Starting phenix.real_space_refine on Sat Mar 16 12:30:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uim_26549/03_2024/7uim_26549_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uim_26549/03_2024/7uim_26549.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uim_26549/03_2024/7uim_26549.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uim_26549/03_2024/7uim_26549.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uim_26549/03_2024/7uim_26549_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uim_26549/03_2024/7uim_26549_updated.pdb" } resolution = 3.1 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= 0.001 sd= 0.015 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 536 5.49 5 Mg 13 5.21 5 S 21 5.16 5 C 7184 2.51 5 N 2736 2.21 5 O 4282 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D GLU 39": "OE1" <-> "OE2" Residue "D GLU 42": "OE1" <-> "OE2" Residue "D ASP 108": "OD1" <-> "OD2" Residue "D ASP 132": "OD1" <-> "OD2" Residue "D ASP 141": "OD1" <-> "OD2" Residue "D ASP 152": "OD1" <-> "OD2" Residue "D ASP 166": "OD1" <-> "OD2" Residue "D TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 319": "OE1" <-> "OE2" Residue "D TYR 420": "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: 14772 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 11624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 11624 Inner-chain residues flagged as termini: ['pdbres=" G B 171 "', 'pdbres=" G B 220 "', 'pdbres=" A B 298 "', 'pdbres=" A B 401 "', 'pdbres=" G B 551 "'] Classifications: {'RNA': 541} Modifications used: {'5*END': 5, 'rna2p_pur': 42, 'rna2p_pyr': 16, 'rna3p_pur': 286, 'rna3p_pyr': 197} Link IDs: {'rna2p': 57, 'rna3p': 483} 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: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Unusual residues: {' MG': 13, 'NH4': 2} Classifications: {'undetermined': 15} Link IDs: {None: 14} Time building chain proxies: 7.69, per 1000 atoms: 0.52 Number of scatterers: 14772 At special positions: 0 Unit cell: (100.672, 153.92, 154.752, 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 536 15.00 Mg 13 11.99 O 4282 8.00 N 2736 7.00 C 7184 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.87 Conformation dependent library (CDL) restraints added in 644.1 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: 20 helices and 2 sheets defined 62.0% alpha, 4.4% beta 159 base pairs and 290 stacking pairs defined. Time for finding SS restraints: 8.42 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 57 removed outlier: 6.359A pdb=" N GLU D 49 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N THR D 50 " --> pdb=" O LYS D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 105 Proline residue: D 100 - end of helix removed outlier: 6.256A pdb=" N GLU D 104 " --> pdb=" O PRO D 100 " (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 161 Processing helix chain 'D' and resid 165 through 176 Processing helix chain 'D' and resid 199 through 217 removed outlier: 3.870A 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 removed outlier: 4.159A pdb=" N GLU D 343 " --> pdb=" O THR D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 373 Processing helix chain 'D' and resid 377 through 386 Processing helix chain 'D' and resid 391 through 395 Processing helix chain 'D' and resid 398 through 402 Processing helix chain 'D' and resid 405 through 411 Processing helix chain 'D' and resid 416 through 422 Processing sheet with id= A, first strand: chain 'D' and resid 136 through 140 removed outlier: 4.571A 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 278 166 hydrogen bonds defined for protein. 489 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 383 hydrogen bonds 574 hydrogen bond angles 0 basepair planarities 159 basepair parallelities 290 stacking parallelities Total time for adding SS restraints: 7.33 Time building geometry restraints manager: 9.39 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: 1918 1.33 - 1.45: 7477 1.45 - 1.57: 5712 1.57 - 1.70: 1072 1.70 - 1.82: 35 Bond restraints: 16214 Sorted by residual: bond pdb=" CB GLU D 39 " pdb=" CG GLU D 39 " ideal model delta sigma weight residual 1.520 1.578 -0.058 3.00e-02 1.11e+03 3.76e+00 bond pdb=" CB ILE D 325 " pdb=" CG2 ILE D 325 " ideal model delta sigma weight residual 1.521 1.461 0.060 3.30e-02 9.18e+02 3.35e+00 bond pdb=" CD2 TYR D 174 " pdb=" CE2 TYR D 174 " ideal model delta sigma weight residual 1.382 1.329 0.053 3.00e-02 1.11e+03 3.16e+00 bond pdb=" CB LYS D 36 " pdb=" CG LYS D 36 " ideal model delta sigma weight residual 1.520 1.568 -0.048 3.00e-02 1.11e+03 2.60e+00 bond pdb=" CB ARG D 377 " pdb=" CG ARG D 377 " ideal model delta sigma weight residual 1.520 1.567 -0.047 3.00e-02 1.11e+03 2.48e+00 ... (remaining 16209 not shown) Histogram of bond angle deviations from ideal: 97.48 - 105.12: 2537 105.12 - 112.77: 9518 112.77 - 120.42: 7029 120.42 - 128.07: 4549 128.07 - 135.71: 956 Bond angle restraints: 24589 Sorted by residual: angle pdb=" CA LYS D 36 " pdb=" CB LYS D 36 " pdb=" CG LYS D 36 " ideal model delta sigma weight residual 114.10 127.56 -13.46 2.00e+00 2.50e-01 4.53e+01 angle pdb=" CA PRO D 281 " pdb=" N PRO D 281 " pdb=" CD PRO D 281 " ideal model delta sigma weight residual 112.00 104.42 7.58 1.40e+00 5.10e-01 2.93e+01 angle pdb=" O3' G B 123 " pdb=" C3' G B 123 " pdb=" C2' G B 123 " ideal model delta sigma weight residual 113.70 121.42 -7.72 1.50e+00 4.44e-01 2.65e+01 angle pdb=" CA ARG D 377 " pdb=" CB ARG D 377 " pdb=" CG ARG D 377 " ideal model delta sigma weight residual 114.10 124.17 -10.07 2.00e+00 2.50e-01 2.54e+01 angle pdb=" CB LYS D 263 " pdb=" CG LYS D 263 " pdb=" CD LYS D 263 " ideal model delta sigma weight residual 111.30 121.59 -10.29 2.30e+00 1.89e-01 2.00e+01 ... (remaining 24584 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.89: 8654 33.89 - 67.78: 1431 67.78 - 101.67: 157 101.67 - 135.57: 2 135.57 - 169.46: 6 Dihedral angle restraints: 10250 sinusoidal: 9126 harmonic: 1124 Sorted by residual: dihedral pdb=" O4' C B 439 " pdb=" C1' C B 439 " pdb=" N1 C B 439 " pdb=" C2 C B 439 " ideal model delta sinusoidal sigma weight residual 232.00 62.54 169.46 1 1.70e+01 3.46e-03 6.59e+01 dihedral pdb=" O4' C B 440 " pdb=" C1' C B 440 " pdb=" N1 C B 440 " pdb=" C2 C B 440 " ideal model delta sinusoidal sigma weight residual -128.00 35.88 -163.88 1 1.70e+01 3.46e-03 6.51e+01 dihedral pdb=" CA PRO D 281 " pdb=" C PRO D 281 " pdb=" N ARG D 282 " pdb=" CA ARG D 282 " ideal model delta harmonic sigma weight residual 180.00 148.62 31.38 0 5.00e+00 4.00e-02 3.94e+01 ... (remaining 10247 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2769 0.062 - 0.124: 324 0.124 - 0.186: 56 0.186 - 0.248: 9 0.248 - 0.310: 7 Chirality restraints: 3165 Sorted by residual: 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 -2.17 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" C3' G B 333 " pdb=" C4' G B 333 " pdb=" O3' G B 333 " pdb=" C2' G B 333 " both_signs ideal model delta sigma weight residual False -2.48 -2.19 -0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" C3' U B 46 " pdb=" C4' U B 46 " pdb=" O3' U B 46 " pdb=" C2' U B 46 " both_signs ideal model delta sigma weight residual False -2.48 -2.20 -0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 3162 not shown) Planarity restraints: 1084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 280 " -0.066 5.00e-02 4.00e+02 9.59e-02 1.47e+01 pdb=" N PRO D 281 " 0.166 5.00e-02 4.00e+02 pdb=" CA PRO D 281 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO D 281 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU D 39 " -0.016 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" CD GLU D 39 " 0.058 2.00e-02 2.50e+03 pdb=" OE1 GLU D 39 " -0.021 2.00e-02 2.50e+03 pdb=" OE2 GLU D 39 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS D 289 " 0.053 5.00e-02 4.00e+02 8.07e-02 1.04e+01 pdb=" N PRO D 290 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO D 290 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO D 290 " 0.044 5.00e-02 4.00e+02 ... (remaining 1081 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 84 2.50 - 3.10: 9433 3.10 - 3.70: 29760 3.70 - 4.30: 41791 4.30 - 4.90: 53756 Nonbonded interactions: 134824 Sorted by model distance: nonbonded pdb=" OP1 C B 581 " pdb="MG MG B 701 " model vdw 1.903 2.170 nonbonded pdb=" O3' U B 638 " pdb="MG MG B 701 " model vdw 1.943 2.170 nonbonded pdb=" OP2 G B 158 " pdb="MG MG B 708 " model vdw 1.984 2.170 nonbonded pdb=" OP2 A B 560 " pdb="MG MG B 705 " model vdw 1.992 2.170 nonbonded pdb=" OP2 A B 323 " pdb="MG MG B 709 " model vdw 2.016 2.170 ... (remaining 134819 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: 2.460 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: 12.150 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 48.420 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4534 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 : 0.005 0.068 16214 Z= 0.292 Angle : 0.871 13.462 24589 Z= 0.437 Chirality : 0.045 0.310 3165 Planarity : 0.007 0.096 1084 Dihedral : 24.926 169.458 9526 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.00 % Allowed : 31.67 % Favored : 68.33 % 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: -1.28 (0.39), residues: 381 helix: -0.58 (0.28), residues: 256 sheet: -1.65 (0.92), residues: 24 loop : -0.87 (0.60), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP D 360 HIS 0.007 0.002 HIS D 291 PHE 0.032 0.003 PHE D 298 TYR 0.032 0.003 TYR D 278 ARG 0.010 0.001 ARG D 377 *********************** 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 126 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 26 ASN cc_start: 0.8204 (m-40) cc_final: 0.8002 (m-40) REVERT: D 175 LEU cc_start: 0.7673 (mt) cc_final: 0.7446 (tp) REVERT: D 270 LEU cc_start: 0.4275 (mt) cc_final: 0.2998 (mt) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.3580 time to fit residues: 60.9310 Evaluate side-chains 71 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.690 ------------------------------------------------------------------------------- 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: 0.0070 chunk 69 optimal weight: 3.9990 chunk 38 optimal weight: 8.9990 chunk 23 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 37 optimal weight: 20.0000 chunk 72 optimal weight: 3.9990 chunk 27 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 overall best weight: 4.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 109 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5299 moved from start: 0.4515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 16214 Z= 0.291 Angle : 0.780 9.371 24589 Z= 0.390 Chirality : 0.039 0.246 3165 Planarity : 0.006 0.063 1084 Dihedral : 25.271 165.167 8721 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 25.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 6.45 % Allowed : 31.38 % Favored : 62.17 % 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: -0.57 (0.41), residues: 381 helix: -0.05 (0.31), residues: 251 sheet: -0.90 (1.00), residues: 24 loop : -0.68 (0.59), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP D 328 HIS 0.008 0.002 HIS D 109 PHE 0.012 0.002 PHE D 106 TYR 0.019 0.002 TYR D 385 ARG 0.011 0.002 ARG D 56 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 70 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 206 MET cc_start: 0.6591 (tpp) cc_final: 0.6361 (tpt) REVERT: D 214 MET cc_start: 0.6731 (mmt) cc_final: 0.6474 (mmt) outliers start: 22 outliers final: 8 residues processed: 85 average time/residue: 0.3029 time to fit residues: 36.2163 Evaluate side-chains 66 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 58 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 33 ASP Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 414 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 chunk 90 optimal weight: 9.9990 chunk 74 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 28 optimal weight: 10.9990 chunk 67 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 107 HIS D 204 ASN D 244 ASN ** D 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5570 moved from start: 0.7304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 16214 Z= 0.337 Angle : 0.821 10.827 24589 Z= 0.411 Chirality : 0.042 0.245 3165 Planarity : 0.006 0.076 1084 Dihedral : 25.676 167.028 8721 Min Nonbonded Distance : 1.172 Molprobity Statistics. All-atom Clashscore : 33.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 8.21 % Allowed : 29.91 % Favored : 61.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.41), residues: 381 helix: -0.26 (0.31), residues: 259 sheet: -0.58 (1.10), residues: 19 loop : -1.62 (0.58), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.005 TRP D 328 HIS 0.008 0.002 HIS D 107 PHE 0.015 0.003 PHE D 146 TYR 0.032 0.004 TYR D 102 ARG 0.006 0.001 ARG D 266 *********************** 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 90 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 62 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 175 LEU cc_start: 0.7894 (mt) cc_final: 0.7455 (tt) REVERT: D 310 TRP cc_start: 0.7337 (OUTLIER) cc_final: 0.6645 (t60) REVERT: D 323 GLN cc_start: 0.6152 (OUTLIER) cc_final: 0.3951 (tm-30) outliers start: 28 outliers final: 13 residues processed: 86 average time/residue: 0.2695 time to fit residues: 33.4983 Evaluate side-chains 67 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 52 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 221 PHE Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 231 MET Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 323 GLN Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 414 ILE Chi-restraints excluded: chain D residue 418 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 43 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 39 optimal weight: 20.0000 chunk 56 optimal weight: 8.9990 chunk 83 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 79 optimal weight: 0.7980 chunk 23 optimal weight: 10.0000 chunk 74 optimal weight: 4.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5567 moved from start: 0.8159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 16214 Z= 0.293 Angle : 0.737 13.369 24589 Z= 0.372 Chirality : 0.038 0.264 3165 Planarity : 0.005 0.054 1084 Dihedral : 25.514 163.371 8721 Min Nonbonded Distance : 0.977 Molprobity Statistics. All-atom Clashscore : 29.95 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.41 % Favored : 96.33 % Rotamer: Outliers : 6.45 % Allowed : 32.55 % 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: -0.78 (0.40), residues: 381 helix: -0.09 (0.31), residues: 251 sheet: -0.35 (0.89), residues: 19 loop : -1.29 (0.57), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP D 328 HIS 0.004 0.001 HIS D 109 PHE 0.015 0.003 PHE D 298 TYR 0.021 0.003 TYR D 37 ARG 0.009 0.001 ARG D 349 *********************** 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 80 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 58 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 173 LYS cc_start: 0.7131 (mttt) cc_final: 0.5947 (mptt) REVERT: D 175 LEU cc_start: 0.8102 (mt) cc_final: 0.7691 (tt) REVERT: D 240 ARG cc_start: 0.5059 (tmm-80) cc_final: 0.4637 (ptt90) REVERT: D 310 TRP cc_start: 0.6962 (OUTLIER) cc_final: 0.6176 (t60) REVERT: D 323 GLN cc_start: 0.6042 (OUTLIER) cc_final: 0.4403 (tm-30) outliers start: 22 outliers final: 13 residues processed: 76 average time/residue: 0.2910 time to fit residues: 31.8120 Evaluate side-chains 68 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 53 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 33 ASP Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 221 PHE Chi-restraints excluded: chain D residue 231 MET Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 285 GLN Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 323 GLN Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 414 ILE Chi-restraints excluded: chain D residue 418 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 66 optimal weight: 0.0570 chunk 36 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 chunk 61 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 overall best weight: 5.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5631 moved from start: 0.9021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 16214 Z= 0.312 Angle : 0.766 12.885 24589 Z= 0.387 Chirality : 0.040 0.265 3165 Planarity : 0.006 0.056 1084 Dihedral : 25.651 163.983 8721 Min Nonbonded Distance : 1.063 Molprobity Statistics. All-atom Clashscore : 33.06 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.94 % Favored : 95.80 % Rotamer: Outliers : 6.16 % Allowed : 33.72 % Favored : 60.12 % 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: -0.49 (0.42), residues: 381 helix: 0.13 (0.32), residues: 250 sheet: 0.19 (0.82), residues: 19 loop : -1.22 (0.61), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP D 328 HIS 0.002 0.001 HIS D 291 PHE 0.013 0.003 PHE D 113 TYR 0.023 0.003 TYR D 392 ARG 0.004 0.001 ARG D 172 *********************** 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 72 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 51 time to evaluate : 0.753 Fit side-chains REVERT: D 310 TRP cc_start: 0.7090 (OUTLIER) cc_final: 0.6321 (t60) REVERT: D 323 GLN cc_start: 0.6001 (OUTLIER) cc_final: 0.4157 (tm-30) outliers start: 21 outliers final: 16 residues processed: 67 average time/residue: 0.2795 time to fit residues: 27.4688 Evaluate side-chains 68 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 50 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 221 PHE Chi-restraints excluded: chain D residue 231 MET Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 280 ASP Chi-restraints excluded: chain D residue 285 GLN Chi-restraints excluded: chain D residue 309 SER Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 323 GLN Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 414 ILE Chi-restraints excluded: chain D residue 418 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 52 optimal weight: 30.0000 chunk 21 optimal weight: 10.0000 chunk 89 optimal weight: 0.2980 chunk 73 optimal weight: 7.9990 chunk 41 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 overall best weight: 5.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 22 GLN ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5653 moved from start: 0.9674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 16214 Z= 0.317 Angle : 0.777 13.443 24589 Z= 0.390 Chirality : 0.040 0.270 3165 Planarity : 0.006 0.052 1084 Dihedral : 25.714 163.291 8721 Min Nonbonded Distance : 0.987 Molprobity Statistics. All-atom Clashscore : 33.10 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.20 % Favored : 95.54 % Rotamer: Outliers : 8.80 % Allowed : 30.79 % Favored : 60.41 % 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: -0.86 (0.41), residues: 381 helix: -0.12 (0.31), residues: 253 sheet: 0.46 (0.92), residues: 14 loop : -1.52 (0.58), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 328 HIS 0.003 0.001 HIS D 291 PHE 0.013 0.003 PHE D 113 TYR 0.022 0.003 TYR D 392 ARG 0.005 0.001 ARG D 172 *********************** 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 84 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 54 time to evaluate : 0.673 Fit side-chains REVERT: D 173 LYS cc_start: 0.7286 (mttt) cc_final: 0.5891 (mptt) REVERT: D 310 TRP cc_start: 0.6927 (OUTLIER) cc_final: 0.6162 (t60) REVERT: D 323 GLN cc_start: 0.6106 (OUTLIER) cc_final: 0.4260 (tm-30) outliers start: 30 outliers final: 22 residues processed: 78 average time/residue: 0.2669 time to fit residues: 30.3858 Evaluate side-chains 77 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 53 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 33 ASP Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 135 ASP Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 221 PHE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 280 ASP Chi-restraints excluded: chain D residue 285 GLN Chi-restraints excluded: chain D residue 309 SER Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 323 GLN Chi-restraints excluded: chain D residue 338 LYS Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 414 ILE Chi-restraints excluded: chain D residue 418 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 10.0000 chunk 50 optimal weight: 20.0000 chunk 65 optimal weight: 7.9990 chunk 74 optimal weight: 0.9990 chunk 49 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 40 optimal weight: 20.0000 chunk 35 optimal weight: 10.0000 chunk 52 optimal weight: 20.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5640 moved from start: 0.9998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 16214 Z= 0.294 Angle : 0.744 13.084 24589 Z= 0.377 Chirality : 0.039 0.265 3165 Planarity : 0.005 0.051 1084 Dihedral : 25.676 163.172 8721 Min Nonbonded Distance : 1.020 Molprobity Statistics. All-atom Clashscore : 32.01 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.51 % Favored : 94.23 % Rotamer: Outliers : 7.92 % Allowed : 34.90 % Favored : 57.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.42), residues: 381 helix: 0.23 (0.33), residues: 246 sheet: 0.59 (0.92), residues: 14 loop : -2.00 (0.53), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 328 HIS 0.003 0.001 HIS D 291 PHE 0.020 0.002 PHE D 113 TYR 0.023 0.003 TYR D 392 ARG 0.005 0.001 ARG D 117 *********************** 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: 27 poor density : 55 time to evaluate : 0.750 Fit side-chains revert: symmetry clash REVERT: D 173 LYS cc_start: 0.6969 (mttt) cc_final: 0.5419 (mptt) REVERT: D 310 TRP cc_start: 0.6893 (OUTLIER) cc_final: 0.6129 (t60) REVERT: D 323 GLN cc_start: 0.6033 (OUTLIER) cc_final: 0.4209 (tm-30) outliers start: 27 outliers final: 16 residues processed: 75 average time/residue: 0.2942 time to fit residues: 32.0149 Evaluate side-chains 71 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 53 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 33 ASP Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 135 ASP Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 221 PHE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 309 SER Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 323 GLN Chi-restraints excluded: chain D residue 338 LYS Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 418 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 8.9990 chunk 17 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 43 optimal weight: 20.0000 chunk 8 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5340 moved from start: 0.9860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 16214 Z= 0.144 Angle : 0.608 15.303 24589 Z= 0.305 Chirality : 0.031 0.298 3165 Planarity : 0.004 0.050 1084 Dihedral : 25.151 169.678 8721 Min Nonbonded Distance : 1.159 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.99 % Favored : 94.75 % Rotamer: Outliers : 3.52 % Allowed : 38.71 % 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: -0.40 (0.42), residues: 381 helix: 0.47 (0.33), residues: 248 sheet: 0.55 (0.94), residues: 24 loop : -2.08 (0.55), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 328 HIS 0.002 0.001 HIS D 291 PHE 0.015 0.002 PHE D 113 TYR 0.016 0.002 TYR D 37 ARG 0.010 0.001 ARG D 172 *********************** 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 70 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 58 time to evaluate : 0.721 Fit side-chains revert: symmetry clash REVERT: D 7 MET cc_start: 0.3064 (tpt) cc_final: 0.2272 (mmm) REVERT: D 136 TRP cc_start: 0.7092 (m100) cc_final: 0.6885 (m100) REVERT: D 310 TRP cc_start: 0.6419 (OUTLIER) cc_final: 0.6140 (t60) outliers start: 12 outliers final: 8 residues processed: 66 average time/residue: 0.3052 time to fit residues: 29.3009 Evaluate side-chains 61 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 52 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 33 ASP Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 135 ASP Chi-restraints excluded: chain D residue 221 PHE Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 418 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 64 optimal weight: 0.9980 chunk 25 optimal weight: 9.9990 chunk 74 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 54 optimal weight: 0.3980 chunk 87 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5485 moved from start: 1.0038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 16214 Z= 0.196 Angle : 0.643 15.743 24589 Z= 0.323 Chirality : 0.033 0.250 3165 Planarity : 0.005 0.050 1084 Dihedral : 25.230 167.623 8721 Min Nonbonded Distance : 1.055 Molprobity Statistics. All-atom Clashscore : 22.99 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.77 % Favored : 93.96 % Rotamer: Outliers : 3.52 % Allowed : 38.71 % 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: -0.21 (0.43), residues: 381 helix: 0.60 (0.33), residues: 244 sheet: 0.67 (0.92), residues: 24 loop : -1.89 (0.56), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.082 0.005 TRP D 328 HIS 0.003 0.001 HIS D 109 PHE 0.022 0.003 PHE D 332 TYR 0.017 0.003 TYR D 331 ARG 0.004 0.001 ARG D 172 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 52 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 310 TRP cc_start: 0.6780 (OUTLIER) cc_final: 0.6213 (t60) outliers start: 12 outliers final: 11 residues processed: 61 average time/residue: 0.2783 time to fit residues: 24.7126 Evaluate side-chains 64 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 52 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 33 ASP Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 135 ASP Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 221 PHE Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 418 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 10.0000 chunk 60 optimal weight: 0.3980 chunk 91 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 72 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 chunk 77 optimal weight: 0.7980 chunk 22 optimal weight: 10.0000 overall best weight: 3.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5507 moved from start: 1.0156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 16214 Z= 0.212 Angle : 0.656 16.714 24589 Z= 0.329 Chirality : 0.034 0.258 3165 Planarity : 0.005 0.049 1084 Dihedral : 25.266 169.832 8721 Min Nonbonded Distance : 1.050 Molprobity Statistics. All-atom Clashscore : 24.08 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.51 % Favored : 94.23 % Rotamer: Outliers : 3.52 % Allowed : 39.30 % Favored : 57.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.42), residues: 381 helix: 0.58 (0.33), residues: 246 sheet: 1.36 (1.08), residues: 14 loop : -2.03 (0.52), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.005 TRP D 328 HIS 0.003 0.001 HIS D 291 PHE 0.016 0.002 PHE D 332 TYR 0.017 0.002 TYR D 392 ARG 0.006 0.001 ARG D 377 ********************** 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 64 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 52 time to evaluate : 0.650 Fit side-chains revert: symmetry clash REVERT: D 7 MET cc_start: 0.2412 (mmm) cc_final: 0.1569 (mmm) REVERT: D 310 TRP cc_start: 0.6751 (OUTLIER) cc_final: 0.6231 (t60) outliers start: 12 outliers final: 10 residues processed: 62 average time/residue: 0.2875 time to fit residues: 25.9825 Evaluate side-chains 60 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 49 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 33 ASP Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 135 ASP Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 221 PHE Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 418 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 75 optimal weight: 0.0970 chunk 9 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 64 optimal weight: 0.9980 chunk 4 optimal weight: 10.0000 chunk 52 optimal weight: 30.0000 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.070097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.056725 restraints weight = 110093.330| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.70 r_work: 0.3642 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 1.0382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16214 Z= 0.233 Angle : 0.682 16.763 24589 Z= 0.342 Chirality : 0.035 0.260 3165 Planarity : 0.005 0.048 1084 Dihedral : 25.342 173.524 8721 Min Nonbonded Distance : 1.036 Molprobity Statistics. All-atom Clashscore : 26.47 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.30 % Favored : 93.44 % Rotamer: Outliers : 3.81 % Allowed : 39.00 % Favored : 57.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.42), residues: 381 helix: 0.45 (0.33), residues: 246 sheet: 1.41 (1.12), residues: 14 loop : -1.91 (0.55), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP D 328 HIS 0.003 0.001 HIS D 109 PHE 0.026 0.003 PHE D 298 TYR 0.018 0.003 TYR D 392 ARG 0.005 0.001 ARG D 377 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2389.82 seconds wall clock time: 44 minutes 42.65 seconds (2682.65 seconds total)