Starting phenix.real_space_refine on Sun May 19 16:30:35 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8jo4_36455.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8jo4_36455.pdb Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- run=minimization_global+local_grid_search+nqh_flips resolution=3.04 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8jo4_36455.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8jo4_36455.map" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8jo4_36455.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8jo4_36455.pdb" } resolution = 3.04 refinement { run = *minimization_global rigid_body *local_grid_search morphing \ simulated_annealing adp occupancy *nqh_flips } 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= 0.021 sd= 0.333 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: 5 Type Number sf(0) Gaussians S 27 5.16 5 C 3596 2.51 5 N 941 2.21 5 O 1093 1.98 5 H 5654 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 11311 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 5717 Classifications: {'peptide': 350} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 338} Chain: "B" Number of atoms: 5594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 5594 Inner-chain residues flagged as termini: ['pdbres="PRO B 40 "', 'pdbres="ASP B 53 "'] Classifications: {'peptide': 359} Modifications used: {'COO': 2, 'NH3': 2} Link IDs: {'PTRANS': 19, 'TRANS': 339} Chain breaks: 1 Time building chain proxies: 1.84, per 1000 atoms: 0.16 Number of scatterers: 11311 At special positions: 0 Unit cell: (65.1, 82.77, 115.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 27 16.00 O 1093 8.00 N 941 7.00 C 3596 6.00 H 5654 1.00 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: 2.85 Conformation dependent library (CDL) restraints added in 354.1 milliseconds 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1348 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 5 sheets defined 52.0% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 5 through 15 Processing helix chain 'A' and resid 21 through 36 Processing helix chain 'A' and resid 42 through 54 Processing helix chain 'A' and resid 58 through 71 Processing helix chain 'A' and resid 73 through 76 No H-bonds generated for 'chain 'A' and resid 73 through 76' Processing helix chain 'A' and resid 78 through 90 removed outlier: 3.669A pdb=" N SER A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN A 90 " --> pdb=" O THR A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 122 through 133 Processing helix chain 'A' and resid 150 through 163 removed outlier: 4.711A pdb=" N VAL A 161 " --> pdb=" O ILE A 157 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N MET A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N LEU A 163 " --> pdb=" O ALA A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 174 Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 229 through 232 No H-bonds generated for 'chain 'A' and resid 229 through 232' Processing helix chain 'A' and resid 244 through 258 removed outlier: 4.065A pdb=" N ASP A 258 " --> pdb=" O LYS A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 283 Processing helix chain 'A' and resid 289 through 296 Processing helix chain 'A' and resid 299 through 307 Processing helix chain 'A' and resid 321 through 351 Processing helix chain 'B' and resid 58 through 62 Processing helix chain 'B' and resid 81 through 93 Processing helix chain 'B' and resid 100 through 102 No H-bonds generated for 'chain 'B' and resid 100 through 102' Processing helix chain 'B' and resid 115 through 127 Processing helix chain 'B' and resid 139 through 147 removed outlier: 3.681A pdb=" N SER B 147 " --> pdb=" O SER B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 197 Processing helix chain 'B' and resid 205 through 217 Processing helix chain 'B' and resid 225 through 234 Processing helix chain 'B' and resid 254 through 263 removed outlier: 3.552A pdb=" N ARG B 258 " --> pdb=" O GLU B 255 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N CYS B 259 " --> pdb=" O ARG B 256 " (cutoff:3.500A) Proline residue: B 260 - end of helix Processing helix chain 'B' and resid 266 through 269 Processing helix chain 'B' and resid 276 through 285 Processing helix chain 'B' and resid 289 through 297 removed outlier: 3.677A pdb=" N ARG B 292 " --> pdb=" O ILE B 289 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N LYS B 293 " --> pdb=" O ASP B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 306 No H-bonds generated for 'chain 'B' and resid 304 through 306' Processing helix chain 'B' and resid 311 through 322 Processing helix chain 'B' and resid 337 through 349 removed outlier: 5.444A pdb=" N VAL B 341 " --> pdb=" O LYS B 338 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA B 349 " --> pdb=" O SER B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 356 removed outlier: 3.823A pdb=" N GLN B 356 " --> pdb=" O THR B 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 353 through 356' Processing helix chain 'B' and resid 361 through 367 Processing helix chain 'B' and resid 369 through 375 removed outlier: 3.871A pdb=" N LYS B 375 " --> pdb=" O VAL B 372 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 190 through 193 Processing sheet with id= B, first strand: chain 'B' and resid 134 through 138 removed outlier: 6.851A pdb=" N THR B 105 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N ALA B 137 " --> pdb=" O THR B 105 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU B 107 " --> pdb=" O ALA B 137 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LEU B 10 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N THR B 108 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N CYS B 12 " --> pdb=" O THR B 108 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 37 through 39 Processing sheet with id= D, first strand: chain 'B' and resid 299 through 302 removed outlier: 6.338A pdb=" N ILE B 153 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N SER B 302 " --> pdb=" O ILE B 153 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N LEU B 155 " --> pdb=" O SER B 302 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 240 through 243 251 hydrogen bonds defined for protein. 642 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.09 Time building geometry restraints manager: 3.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.14: 5647 1.14 - 1.31: 974 1.31 - 1.48: 2221 1.48 - 1.64: 2533 1.64 - 1.81: 47 Bond restraints: 11422 Sorted by residual: bond pdb=" N GLY B 345 " pdb=" H GLY B 345 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.78e+01 bond pdb=" N VAL A 250 " pdb=" H VAL A 250 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.71e+01 bond pdb=" N VAL A 251 " pdb=" H VAL A 251 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.69e+01 bond pdb=" N ILE B 343 " pdb=" H ILE B 343 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.68e+01 bond pdb=" N ASP A 15 " pdb=" H ASP A 15 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.68e+01 ... (remaining 11417 not shown) Histogram of bond angle deviations from ideal: 98.62 - 105.70: 113 105.70 - 112.78: 13541 112.78 - 119.85: 2950 119.85 - 126.93: 4031 126.93 - 134.01: 57 Bond angle restraints: 20692 Sorted by residual: angle pdb=" N VAL B 341 " pdb=" CA VAL B 341 " pdb=" C VAL B 341 " ideal model delta sigma weight residual 110.23 107.92 2.31 1.04e+00 9.25e-01 4.92e+00 angle pdb=" CA VAL B 165 " pdb=" C VAL B 165 " pdb=" O VAL B 165 " ideal model delta sigma weight residual 120.88 119.58 1.30 6.80e-01 2.16e+00 3.65e+00 angle pdb=" CA TRP B 358 " pdb=" CB TRP B 358 " pdb=" CG TRP B 358 " ideal model delta sigma weight residual 113.60 116.67 -3.07 1.90e+00 2.77e-01 2.61e+00 angle pdb=" CA VAL B 165 " pdb=" C VAL B 165 " pdb=" N PRO B 166 " ideal model delta sigma weight residual 118.12 119.42 -1.30 8.10e-01 1.52e+00 2.56e+00 angle pdb=" N VAL A 239 " pdb=" CA VAL A 239 " pdb=" C VAL A 239 " ideal model delta sigma weight residual 111.58 109.94 1.64 1.06e+00 8.90e-01 2.39e+00 ... (remaining 20687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 5011 17.93 - 35.86: 236 35.86 - 53.80: 99 53.80 - 71.73: 23 71.73 - 89.66: 4 Dihedral angle restraints: 5373 sinusoidal: 2943 harmonic: 2430 Sorted by residual: dihedral pdb=" CA VAL A 239 " pdb=" C VAL A 239 " pdb=" N ALA A 240 " pdb=" CA ALA A 240 " ideal model delta harmonic sigma weight residual 180.00 162.48 17.52 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" N ASP A 321 " pdb=" CA ASP A 321 " pdb=" CB ASP A 321 " pdb=" CG ASP A 321 " ideal model delta sinusoidal sigma weight residual -180.00 -120.45 -59.55 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N GLN A 82 " pdb=" CA GLN A 82 " pdb=" CB GLN A 82 " pdb=" CG GLN A 82 " ideal model delta sinusoidal sigma weight residual -180.00 -121.03 -58.97 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 5370 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 555 0.029 - 0.057: 215 0.057 - 0.086: 55 0.086 - 0.114: 38 0.114 - 0.143: 14 Chirality restraints: 877 Sorted by residual: chirality pdb=" CA ILE B 167 " pdb=" N ILE B 167 " pdb=" C ILE B 167 " pdb=" CB ILE B 167 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.09e-01 chirality pdb=" CA ILE B 359 " pdb=" N ILE B 359 " pdb=" C ILE B 359 " pdb=" CB ILE B 359 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.99e-01 chirality pdb=" CA VAL A 236 " pdb=" N VAL A 236 " pdb=" C VAL A 236 " pdb=" CB VAL A 236 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.00e-01 ... (remaining 874 not shown) Planarity restraints: 1680 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 165 " -0.027 5.00e-02 4.00e+02 4.07e-02 2.66e+00 pdb=" N PRO B 166 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 166 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 166 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 211 " -0.025 5.00e-02 4.00e+02 3.83e-02 2.35e+00 pdb=" N PRO A 212 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 212 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 212 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 16 " 0.016 5.00e-02 4.00e+02 2.39e-02 9.16e-01 pdb=" N PRO A 17 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO A 17 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 17 " 0.013 5.00e-02 4.00e+02 ... (remaining 1677 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.12: 782 2.12 - 2.74: 19720 2.74 - 3.36: 34527 3.36 - 3.98: 46578 3.98 - 4.60: 69628 Nonbonded interactions: 171235 Sorted by model distance: nonbonded pdb=" HG SER A 175 " pdb=" OD2 ASP A 298 " model vdw 1.495 1.850 nonbonded pdb=" O ILE B 319 " pdb=" H ALA B 323 " model vdw 1.497 1.850 nonbonded pdb=" OE1 GLU A 343 " pdb=" HG1 THR B 353 " model vdw 1.513 1.850 nonbonded pdb="HH22 ARG B 118 " pdb=" O CYS B 376 " model vdw 1.524 1.850 nonbonded pdb=" O THR B 8 " pdb=" HD1 HIS B 103 " model vdw 1.534 1.850 ... (remaining 171230 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: 5 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.50 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will not be refined 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: 0.020 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: 0.060 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 14.150 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 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:0.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:8.710 Internal consistency checks: 0.000 Total: 23.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 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 : 0.002 0.035 5768 Z= 0.135 Angle : 0.434 4.101 7805 Z= 0.237 Chirality : 0.039 0.143 877 Planarity : 0.003 0.041 1004 Dihedral : 11.622 89.662 2177 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.84 % Favored : 97.01 % Rotamer: Outliers : 2.09 % Allowed : 4.82 % Favored : 93.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.31), residues: 703 helix: 0.39 (0.26), residues: 379 sheet: -0.52 (0.59), residues: 64 loop : 0.27 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 337 TYR 0.007 0.001 TYR A 132 PHE 0.009 0.001 PHE A 125 TRP 0.009 0.001 TRP B 358 HIS 0.004 0.001 HIS A 300 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 143 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 GLU cc_start: 0.7427 (mt-10) cc_final: 0.7177 (mt-10) REVERT: A 129 ASN cc_start: 0.6955 (t0) cc_final: 0.6668 (t0) REVERT: A 217 ASP cc_start: 0.7818 (m-30) cc_final: 0.7606 (m-30) REVERT: A 247 TYR cc_start: 0.8407 (m-80) cc_final: 0.8162 (m-80) REVERT: A 272 ASN cc_start: 0.8025 (t0) cc_final: 0.7812 (t0) REVERT: B 269 ILE cc_start: 0.8477 (pt) cc_final: 0.8157 (tt) REVERT: B 298 ASN cc_start: 0.7560 (m-40) cc_final: 0.7304 (m-40) REVERT: B 362 GLN cc_start: 0.6934 (tt0) cc_final: 0.6610 (tp-100) outliers start: 13 outliers final: 8 residues processed: 152 average time/residue: 0.2475 time to fit residues: 49.6494 Evaluate side-chains 112 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 104 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain B residue 259 CYS Chi-restraints excluded: chain B residue 315 MET Chi-restraints excluded: chain B residue 346 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN A 174 GLN B 355 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 5768 Z= 0.306 Angle : 0.495 4.635 7805 Z= 0.261 Chirality : 0.041 0.143 877 Planarity : 0.004 0.042 1004 Dihedral : 6.738 85.026 787 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.28 % Favored : 97.58 % Rotamer: Outliers : 2.57 % Allowed : 8.83 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.32), residues: 703 helix: 0.65 (0.26), residues: 378 sheet: -0.60 (0.59), residues: 66 loop : 0.41 (0.41), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 101 TYR 0.009 0.001 TYR A 139 PHE 0.012 0.002 PHE A 125 TRP 0.008 0.002 TRP A 277 HIS 0.004 0.001 HIS A 300 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 103 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7468 (tt) REVERT: A 129 ASN cc_start: 0.7103 (t0) cc_final: 0.6763 (t0) REVERT: B 269 ILE cc_start: 0.8558 (pt) cc_final: 0.8252 (tt) REVERT: B 298 ASN cc_start: 0.7715 (m-40) cc_final: 0.7466 (m-40) REVERT: B 362 GLN cc_start: 0.6966 (tt0) cc_final: 0.6582 (tp-100) outliers start: 16 outliers final: 11 residues processed: 114 average time/residue: 0.2761 time to fit residues: 42.2385 Evaluate side-chains 106 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 94 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 174 GLN Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain B residue 315 MET Chi-restraints excluded: chain B residue 346 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 64 optimal weight: 0.8980 chunk 17 optimal weight: 9.9990 chunk 36 optimal weight: 0.0030 chunk 12 optimal weight: 9.9990 chunk 32 optimal weight: 8.9990 chunk 68 optimal weight: 0.9980 chunk 18 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 42 optimal weight: 9.9990 chunk 60 optimal weight: 9.9990 overall best weight: 3.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN A 322 HIS B 355 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5768 Z= 0.203 Angle : 0.460 4.308 7805 Z= 0.241 Chirality : 0.040 0.141 877 Planarity : 0.004 0.043 1004 Dihedral : 6.289 80.741 781 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.28 % Favored : 97.58 % Rotamer: Outliers : 1.77 % Allowed : 10.59 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.32), residues: 703 helix: 0.90 (0.27), residues: 378 sheet: -0.48 (0.60), residues: 66 loop : 0.56 (0.41), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 136 TYR 0.008 0.001 TYR A 330 PHE 0.011 0.001 PHE A 125 TRP 0.008 0.002 TRP B 358 HIS 0.004 0.001 HIS A 300 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 98 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7406 (tt) REVERT: A 129 ASN cc_start: 0.7044 (t0) cc_final: 0.6675 (t0) REVERT: A 247 TYR cc_start: 0.8471 (m-80) cc_final: 0.8196 (m-80) REVERT: A 272 ASN cc_start: 0.8126 (t0) cc_final: 0.7888 (t0) REVERT: B 269 ILE cc_start: 0.8539 (pt) cc_final: 0.8247 (tt) REVERT: B 298 ASN cc_start: 0.7696 (m-40) cc_final: 0.7452 (m-40) REVERT: B 362 GLN cc_start: 0.6943 (tt0) cc_final: 0.6560 (tp-100) outliers start: 11 outliers final: 8 residues processed: 106 average time/residue: 0.1988 time to fit residues: 28.5503 Evaluate side-chains 106 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 97 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain B residue 315 MET Chi-restraints excluded: chain B residue 346 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 12 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 40 optimal weight: 8.9990 chunk 26 optimal weight: 8.9990 chunk 61 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 66 optimal weight: 0.0070 chunk 33 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 overall best weight: 6.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 355 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5768 Z= 0.304 Angle : 0.496 4.639 7805 Z= 0.261 Chirality : 0.041 0.142 877 Planarity : 0.004 0.039 1004 Dihedral : 6.267 70.112 781 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.70 % Favored : 97.16 % Rotamer: Outliers : 2.57 % Allowed : 10.27 % Favored : 87.16 % 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: 0.54 (0.32), residues: 703 helix: 0.70 (0.27), residues: 379 sheet: -0.57 (0.60), residues: 66 loop : 0.36 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 136 TYR 0.009 0.001 TYR A 330 PHE 0.011 0.002 PHE A 125 TRP 0.008 0.002 TRP B 81 HIS 0.005 0.001 HIS A 300 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 99 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7434 (tt) REVERT: A 129 ASN cc_start: 0.7088 (t0) cc_final: 0.6697 (t0) REVERT: A 162 MET cc_start: 0.6631 (OUTLIER) cc_final: 0.6408 (mtp) REVERT: B 269 ILE cc_start: 0.8557 (pt) cc_final: 0.8293 (tt) REVERT: B 298 ASN cc_start: 0.7798 (m-40) cc_final: 0.7575 (m-40) REVERT: B 362 GLN cc_start: 0.6963 (tt0) cc_final: 0.6537 (tp-100) REVERT: B 377 PHE cc_start: 0.7797 (p90) cc_final: 0.7523 (p90) outliers start: 16 outliers final: 11 residues processed: 110 average time/residue: 0.1733 time to fit residues: 25.4559 Evaluate side-chains 109 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 96 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 259 CYS Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain B residue 346 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 11 optimal weight: 9.9990 chunk 51 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 chunk 42 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 30 optimal weight: 0.4980 overall best weight: 5.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5768 Z= 0.295 Angle : 0.504 4.400 7805 Z= 0.264 Chirality : 0.041 0.156 877 Planarity : 0.004 0.038 1004 Dihedral : 5.822 59.371 778 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.70 % Favored : 97.16 % Rotamer: Outliers : 2.25 % Allowed : 10.91 % Favored : 86.84 % 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: 0.44 (0.32), residues: 703 helix: 0.61 (0.27), residues: 378 sheet: -0.57 (0.61), residues: 66 loop : 0.31 (0.40), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 136 TYR 0.009 0.001 TYR A 330 PHE 0.010 0.002 PHE A 125 TRP 0.007 0.002 TRP B 81 HIS 0.004 0.001 HIS A 300 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 95 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7414 (tt) REVERT: A 129 ASN cc_start: 0.7115 (t0) cc_final: 0.6715 (t0) REVERT: A 162 MET cc_start: 0.6603 (OUTLIER) cc_final: 0.6380 (mtp) REVERT: A 247 TYR cc_start: 0.8492 (m-80) cc_final: 0.8207 (m-80) REVERT: B 269 ILE cc_start: 0.8573 (pt) cc_final: 0.8307 (tt) REVERT: B 362 GLN cc_start: 0.6809 (tt0) cc_final: 0.6378 (tp-100) REVERT: B 377 PHE cc_start: 0.7896 (p90) cc_final: 0.7560 (p90) outliers start: 14 outliers final: 12 residues processed: 107 average time/residue: 0.1754 time to fit residues: 25.2339 Evaluate side-chains 107 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 93 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 259 CYS Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain B residue 346 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 18 optimal weight: 9.9990 chunk 69 optimal weight: 9.9990 chunk 57 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 355 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5768 Z= 0.261 Angle : 0.493 4.302 7805 Z= 0.257 Chirality : 0.041 0.167 877 Planarity : 0.004 0.037 1004 Dihedral : 5.667 58.935 778 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.84 % Favored : 97.01 % Rotamer: Outliers : 2.25 % Allowed : 10.75 % Favored : 87.00 % 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: 0.48 (0.32), residues: 703 helix: 0.64 (0.27), residues: 378 sheet: -0.62 (0.60), residues: 66 loop : 0.34 (0.40), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 136 TYR 0.009 0.001 TYR A 42 PHE 0.010 0.001 PHE A 125 TRP 0.007 0.002 TRP B 358 HIS 0.004 0.001 HIS A 300 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 833.14 seconds wall clock time: 14 minutes 54.28 seconds (894.28 seconds total)