Starting phenix.real_space_refine on Sun May 19 16:30:36 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6y9x_10740.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6y9x_10740.pdb Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- run=minimization_global+local_grid_search+nqh_flips resolution=4.4 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6y9x_10740.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6y9x_10740.map" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6y9x_10740.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6y9x_10740.pdb" } resolution = 4.4 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= 0.003 sd= 0.006 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 26 5.16 5 C 2162 2.51 5 N 598 2.21 5 O 649 1.98 5 H 3432 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6867 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2265 Classifications: {'peptide': 146} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 134} Chain: "B" Number of atoms: 3432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 3432 Classifications: {'peptide': 220} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 202} Chain: "N" Number of atoms: 1170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1170 Classifications: {'peptide': 74} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 4, 'TRANS': 69} Time building chain proxies: 1.17, per 1000 atoms: 0.17 Number of scatterers: 6867 At special positions: 0 Unit cell: (95.4, 125.08, 85.86, 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 26 16.00 O 649 8.00 N 598 7.00 C 2162 6.00 H 3432 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 198 " - pdb=" SG CYS B 218 " distance=2.04 Simple disulfide: pdb=" SG CYS N 198 " - pdb=" SG CYS N 218 " distance=2.04 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: 1.47 Conformation dependent library (CDL) restraints added in 210.4 milliseconds 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 824 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 1 sheets defined 57.5% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 17 through 30 Processing helix chain 'A' and resid 35 through 43 Processing helix chain 'A' and resid 49 through 57 Processing helix chain 'A' and resid 63 through 83 Processing helix chain 'A' and resid 101 through 104 No H-bonds generated for 'chain 'A' and resid 101 through 104' Processing helix chain 'A' and resid 111 through 119 Processing helix chain 'A' and resid 126 through 144 Processing helix chain 'B' and resid 17 through 26 Processing helix chain 'B' and resid 34 through 43 removed outlier: 3.765A pdb=" N ILE B 37 " --> pdb=" O PRO B 34 " (cutoff:3.500A) Proline residue: B 38 - end of helix Processing helix chain 'B' and resid 49 through 57 Processing helix chain 'B' and resid 63 through 83 Processing helix chain 'B' and resid 111 through 119 Processing helix chain 'B' and resid 126 through 144 Processing helix chain 'B' and resid 150 through 152 No H-bonds generated for 'chain 'B' and resid 150 through 152' Processing helix chain 'B' and resid 161 through 174 Processing helix chain 'B' and resid 179 through 189 removed outlier: 3.704A pdb=" N TRP B 184 " --> pdb=" O GLU B 180 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU B 187 " --> pdb=" O ASN B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 205 removed outlier: 3.552A pdb=" N LEU B 205 " --> pdb=" O ILE B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 217 Processing helix chain 'N' and resid 150 through 152 No H-bonds generated for 'chain 'N' and resid 150 through 152' Processing helix chain 'N' and resid 161 through 174 Processing helix chain 'N' and resid 179 through 189 removed outlier: 3.709A pdb=" N TRP N 184 " --> pdb=" O GLU N 180 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU N 187 " --> pdb=" O ASN N 183 " (cutoff:3.500A) Processing helix chain 'N' and resid 196 through 205 removed outlier: 3.552A pdb=" N LEU N 205 " --> pdb=" O ILE N 201 " (cutoff:3.500A) Processing helix chain 'N' and resid 211 through 217 Processing sheet with id= A, first strand: chain 'A' and resid 2 through 4 156 hydrogen bonds defined for protein. 459 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: 1.09 Time building geometry restraints manager: 1.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.15: 3432 1.15 - 1.32: 591 1.32 - 1.49: 1346 1.49 - 1.65: 1525 1.65 - 1.82: 48 Bond restraints: 6942 Sorted by residual: bond pdb=" N VAL B 27 " pdb=" H VAL B 27 " ideal model delta sigma weight residual 0.860 1.030 -0.170 2.00e-02 2.50e+03 7.26e+01 bond pdb=" N ILE B 37 " pdb=" H ILE B 37 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.84e+01 bond pdb=" N GLU B 28 " pdb=" H GLU B 28 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.80e+01 bond pdb=" N PHE B 32 " pdb=" H PHE B 32 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.79e+01 bond pdb=" N ALA B 47 " pdb=" H ALA B 47 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.65e+01 ... (remaining 6937 not shown) Histogram of bond angle deviations from ideal: 100.27 - 107.01: 202 107.01 - 113.75: 8403 113.75 - 120.49: 2188 120.49 - 127.23: 1768 127.23 - 133.96: 58 Bond angle restraints: 12619 Sorted by residual: angle pdb=" C ALA A 31 " pdb=" CA ALA A 31 " pdb=" CB ALA A 31 " ideal model delta sigma weight residual 117.23 111.35 5.88 1.36e+00 5.41e-01 1.87e+01 angle pdb=" C ILE B 6 " pdb=" N GLN B 7 " pdb=" CA GLN B 7 " ideal model delta sigma weight residual 121.70 126.70 -5.00 1.80e+00 3.09e-01 7.73e+00 angle pdb=" N VAL A 83 " pdb=" CA VAL A 83 " pdb=" C VAL A 83 " ideal model delta sigma weight residual 112.29 110.01 2.28 9.40e-01 1.13e+00 5.90e+00 angle pdb=" CA ALA A 31 " pdb=" C ALA A 31 " pdb=" N PHE A 32 " ideal model delta sigma weight residual 119.98 118.01 1.97 8.50e-01 1.38e+00 5.38e+00 angle pdb=" C ILE B 37 " pdb=" N PRO B 38 " pdb=" CA PRO B 38 " ideal model delta sigma weight residual 118.97 120.83 -1.86 1.04e+00 9.25e-01 3.21e+00 ... (remaining 12614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.70: 2918 14.70 - 29.40: 216 29.40 - 44.10: 100 44.10 - 58.81: 42 58.81 - 73.51: 2 Dihedral angle restraints: 3278 sinusoidal: 1853 harmonic: 1425 Sorted by residual: dihedral pdb=" CB CYS B 198 " pdb=" SG CYS B 198 " pdb=" SG CYS B 218 " pdb=" CB CYS B 218 " ideal model delta sinusoidal sigma weight residual -86.00 -111.00 25.00 1 1.00e+01 1.00e-02 8.99e+00 dihedral pdb=" CB CYS N 198 " pdb=" SG CYS N 198 " pdb=" SG CYS N 218 " pdb=" CB CYS N 218 " ideal model delta sinusoidal sigma weight residual -86.00 -110.92 24.92 1 1.00e+01 1.00e-02 8.94e+00 dihedral pdb=" CB MET N 215 " pdb=" CG MET N 215 " pdb=" SD MET N 215 " pdb=" CE MET N 215 " ideal model delta sinusoidal sigma weight residual -180.00 -131.88 -48.12 3 1.50e+01 4.44e-03 8.59e+00 ... (remaining 3275 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 348 0.027 - 0.055: 121 0.055 - 0.082: 33 0.082 - 0.110: 26 0.110 - 0.137: 6 Chirality restraints: 534 Sorted by residual: chirality pdb=" CA ILE B 124 " pdb=" N ILE B 124 " pdb=" C ILE B 124 " pdb=" CB ILE B 124 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.72e-01 chirality pdb=" CA ILE A 2 " pdb=" N ILE A 2 " pdb=" C ILE A 2 " pdb=" CB ILE A 2 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.29e-01 chirality pdb=" CA ILE A 124 " pdb=" N ILE A 124 " pdb=" C ILE A 124 " pdb=" CB ILE A 124 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.98e-01 ... (remaining 531 not shown) Planarity restraints: 1031 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 37 " 0.031 5.00e-02 4.00e+02 4.72e-02 3.56e+00 pdb=" N PRO A 38 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 38 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 38 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 33 " 0.019 5.00e-02 4.00e+02 2.93e-02 1.37e+00 pdb=" N PRO A 34 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 34 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 34 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 37 " 0.018 5.00e-02 4.00e+02 2.77e-02 1.23e+00 pdb=" N PRO B 38 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO B 38 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 38 " 0.015 5.00e-02 4.00e+02 ... (remaining 1028 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.12: 358 2.12 - 2.74: 11148 2.74 - 3.36: 18893 3.36 - 3.98: 23483 3.98 - 4.60: 35273 Nonbonded interactions: 89155 Sorted by model distance: nonbonded pdb=" OE1 GLN N 179 " pdb="HD21 ASN N 183 " model vdw 1.503 1.850 nonbonded pdb=" OE1 GLN B 179 " pdb="HD21 ASN B 183 " model vdw 1.509 1.850 nonbonded pdb=" O ASN B 195 " pdb=" H LYS B 199 " model vdw 1.536 1.850 nonbonded pdb=" O ASN N 195 " pdb=" H LYS N 199 " model vdw 1.536 1.850 nonbonded pdb=" O SER A 44 " pdb=" HZ3 LYS A 131 " model vdw 1.593 1.850 ... (remaining 89150 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: 0.030 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: 0.040 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.420 Find NCS groups from input model: 0.040 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:0.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:5.430 Internal consistency checks: 0.000 Total: 14.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 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 0.024 3510 Z= 0.146 Angle : 0.446 5.882 4772 Z= 0.241 Chirality : 0.037 0.137 534 Planarity : 0.004 0.047 625 Dihedral : 11.743 73.507 1334 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 1.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.80 % Allowed : 2.67 % Favored : 96.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.25 % 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: -0.68 (0.38), residues: 434 helix: -0.08 (0.30), residues: 280 sheet: -3.36 (0.65), residues: 9 loop : -0.74 (0.48), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 18 TYR 0.006 0.001 TYR B 145 PHE 0.004 0.001 PHE A 32 TRP 0.005 0.001 TRP B 117 HIS 0.002 0.000 HIS B 12 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 232 time to evaluate : 0.164 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.9621 (mt) cc_final: 0.9267 (mt) REVERT: A 96 MET cc_start: -0.1400 (mpp) cc_final: -0.1860 (mmt) REVERT: A 103 ASP cc_start: 0.7770 (m-30) cc_final: 0.7379 (m-30) REVERT: B 51 ASP cc_start: 0.9327 (m-30) cc_final: 0.9068 (m-30) REVERT: B 63 GLN cc_start: 0.8248 (mm-40) cc_final: 0.7353 (pt0) REVERT: B 74 ASN cc_start: 0.9180 (m-40) cc_final: 0.8945 (m110) REVERT: B 100 ARG cc_start: 0.7976 (mtm110) cc_final: 0.7500 (mtp85) REVERT: B 131 LYS cc_start: 0.9596 (ttmt) cc_final: 0.9350 (mttt) REVERT: B 139 ASN cc_start: 0.9158 (m-40) cc_final: 0.8875 (m110) REVERT: B 153 ILE cc_start: 0.8579 (mm) cc_final: 0.8106 (mm) REVERT: N 175 GLU cc_start: 0.6760 (tm-30) cc_final: 0.6009 (mm-30) outliers start: 3 outliers final: 1 residues processed: 234 average time/residue: 0.2575 time to fit residues: 69.2143 Evaluate side-chains 184 residues out of total 374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 183 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 8.9990 chunk 26 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 16 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 chunk 25 optimal weight: 8.9990 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 chunk 37 optimal weight: 8.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN B 193 ASN N 183 ASN N 193 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.4986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3510 Z= 0.214 Angle : 0.518 4.526 4772 Z= 0.269 Chirality : 0.038 0.127 534 Planarity : 0.004 0.041 625 Dihedral : 3.745 30.403 468 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.25 % 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 (0.40), residues: 434 helix: 0.68 (0.31), residues: 281 sheet: -2.49 (0.95), residues: 9 loop : 0.02 (0.50), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 167 TYR 0.007 0.001 TYR N 169 PHE 0.010 0.001 PHE A 32 TRP 0.017 0.001 TRP A 23 HIS 0.003 0.001 HIS B 62 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 0.334 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: 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: 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 23 TRP cc_start: 0.9439 (t-100) cc_final: 0.9143 (t-100) REVERT: A 27 VAL cc_start: 0.9512 (t) cc_final: 0.9172 (t) REVERT: A 50 GLN cc_start: 0.9308 (tm-30) cc_final: 0.9040 (tm-30) REVERT: A 113 GLU cc_start: 0.9271 (mt-10) cc_final: 0.8939 (mt-10) REVERT: B 2 ILE cc_start: 0.7843 (pt) cc_final: 0.7478 (pt) REVERT: B 63 GLN cc_start: 0.8385 (mm-40) cc_final: 0.7571 (pt0) REVERT: B 74 ASN cc_start: 0.9312 (m-40) cc_final: 0.9063 (m110) REVERT: B 100 ARG cc_start: 0.8271 (mtm110) cc_final: 0.7843 (mtp85) REVERT: B 114 GLN cc_start: 0.8866 (mt0) cc_final: 0.8626 (mt0) REVERT: B 118 MET cc_start: 0.8950 (mtm) cc_final: 0.8378 (ptp) REVERT: B 131 LYS cc_start: 0.9622 (ttmt) cc_final: 0.9338 (tttt) REVERT: B 153 ILE cc_start: 0.8476 (mm) cc_final: 0.8141 (mm) REVERT: N 188 THR cc_start: 0.8992 (m) cc_final: 0.8761 (m) REVERT: N 203 LYS cc_start: 0.8679 (mtpt) cc_final: 0.8417 (mtpt) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.3032 time to fit residues: 73.4492 Evaluate side-chains 169 residues out of total 374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 13 optimal weight: 30.0000 chunk 32 optimal weight: 9.9990 chunk 8 optimal weight: 0.1980 chunk 18 optimal weight: 20.0000 chunk 6 optimal weight: 9.9990 chunk 39 optimal weight: 20.0000 chunk 16 optimal weight: 20.0000 chunk 34 optimal weight: 7.9990 chunk 38 optimal weight: 20.0000 chunk 9 optimal weight: 0.5980 chunk 19 optimal weight: 4.9990 overall best weight: 4.7586 ------------------------------------------------------------------------------- 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: 0.7846 moved from start: 0.5707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3510 Z= 0.164 Angle : 0.515 6.561 4772 Z= 0.262 Chirality : 0.038 0.136 534 Planarity : 0.004 0.048 625 Dihedral : 3.593 24.743 468 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.25 % 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: 0.90 (0.40), residues: 434 helix: 0.93 (0.31), residues: 280 sheet: -2.04 (1.15), residues: 9 loop : 0.37 (0.52), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 132 TYR 0.022 0.002 TYR N 164 PHE 0.009 0.002 PHE N 168 TRP 0.011 0.001 TRP A 23 HIS 0.002 0.001 HIS B 12 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 0.296 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: 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: 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 23 TRP cc_start: 0.9437 (t-100) cc_final: 0.9028 (t-100) REVERT: A 27 VAL cc_start: 0.9544 (t) cc_final: 0.9253 (t) REVERT: A 50 GLN cc_start: 0.9318 (tm-30) cc_final: 0.9047 (tm-30) REVERT: A 113 GLU cc_start: 0.9350 (mt-10) cc_final: 0.8973 (mt-10) REVERT: B 43 LEU cc_start: 0.9565 (tp) cc_final: 0.9348 (tp) REVERT: B 45 GLU cc_start: 0.8776 (mm-30) cc_final: 0.7649 (tm-30) REVERT: B 63 GLN cc_start: 0.8430 (mm-40) cc_final: 0.7555 (pt0) REVERT: B 74 ASN cc_start: 0.9347 (m-40) cc_final: 0.9089 (m110) REVERT: B 153 ILE cc_start: 0.8533 (mm) cc_final: 0.8243 (mm) REVERT: N 188 THR cc_start: 0.8977 (m) cc_final: 0.8754 (m) REVERT: N 203 LYS cc_start: 0.8538 (mtpt) cc_final: 0.8263 (mtpt) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.2251 time to fit residues: 54.1295 Evaluate side-chains 178 residues out of total 374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 6 optimal weight: 20.0000 chunk 4 optimal weight: 20.0000 chunk 21 optimal weight: 20.0000 chunk 30 optimal weight: 7.9990 chunk 35 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 27 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 39 optimal weight: 20.0000 chunk 40 optimal weight: 7.9990 chunk 13 optimal weight: 20.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN N 179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.6300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3510 Z= 0.197 Angle : 0.534 6.330 4772 Z= 0.275 Chirality : 0.038 0.141 534 Planarity : 0.005 0.048 625 Dihedral : 3.542 17.540 468 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.25 % 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: 1.14 (0.39), residues: 434 helix: 1.10 (0.31), residues: 279 sheet: -1.86 (1.39), residues: 9 loop : 0.50 (0.50), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 162 TYR 0.013 0.002 TYR N 164 PHE 0.008 0.001 PHE B 40 TRP 0.006 0.001 TRP A 23 HIS 0.003 0.001 HIS B 62 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 0.170 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 TRP cc_start: 0.9501 (t-100) cc_final: 0.9147 (t-100) REVERT: A 40 PHE cc_start: 0.9526 (t80) cc_final: 0.9287 (t80) REVERT: A 50 GLN cc_start: 0.9322 (tm-30) cc_final: 0.9072 (tm-30) REVERT: A 56 LEU cc_start: 0.9646 (mt) cc_final: 0.9442 (mt) REVERT: A 68 MET cc_start: 0.9234 (mtt) cc_final: 0.8910 (mtt) REVERT: A 113 GLU cc_start: 0.9330 (mt-10) cc_final: 0.8918 (mt-10) REVERT: B 2 ILE cc_start: 0.8091 (pt) cc_final: 0.7804 (pt) REVERT: B 63 GLN cc_start: 0.8569 (mm-40) cc_final: 0.7622 (pt0) REVERT: B 74 ASN cc_start: 0.9388 (m-40) cc_final: 0.9100 (m110) REVERT: B 100 ARG cc_start: 0.8374 (ttm110) cc_final: 0.8170 (ttm-80) REVERT: B 131 LYS cc_start: 0.9616 (ttmt) cc_final: 0.9398 (tttt) REVERT: B 134 ILE cc_start: 0.9553 (mm) cc_final: 0.9327 (mm) REVERT: B 153 ILE cc_start: 0.8668 (mm) cc_final: 0.8375 (mm) REVERT: B 215 MET cc_start: 0.8768 (mtp) cc_final: 0.8455 (tmm) REVERT: N 188 THR cc_start: 0.9055 (m) cc_final: 0.8812 (m) REVERT: N 189 LEU cc_start: 0.9008 (mm) cc_final: 0.8801 (mm) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.1654 time to fit residues: 38.7807 Evaluate side-chains 171 residues out of total 374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 35 optimal weight: 20.0000 chunk 30 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 33 optimal weight: 20.0000 chunk 16 optimal weight: 8.9990 chunk 3 optimal weight: 0.8980 chunk 0 optimal weight: 30.0000 chunk 5 optimal weight: 20.0000 chunk 25 optimal weight: 20.0000 chunk 42 optimal weight: 20.0000 chunk 40 optimal weight: 30.0000 overall best weight: 8.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN N 195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.6922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3510 Z= 0.219 Angle : 0.546 5.826 4772 Z= 0.287 Chirality : 0.038 0.140 534 Planarity : 0.006 0.073 625 Dihedral : 3.600 13.243 468 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.25 % 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: 1.12 (0.39), residues: 434 helix: 1.09 (0.31), residues: 278 sheet: -1.33 (1.62), residues: 9 loop : 0.44 (0.50), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 82 TYR 0.014 0.002 TYR N 164 PHE 0.009 0.002 PHE B 168 TRP 0.008 0.001 TRP B 23 HIS 0.003 0.001 HIS B 62 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 0.166 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: 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: 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 50 GLN cc_start: 0.9316 (tm-30) cc_final: 0.9078 (tm-30) REVERT: A 51 ASP cc_start: 0.9552 (m-30) cc_final: 0.9327 (m-30) REVERT: A 56 LEU cc_start: 0.9667 (mt) cc_final: 0.9464 (mt) REVERT: A 113 GLU cc_start: 0.9336 (mt-10) cc_final: 0.8906 (mt-10) REVERT: B 50 GLN cc_start: 0.9036 (mt0) cc_final: 0.8829 (mt0) REVERT: B 63 GLN cc_start: 0.8606 (mm-40) cc_final: 0.7775 (pt0) REVERT: B 74 ASN cc_start: 0.9385 (m-40) cc_final: 0.9080 (m110) REVERT: B 128 GLU cc_start: 0.8438 (tm-30) cc_final: 0.8033 (tm-30) REVERT: B 134 ILE cc_start: 0.9556 (mm) cc_final: 0.9354 (mm) REVERT: N 188 THR cc_start: 0.9082 (m) cc_final: 0.8845 (m) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.1593 time to fit residues: 37.3674 Evaluate side-chains 168 residues out of total 374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 0 optimal weight: 40.0000 chunk 39 optimal weight: 0.4980 chunk 31 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 12 optimal weight: 8.9990 chunk 36 optimal weight: 20.0000 chunk 14 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 overall best weight: 4.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN N 193 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.7201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3510 Z= 0.176 Angle : 0.577 10.707 4772 Z= 0.289 Chirality : 0.039 0.145 534 Planarity : 0.006 0.056 625 Dihedral : 3.700 15.642 468 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.40), residues: 434 helix: 1.29 (0.31), residues: 277 sheet: -1.22 (1.69), residues: 9 loop : 0.71 (0.50), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 82 TYR 0.008 0.001 TYR B 130 PHE 0.012 0.002 PHE A 40 TRP 0.005 0.001 TRP B 184 HIS 0.002 0.001 HIS B 12 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 717.83 seconds wall clock time: 12 minutes 40.55 seconds (760.55 seconds total)