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5268 moved from start: 2.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 16327 Z= 0.298 Angle : 1.020 10.423 24756 Z= 0.504 Chirality : 0.052 0.478 3195 Planarity : 0.007 0.077 1089 Dihedral : 26.889 174.188 8809 Min Nonbonded Distance : 1.458 Molprobity Statistics. All-atom Clashscore : 30.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 8.21 % Allowed : 38.12 % Favored : 53.67 % 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: -1.70 (0.40), residues: 381 helix: -0.47 (0.32), residues: 221 sheet: None (None), residues: 0 loop : -2.03 (0.47), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.004 TRP D 136 HIS 0.050 0.007 HIS D 291 PHE 0.023 0.004 PHE D 279 TYR 0.030 0.003 TYR D 278 ARG 0.009 0.001 ARG D 266 *********************** 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 82 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 54 time to evaluate : 0.685 Fit side-chains revert: symmetry clash REVERT: D 89 PHE cc_start: 0.8697 (t80) cc_final: 0.8438 (t80) REVERT: D 224 TYR cc_start: 0.7186 (OUTLIER) cc_final: 0.4801 (m-80) REVERT: D 236 MET cc_start: 0.3479 (mtt) cc_final: 0.3218 (ptt) REVERT: D 272 TYR cc_start: 0.3652 (t80) cc_final: 0.2660 (t80) REVERT: D 361 LYS cc_start: 0.5341 (OUTLIER) cc_final: 0.5089 (ptmt) REVERT: D 381 ARG cc_start: 0.6202 (ttp80) cc_final: 0.5849 (mpt180) outliers start: 28 outliers final: 8 residues processed: 74 average time/residue: 1.1364 time to fit residues: 93.5120 Evaluate side-chains 47 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 37 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 224 TYR Chi-restraints excluded: chain D residue 228 CYS Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 280 ASP Chi-restraints excluded: chain D residue 361 LYS 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: 5.9990 chunk 60 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 82 optimal weight: 0.0270 overall best weight: 1.5842 ------------------------------------------------------------------------------- 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 291 HIS ** D 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5343 moved from start: 2.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 16327 Z= 0.232 Angle : 0.864 12.198 24756 Z= 0.432 Chirality : 0.044 0.354 3195 Planarity : 0.007 0.082 1089 Dihedral : 26.583 178.818 8809 Min Nonbonded Distance : 1.195 Molprobity Statistics. All-atom Clashscore : 25.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 5.28 % Allowed : 43.70 % Favored : 51.03 % 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: -1.52 (0.41), residues: 381 helix: -0.30 (0.33), residues: 224 sheet: None (None), residues: 0 loop : -2.00 (0.48), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP D 328 HIS 0.016 0.003 HIS D 284 PHE 0.015 0.003 PHE D 145 TYR 0.034 0.003 TYR D 102 ARG 0.005 0.001 ARG D 347 *********************** 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 66 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 48 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 7 MET cc_start: 0.4042 (mpt) cc_final: 0.3089 (mtt) REVERT: D 89 PHE cc_start: 0.8699 (t80) cc_final: 0.8405 (t80) REVERT: D 206 MET cc_start: 0.7140 (ttt) cc_final: 0.6925 (ttm) REVERT: D 337 MET cc_start: 0.4780 (OUTLIER) cc_final: 0.3336 (tpp) outliers start: 18 outliers final: 6 residues processed: 58 average time/residue: 1.0289 time to fit residues: 67.6393 Evaluate side-chains 43 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 36 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 224 TYR Chi-restraints excluded: chain D residue 228 CYS Chi-restraints excluded: chain D residue 337 MET 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: 6.9990 chunk 35 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 74 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5700 moved from start: 2.5948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 16327 Z= 0.258 Angle : 0.872 11.026 24756 Z= 0.433 Chirality : 0.044 0.324 3195 Planarity : 0.006 0.072 1089 Dihedral : 26.487 178.447 8809 Min Nonbonded Distance : 1.015 Molprobity Statistics. All-atom Clashscore : 25.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 4.40 % Allowed : 45.16 % 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: -1.93 (0.40), residues: 381 helix: -0.70 (0.31), residues: 231 sheet: -3.67 (1.28), residues: 10 loop : -1.93 (0.51), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.004 TRP D 328 HIS 0.015 0.003 HIS D 291 PHE 0.017 0.003 PHE D 106 TYR 0.019 0.003 TYR D 102 ARG 0.021 0.002 ARG D 347 *********************** 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: 15 poor density : 47 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 7 MET cc_start: 0.4026 (mpt) cc_final: 0.3356 (mpt) REVERT: D 206 MET cc_start: 0.7603 (ttt) cc_final: 0.7123 (tpp) REVERT: D 268 SER cc_start: 0.8221 (m) cc_final: 0.7973 (p) outliers start: 15 outliers final: 6 residues processed: 58 average time/residue: 1.2748 time to fit residues: 81.8809 Evaluate side-chains 40 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 34 time to evaluate : 0.624 ------------------------------------------------------------------------------- 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 157 LEU Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 224 TYR Chi-restraints excluded: chain D residue 257 VAL 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: 5.9990 chunk 91 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 77 optimal weight: 0.4980 chunk 22 optimal weight: 7.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- 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 395 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5714 moved from start: 2.6500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 16327 Z= 0.201 Angle : 0.768 8.359 24756 Z= 0.382 Chirality : 0.039 0.343 3195 Planarity : 0.006 0.066 1089 Dihedral : 26.222 177.995 8809 Min Nonbonded Distance : 1.025 Molprobity Statistics. All-atom Clashscore : 22.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.35 % Allowed : 48.39 % Favored : 49.27 % 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: -1.81 (0.40), residues: 381 helix: -0.69 (0.31), residues: 233 sheet: None (None), residues: 0 loop : -1.92 (0.50), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP D 328 HIS 0.002 0.001 HIS D 151 PHE 0.036 0.003 PHE D 298 TYR 0.025 0.003 TYR D 392 ARG 0.010 0.001 ARG D 301 ********************** 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 45 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 37 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 7 MET cc_start: 0.3684 (mpt) cc_final: 0.2887 (mpt) REVERT: D 206 MET cc_start: 0.7774 (ttt) cc_final: 0.7532 (tpp) REVERT: D 354 MET cc_start: 0.5093 (tmm) cc_final: 0.3978 (tmt) outliers start: 8 outliers final: 6 residues processed: 43 average time/residue: 0.9242 time to fit residues: 45.6861 Evaluate side-chains 41 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 35 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 224 TYR Chi-restraints excluded: chain D residue 242 MET Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 264 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 73 optimal weight: 8.9990 chunk 30 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 chunk 9 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 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 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 ASN ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.130791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.111233 restraints weight = 52265.135| |-----------------------------------------------------------------------------| r_work (start): 0.4129 rms_B_bonded: 1.80 r_work: 0.4026 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.4026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 2.9740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 16327 Z= 0.434 Angle : 1.271 12.737 24756 Z= 0.617 Chirality : 0.062 0.420 3195 Planarity : 0.008 0.073 1089 Dihedral : 27.252 179.037 8809 Min Nonbonded Distance : 0.920 Molprobity Statistics. All-atom Clashscore : 37.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 5.28 % Allowed : 45.45 % Favored : 49.27 % 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: -2.15 (0.40), residues: 381 helix: -0.97 (0.32), residues: 231 sheet: None (None), residues: 0 loop : -2.04 (0.48), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.006 TRP D 328 HIS 0.009 0.003 HIS D 291 PHE 0.025 0.004 PHE D 106 TYR 0.034 0.004 TYR D 392 ARG 0.011 0.002 ARG D 351 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3244.98 seconds wall clock time: 59 minutes 30.06 seconds (3570.06 seconds total)