Starting phenix.real_space_refine on Wed Mar 12 10:46:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ej6_31153/03_2025/7ej6_31153_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ej6_31153/03_2025/7ej6_31153.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ej6_31153/03_2025/7ej6_31153.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ej6_31153/03_2025/7ej6_31153.map" model { file = "/net/cci-nas-00/data/ceres_data/7ej6_31153/03_2025/7ej6_31153_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ej6_31153/03_2025/7ej6_31153_trim.cif" } resolution = 3.21 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= 0.010 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 18 5.49 5 Mg 3 5.21 5 S 39 5.16 5 C 4674 2.51 5 N 1326 2.21 5 O 1524 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7584 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2436 Classifications: {'peptide': 316} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 306} Chain: "C" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2436 Classifications: {'peptide': 316} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 306} Chain: "A" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2436 Classifications: {'peptide': 316} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 306} Chain: "D" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 180 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.50, per 1000 atoms: 0.86 Number of scatterers: 7584 At special positions: 0 Unit cell: (84.96, 97.35, 111.51, 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 39 16.00 P 18 15.00 Mg 3 11.99 O 1524 8.00 N 1326 7.00 C 4674 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 - 3.00 Amino acid : True - 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.57 Conformation dependent library (CDL) restraints added in 1.1 seconds 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1716 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 6 sheets defined 48.3% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'B' and resid 20 through 25 removed outlier: 3.600A pdb=" N TYR B 25 " --> pdb=" O LEU B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 38 removed outlier: 3.920A pdb=" N LYS B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 48 Processing helix chain 'B' and resid 50 through 55 Processing helix chain 'B' and resid 61 through 76 Processing helix chain 'B' and resid 83 through 90 Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 100 through 108 Processing helix chain 'B' and resid 126 through 137 removed outlier: 3.981A pdb=" N HIS B 132 " --> pdb=" O THR B 128 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL B 136 " --> pdb=" O HIS B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 145 Processing helix chain 'B' and resid 161 through 171 Processing helix chain 'B' and resid 175 through 181 Processing helix chain 'B' and resid 190 through 205 removed outlier: 3.594A pdb=" N VAL B 198 " --> pdb=" O GLN B 194 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU B 203 " --> pdb=" O GLU B 199 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLU B 204 " --> pdb=" O GLN B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 226 removed outlier: 3.727A pdb=" N VAL B 224 " --> pdb=" O ALA B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 253 removed outlier: 3.693A pdb=" N ARG B 235 " --> pdb=" O GLU B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 291 removed outlier: 3.579A pdb=" N ALA B 288 " --> pdb=" O GLY B 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 25 removed outlier: 3.601A pdb=" N TYR C 25 " --> pdb=" O LEU C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 38 removed outlier: 3.920A pdb=" N LYS C 34 " --> pdb=" O SER C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 48 Processing helix chain 'C' and resid 50 through 55 Processing helix chain 'C' and resid 61 through 76 Processing helix chain 'C' and resid 83 through 90 Processing helix chain 'C' and resid 91 through 93 No H-bonds generated for 'chain 'C' and resid 91 through 93' Processing helix chain 'C' and resid 100 through 108 Processing helix chain 'C' and resid 129 through 137 removed outlier: 3.668A pdb=" N VAL C 136 " --> pdb=" O HIS C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 145 Processing helix chain 'C' and resid 161 through 171 Processing helix chain 'C' and resid 175 through 181 Processing helix chain 'C' and resid 190 through 205 removed outlier: 3.594A pdb=" N VAL C 198 " --> pdb=" O GLN C 194 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU C 203 " --> pdb=" O GLU C 199 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU C 204 " --> pdb=" O GLN C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 226 removed outlier: 3.727A pdb=" N VAL C 224 " --> pdb=" O ALA C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 253 removed outlier: 3.693A pdb=" N ARG C 235 " --> pdb=" O GLU C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 291 removed outlier: 3.579A pdb=" N ALA C 288 " --> pdb=" O GLY C 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 25 removed outlier: 3.599A pdb=" N TYR A 25 " --> pdb=" O LEU A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 38 removed outlier: 3.919A pdb=" N LYS A 34 " --> pdb=" O SER A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 48 Processing helix chain 'A' and resid 50 through 55 Processing helix chain 'A' and resid 61 through 76 Processing helix chain 'A' and resid 83 through 90 Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 100 through 108 Processing helix chain 'A' and resid 127 through 137 removed outlier: 3.667A pdb=" N VAL A 136 " --> pdb=" O HIS A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 145 Processing helix chain 'A' and resid 161 through 171 Processing helix chain 'A' and resid 175 through 181 Processing helix chain 'A' and resid 190 through 205 removed outlier: 3.594A pdb=" N VAL A 198 " --> pdb=" O GLN A 194 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU A 203 " --> pdb=" O GLU A 199 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU A 204 " --> pdb=" O GLN A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 226 removed outlier: 3.727A pdb=" N VAL A 224 " --> pdb=" O ALA A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 253 removed outlier: 3.693A pdb=" N ARG A 235 " --> pdb=" O GLU A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 291 removed outlier: 3.579A pdb=" N ALA A 288 " --> pdb=" O GLY A 284 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 183 through 187 removed outlier: 5.748A pdb=" N LYS B 150 " --> pdb=" O TYR B 210 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU B 212 " --> pdb=" O LYS B 150 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N SER B 115 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N LEU B 259 " --> pdb=" O SER B 115 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N THR B 117 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ASN B 261 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL B 119 " --> pdb=" O ASN B 261 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ARG B 294 " --> pdb=" O GLN B 310 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LYS B 318 " --> pdb=" O LEU B 309 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 263 through 264 removed outlier: 5.007A pdb=" N LYS B 280 " --> pdb=" O GLN B 264 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 183 through 187 removed outlier: 5.747A pdb=" N LYS C 150 " --> pdb=" O TYR C 210 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU C 212 " --> pdb=" O LYS C 150 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N SER C 115 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N LEU C 259 " --> pdb=" O SER C 115 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N THR C 117 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ASN C 261 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL C 119 " --> pdb=" O ASN C 261 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ARG C 294 " --> pdb=" O GLN C 310 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LYS C 318 " --> pdb=" O LEU C 309 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 263 through 264 removed outlier: 5.006A pdb=" N LYS C 280 " --> pdb=" O GLN C 264 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 183 through 187 removed outlier: 5.748A pdb=" N LYS A 150 " --> pdb=" O TYR A 210 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU A 212 " --> pdb=" O LYS A 150 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N SER A 115 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N LEU A 259 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N THR A 117 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ASN A 261 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL A 119 " --> pdb=" O ASN A 261 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ARG A 294 " --> pdb=" O GLN A 310 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LYS A 318 " --> pdb=" O LEU A 309 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 263 through 264 removed outlier: 5.007A pdb=" N LYS A 280 " --> pdb=" O GLN A 264 " (cutoff:3.500A) 340 hydrogen bonds defined for protein. 966 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: 2.14 Time building geometry restraints manager: 2.84 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: 2215 1.33 - 1.45: 1087 1.45 - 1.57: 4303 1.57 - 1.69: 32 1.69 - 1.81: 60 Bond restraints: 7697 Sorted by residual: bond pdb=" C4 ATP B 602 " pdb=" C5 ATP B 602 " ideal model delta sigma weight residual 1.388 1.457 -0.069 1.00e-02 1.00e+04 4.73e+01 bond pdb=" C4 ATP C 402 " pdb=" C5 ATP C 402 " ideal model delta sigma weight residual 1.388 1.457 -0.069 1.00e-02 1.00e+04 4.70e+01 bond pdb=" C4 ATP C 401 " pdb=" C5 ATP C 401 " ideal model delta sigma weight residual 1.388 1.456 -0.068 1.00e-02 1.00e+04 4.67e+01 bond pdb=" C5 ATP C 402 " pdb=" C6 ATP C 402 " ideal model delta sigma weight residual 1.409 1.474 -0.065 1.00e-02 1.00e+04 4.29e+01 bond pdb=" C5 ATP B 602 " pdb=" C6 ATP B 602 " ideal model delta sigma weight residual 1.409 1.474 -0.065 1.00e-02 1.00e+04 4.28e+01 ... (remaining 7692 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.80: 10300 3.80 - 7.60: 98 7.60 - 11.40: 10 11.40 - 15.20: 1 15.20 - 18.99: 6 Bond angle restraints: 10415 Sorted by residual: angle pdb=" PA ATP B 602 " pdb=" O3A ATP B 602 " pdb=" PB ATP B 602 " ideal model delta sigma weight residual 136.83 117.84 18.99 1.00e+00 1.00e+00 3.61e+02 angle pdb=" PA ATP C 401 " pdb=" O3A ATP C 401 " pdb=" PB ATP C 401 " ideal model delta sigma weight residual 136.83 117.85 18.98 1.00e+00 1.00e+00 3.60e+02 angle pdb=" PA ATP C 402 " pdb=" O3A ATP C 402 " pdb=" PB ATP C 402 " ideal model delta sigma weight residual 136.83 117.86 18.97 1.00e+00 1.00e+00 3.60e+02 angle pdb=" PB ATP C 402 " pdb=" O3B ATP C 402 " pdb=" PG ATP C 402 " ideal model delta sigma weight residual 139.87 121.14 18.73 1.00e+00 1.00e+00 3.51e+02 angle pdb=" PB ATP C 401 " pdb=" O3B ATP C 401 " pdb=" PG ATP C 401 " ideal model delta sigma weight residual 139.87 121.17 18.70 1.00e+00 1.00e+00 3.50e+02 ... (remaining 10410 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 4134 17.88 - 35.76: 422 35.76 - 53.64: 132 53.64 - 71.53: 13 71.53 - 89.41: 24 Dihedral angle restraints: 4725 sinusoidal: 2037 harmonic: 2688 Sorted by residual: dihedral pdb=" CA PRO B 82 " pdb=" C PRO B 82 " pdb=" N ALA B 83 " pdb=" CA ALA B 83 " ideal model delta harmonic sigma weight residual 180.00 158.72 21.28 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA PRO A 82 " pdb=" C PRO A 82 " pdb=" N ALA A 83 " pdb=" CA ALA A 83 " ideal model delta harmonic sigma weight residual 180.00 158.75 21.25 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA PRO C 82 " pdb=" C PRO C 82 " pdb=" N ALA C 83 " pdb=" CA ALA C 83 " ideal model delta harmonic sigma weight residual 180.00 158.79 21.21 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 4722 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1002 0.066 - 0.131: 164 0.131 - 0.197: 9 0.197 - 0.263: 6 0.263 - 0.328: 1 Chirality restraints: 1182 Sorted by residual: chirality pdb=" CA THR C 128 " pdb=" N THR C 128 " pdb=" C THR C 128 " pdb=" CB THR C 128 " both_signs ideal model delta sigma weight residual False 2.53 2.20 0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" CA THR A 128 " pdb=" N THR A 128 " pdb=" C THR A 128 " pdb=" CB THR A 128 " both_signs ideal model delta sigma weight residual False 2.53 2.77 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" C2' ATP C 401 " pdb=" C1' ATP C 401 " pdb=" C3' ATP C 401 " pdb=" O2' ATP C 401 " both_signs ideal model delta sigma weight residual False -2.68 -2.47 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 1179 not shown) Planarity restraints: 1314 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 124 " 0.024 2.00e-02 2.50e+03 5.02e-02 2.52e+01 pdb=" C ARG C 124 " -0.087 2.00e-02 2.50e+03 pdb=" O ARG C 124 " 0.034 2.00e-02 2.50e+03 pdb=" N CYS C 125 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 315 " 0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C MET A 315 " -0.059 2.00e-02 2.50e+03 pdb=" O MET A 315 " 0.022 2.00e-02 2.50e+03 pdb=" N PRO A 316 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 315 " -0.017 2.00e-02 2.50e+03 3.40e-02 1.16e+01 pdb=" C MET B 315 " 0.059 2.00e-02 2.50e+03 pdb=" O MET B 315 " -0.022 2.00e-02 2.50e+03 pdb=" N PRO B 316 " -0.020 2.00e-02 2.50e+03 ... (remaining 1311 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 217 2.60 - 3.17: 7583 3.17 - 3.75: 11248 3.75 - 4.32: 16575 4.32 - 4.90: 27290 Nonbonded interactions: 62913 Sorted by model distance: nonbonded pdb="MG MG B 601 " pdb=" O3B ATP C 401 " model vdw 2.019 2.170 nonbonded pdb=" O3B ATP B 602 " pdb="MG MG A 601 " model vdw 2.020 2.170 nonbonded pdb=" O3B ATP C 402 " pdb="MG MG C 403 " model vdw 2.020 2.170 nonbonded pdb=" O TYR A 94 " pdb=" OG1 THR A 113 " model vdw 2.079 3.040 nonbonded pdb=" O TYR C 94 " pdb=" OG1 THR C 113 " model vdw 2.080 3.040 ... (remaining 62908 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 16 through 334) selection = (chain 'B' and resid 16 through 334) selection = (chain 'C' and resid 16 through 334) } 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=1.00 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: 0.010 Normalize map: mean=0, sd=1: 4.130 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: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.750 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 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 : 0.008 0.069 7697 Z= 0.503 Angle : 1.028 18.994 10415 Z= 0.749 Chirality : 0.048 0.328 1182 Planarity : 0.004 0.050 1314 Dihedral : 16.919 89.407 3009 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 51.68 Ramachandran Plot: Outliers : 0.74 % Allowed : 12.10 % Favored : 87.15 % Rotamer: Outliers : 1.13 % Allowed : 6.02 % Favored : 92.86 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: -4.78 (0.21), residues: 942 helix: -3.46 (0.16), residues: 435 sheet: 0.42 (0.43), residues: 153 loop : -4.39 (0.23), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 193 PHE 0.005 0.001 PHE A 123 TYR 0.010 0.001 TYR C 41 ARG 0.004 0.001 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.812 Fit side-chains REVERT: B 178 SER cc_start: 0.8980 (OUTLIER) cc_final: 0.8742 (m) REVERT: C 178 SER cc_start: 0.9059 (OUTLIER) cc_final: 0.8834 (t) REVERT: A 127 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.7994 (mtpt) REVERT: A 178 SER cc_start: 0.8918 (OUTLIER) cc_final: 0.8669 (m) outliers start: 9 outliers final: 4 residues processed: 85 average time/residue: 0.1659 time to fit residues: 20.7166 Evaluate side-chains 61 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 127 LYS Chi-restraints excluded: chain A residue 178 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 GLN B 132 HIS B 182 ASN B 194 GLN B 236 GLN B 242 HIS ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 GLN C 132 HIS C 182 ASN C 194 GLN C 236 GLN C 242 HIS ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 102 GLN ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 182 ASN A 194 GLN A 236 GLN A 242 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.075305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.059020 restraints weight = 19906.991| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.94 r_work: 0.2776 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7697 Z= 0.210 Angle : 0.711 8.142 10415 Z= 0.372 Chirality : 0.046 0.169 1182 Planarity : 0.005 0.033 1314 Dihedral : 15.310 86.469 1229 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.64 % Allowed : 7.96 % Favored : 91.40 % Rotamer: Outliers : 1.50 % Allowed : 10.53 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.25), residues: 942 helix: -1.13 (0.23), residues: 450 sheet: 0.88 (0.44), residues: 147 loop : -3.92 (0.26), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 193 PHE 0.006 0.001 PHE A 123 TYR 0.014 0.001 TYR C 94 ARG 0.003 0.001 ARG C 52 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.846 Fit side-chains REVERT: C 28 ASN cc_start: 0.8395 (p0) cc_final: 0.7997 (p0) REVERT: A 28 ASN cc_start: 0.8133 (p0) cc_final: 0.7922 (p0) REVERT: A 41 TYR cc_start: 0.7780 (m-80) cc_final: 0.7562 (m-80) outliers start: 12 outliers final: 2 residues processed: 84 average time/residue: 0.1516 time to fit residues: 19.0648 Evaluate side-chains 53 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain C residue 324 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 25 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 73 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.072978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.056439 restraints weight = 20212.400| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 2.96 r_work: 0.2700 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 7697 Z= 0.305 Angle : 0.675 7.141 10415 Z= 0.355 Chirality : 0.047 0.171 1182 Planarity : 0.005 0.050 1314 Dihedral : 14.468 80.098 1219 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.64 % Allowed : 7.11 % Favored : 92.25 % Rotamer: Outliers : 3.01 % Allowed : 12.53 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: -1.90 (0.27), residues: 942 helix: -0.23 (0.25), residues: 456 sheet: 0.66 (0.43), residues: 153 loop : -3.76 (0.27), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 193 PHE 0.011 0.001 PHE A 123 TYR 0.011 0.001 TYR B 94 ARG 0.003 0.000 ARG B 187 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 58 time to evaluate : 0.872 Fit side-chains revert: symmetry clash REVERT: C 17 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8641 (pt) REVERT: C 28 ASN cc_start: 0.8449 (p0) cc_final: 0.8165 (p0) REVERT: A 22 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8902 (tt) REVERT: A 41 TYR cc_start: 0.7868 (m-80) cc_final: 0.7632 (m-80) outliers start: 24 outliers final: 9 residues processed: 79 average time/residue: 0.1297 time to fit residues: 16.3185 Evaluate side-chains 64 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 114 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 26 optimal weight: 0.0670 chunk 77 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 chunk 87 optimal weight: 0.4980 chunk 2 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 overall best weight: 1.0922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.075601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.059487 restraints weight = 19963.178| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 2.94 r_work: 0.2770 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7697 Z= 0.174 Angle : 0.600 8.648 10415 Z= 0.312 Chirality : 0.043 0.158 1182 Planarity : 0.004 0.029 1314 Dihedral : 13.851 73.648 1218 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.64 % Allowed : 6.26 % Favored : 93.10 % Rotamer: Outliers : 3.26 % Allowed : 12.66 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: -1.31 (0.27), residues: 942 helix: 0.29 (0.26), residues: 456 sheet: 0.98 (0.44), residues: 144 loop : -3.44 (0.27), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 132 PHE 0.005 0.001 PHE A 123 TYR 0.012 0.001 TYR A 94 ARG 0.002 0.000 ARG B 187 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 58 time to evaluate : 0.821 Fit side-chains REVERT: A 41 TYR cc_start: 0.7843 (m-80) cc_final: 0.7612 (m-80) REVERT: A 144 MET cc_start: 0.9055 (mmm) cc_final: 0.8769 (mtp) outliers start: 26 outliers final: 12 residues processed: 81 average time/residue: 0.1348 time to fit residues: 17.1106 Evaluate side-chains 63 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 125 CYS Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 197 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 50 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 39 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 64 optimal weight: 0.6980 chunk 78 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.072233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.055698 restraints weight = 20012.632| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 2.95 r_work: 0.2678 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 7697 Z= 0.383 Angle : 0.678 8.017 10415 Z= 0.354 Chirality : 0.047 0.246 1182 Planarity : 0.005 0.050 1314 Dihedral : 14.486 77.621 1218 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.64 % Allowed : 8.81 % Favored : 90.55 % Rotamer: Outliers : 3.26 % Allowed : 13.03 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: -1.36 (0.28), residues: 942 helix: 0.17 (0.25), residues: 459 sheet: 0.72 (0.44), residues: 153 loop : -3.34 (0.29), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 193 PHE 0.009 0.001 PHE B 123 TYR 0.013 0.001 TYR A 94 ARG 0.003 0.000 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 57 time to evaluate : 0.820 Fit side-chains revert: symmetry clash REVERT: A 41 TYR cc_start: 0.7939 (m-80) cc_final: 0.7679 (m-80) REVERT: A 144 MET cc_start: 0.9056 (mmm) cc_final: 0.8819 (mtp) outliers start: 26 outliers final: 16 residues processed: 75 average time/residue: 0.1278 time to fit residues: 15.3776 Evaluate side-chains 68 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 114 MET Chi-restraints excluded: chain C residue 125 CYS Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 114 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 88 optimal weight: 3.9990 chunk 47 optimal weight: 0.0970 chunk 60 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 19 optimal weight: 0.5980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.076798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.060349 restraints weight = 19920.938| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 2.97 r_work: 0.2795 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 7697 Z= 0.156 Angle : 0.581 7.716 10415 Z= 0.301 Chirality : 0.043 0.155 1182 Planarity : 0.003 0.028 1314 Dihedral : 13.546 73.556 1218 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.64 % Allowed : 6.05 % Favored : 93.31 % Rotamer: Outliers : 3.63 % Allowed : 12.41 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: -1.07 (0.28), residues: 942 helix: 0.44 (0.26), residues: 462 sheet: 0.98 (0.46), residues: 144 loop : -3.24 (0.27), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 193 PHE 0.006 0.001 PHE A 253 TYR 0.007 0.001 TYR C 41 ARG 0.002 0.000 ARG C 124 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 60 time to evaluate : 0.880 Fit side-chains revert: symmetry clash REVERT: B 164 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.8576 (tpt170) REVERT: A 41 TYR cc_start: 0.7799 (m-80) cc_final: 0.7569 (m-80) REVERT: A 144 MET cc_start: 0.8988 (mmm) cc_final: 0.8729 (mtp) REVERT: A 164 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.8731 (tpt170) outliers start: 29 outliers final: 15 residues processed: 81 average time/residue: 0.2714 time to fit residues: 31.3889 Evaluate side-chains 70 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 53 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 179 CYS Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 114 MET Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain A residue 197 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 92 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 39 optimal weight: 9.9990 chunk 43 optimal weight: 0.4980 chunk 65 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 GLN C 200 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.073833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.057275 restraints weight = 20073.426| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 2.98 r_work: 0.2719 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7697 Z= 0.272 Angle : 0.629 7.539 10415 Z= 0.327 Chirality : 0.045 0.195 1182 Planarity : 0.004 0.039 1314 Dihedral : 14.041 74.380 1218 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.64 % Allowed : 6.90 % Favored : 92.46 % Rotamer: Outliers : 2.76 % Allowed : 14.04 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: -1.07 (0.27), residues: 942 helix: 0.43 (0.25), residues: 456 sheet: 1.03 (0.46), residues: 144 loop : -3.19 (0.28), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 193 PHE 0.007 0.001 PHE C 253 TYR 0.010 0.001 TYR A 94 ARG 0.003 0.000 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 58 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 164 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.7931 (mmm160) REVERT: A 41 TYR cc_start: 0.7886 (m-80) cc_final: 0.7639 (m-80) REVERT: A 144 MET cc_start: 0.9046 (mmm) cc_final: 0.8800 (mtp) REVERT: A 164 ARG cc_start: 0.9054 (OUTLIER) cc_final: 0.8628 (tpt170) outliers start: 22 outliers final: 15 residues processed: 74 average time/residue: 0.1679 time to fit residues: 18.6115 Evaluate side-chains 70 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 53 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 179 CYS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain C residue 114 MET Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 317 GLU Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain A residue 212 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 89 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 GLN A 28 ASN A 285 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.072985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.056459 restraints weight = 20265.771| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 2.99 r_work: 0.2695 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 7697 Z= 0.318 Angle : 0.663 8.631 10415 Z= 0.340 Chirality : 0.045 0.224 1182 Planarity : 0.004 0.044 1314 Dihedral : 14.634 79.348 1218 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.64 % Allowed : 7.11 % Favored : 92.25 % Rotamer: Outliers : 3.63 % Allowed : 13.03 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: -1.11 (0.28), residues: 942 helix: 0.40 (0.25), residues: 456 sheet: 0.77 (0.45), residues: 150 loop : -3.17 (0.29), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 193 PHE 0.007 0.001 PHE A 123 TYR 0.014 0.001 TYR A 94 ARG 0.003 0.000 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 54 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 164 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.7936 (mmm160) REVERT: C 94 TYR cc_start: 0.8414 (OUTLIER) cc_final: 0.7378 (t80) REVERT: C 173 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8604 (pp20) REVERT: C 219 MET cc_start: 0.8986 (OUTLIER) cc_final: 0.8198 (mtp) REVERT: A 41 TYR cc_start: 0.7923 (m-80) cc_final: 0.7669 (m-80) REVERT: A 144 MET cc_start: 0.9055 (mmm) cc_final: 0.8790 (mtp) REVERT: A 164 ARG cc_start: 0.9065 (OUTLIER) cc_final: 0.8203 (mmm160) outliers start: 29 outliers final: 19 residues processed: 74 average time/residue: 0.1641 time to fit residues: 18.3072 Evaluate side-chains 75 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 51 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 179 CYS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 114 MET Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 317 GLU Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 324 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 87 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 76 optimal weight: 8.9990 chunk 30 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 GLN A 28 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.074793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.058264 restraints weight = 20361.780| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 3.01 r_work: 0.2742 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7697 Z= 0.199 Angle : 0.619 8.511 10415 Z= 0.318 Chirality : 0.044 0.177 1182 Planarity : 0.004 0.030 1314 Dihedral : 14.126 75.444 1218 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.64 % Allowed : 6.37 % Favored : 92.99 % Rotamer: Outliers : 3.63 % Allowed : 12.78 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: -0.94 (0.28), residues: 942 helix: 0.59 (0.25), residues: 456 sheet: 0.97 (0.45), residues: 144 loop : -3.15 (0.28), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 193 PHE 0.006 0.001 PHE A 253 TYR 0.010 0.001 TYR A 94 ARG 0.002 0.000 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 58 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 164 ARG cc_start: 0.8908 (OUTLIER) cc_final: 0.8474 (tpt170) REVERT: C 94 TYR cc_start: 0.8379 (OUTLIER) cc_final: 0.7321 (t80) REVERT: A 41 TYR cc_start: 0.7860 (m-80) cc_final: 0.7628 (m-80) REVERT: A 144 MET cc_start: 0.9056 (mmm) cc_final: 0.8806 (mtp) REVERT: A 164 ARG cc_start: 0.9039 (OUTLIER) cc_final: 0.8692 (tpt170) outliers start: 29 outliers final: 18 residues processed: 78 average time/residue: 0.1874 time to fit residues: 21.2813 Evaluate side-chains 74 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 53 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 179 CYS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 114 MET Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 317 GLU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 324 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 24 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 33 optimal weight: 7.9990 chunk 56 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 37 optimal weight: 0.4980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.076773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.060340 restraints weight = 20264.247| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 3.01 r_work: 0.2796 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7697 Z= 0.167 Angle : 0.609 9.543 10415 Z= 0.311 Chirality : 0.043 0.172 1182 Planarity : 0.003 0.028 1314 Dihedral : 13.485 72.595 1218 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.05 % Favored : 93.42 % Rotamer: Outliers : 2.38 % Allowed : 14.16 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: -0.83 (0.28), residues: 942 helix: 0.67 (0.25), residues: 462 sheet: 0.91 (0.46), residues: 144 loop : -3.07 (0.29), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 193 PHE 0.006 0.001 PHE C 253 TYR 0.007 0.001 TYR A 94 ARG 0.002 0.000 ARG C 124 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 164 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.8504 (tpt170) REVERT: C 200 GLN cc_start: 0.8501 (mt0) cc_final: 0.8263 (mm-40) REVERT: A 41 TYR cc_start: 0.7800 (m-80) cc_final: 0.7564 (m-80) REVERT: A 144 MET cc_start: 0.9053 (mmm) cc_final: 0.8794 (mtp) REVERT: A 164 ARG cc_start: 0.9032 (OUTLIER) cc_final: 0.8722 (tpt170) outliers start: 19 outliers final: 15 residues processed: 72 average time/residue: 0.1643 time to fit residues: 17.4164 Evaluate side-chains 72 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 179 CYS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 114 MET Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 317 GLU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 272 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 51 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.074242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.057737 restraints weight = 20053.890| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 2.98 r_work: 0.2726 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7697 Z= 0.264 Angle : 0.641 8.913 10415 Z= 0.329 Chirality : 0.045 0.195 1182 Planarity : 0.004 0.035 1314 Dihedral : 14.108 75.629 1218 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.64 % Allowed : 7.01 % Favored : 92.36 % Rotamer: Outliers : 2.63 % Allowed : 13.78 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: -0.89 (0.28), residues: 942 helix: 0.64 (0.25), residues: 459 sheet: 0.93 (0.45), residues: 144 loop : -3.14 (0.29), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 193 PHE 0.006 0.001 PHE B 123 TYR 0.012 0.001 TYR A 94 ARG 0.003 0.000 ARG A 142 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3218.73 seconds wall clock time: 57 minutes 17.76 seconds (3437.76 seconds total)