Starting phenix.real_space_refine on Wed Mar 4 18:48:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uzy_26922/03_2026/7uzy_26922.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uzy_26922/03_2026/7uzy_26922.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7uzy_26922/03_2026/7uzy_26922.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uzy_26922/03_2026/7uzy_26922.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uzy_26922/03_2026/7uzy_26922.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uzy_26922/03_2026/7uzy_26922.map" } resolution = 4.05 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.029 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 P 44 5.49 5 S 39 5.16 5 C 9578 2.51 5 N 2599 2.21 5 O 3072 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15332 Number of models: 1 Model: "" Number of chains: 11 Chain: "F" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3353 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 3, 'TRANS': 410} Chain breaks: 7 Chain: "J" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 871 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 1, 'TRANS': 100} Chain breaks: 2 Chain: "I" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 937 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 1, 'TRANS': 108} Chain breaks: 1 Chain: "K" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 505 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 1, 'TRANS': 57} Chain breaks: 1 Chain: "D" Number of atoms: 1572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1572 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 4, 'TRANS': 193} Chain breaks: 1 Chain: "C" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1628 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 200} Chain breaks: 1 Chain: "A" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1628 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 200} Chain breaks: 1 Chain: "B" Number of atoms: 1523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1523 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 187} Chain breaks: 2 Chain: "H" Number of atoms: 2378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2378 Classifications: {'peptide': 296} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 286} Chain breaks: 1 Chain: "G" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 637 Classifications: {'RNA': 30} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 5, 'rna3p_pur': 11, 'rna3p_pyr': 9} Link IDs: {'rna2p': 10, 'rna3p': 19} Chain: "L" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 300 Classifications: {'RNA': 14} Modifications used: {'rna2p_pur': 3, 'rna3p_pur': 6, 'rna3p_pyr': 5} Link IDs: {'rna2p': 3, 'rna3p': 10} Chain breaks: 1 Time building chain proxies: 3.66, per 1000 atoms: 0.24 Number of scatterers: 15332 At special positions: 0 Unit cell: (96.8, 122.1, 188.1, 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 39 16.00 P 44 15.00 O 3072 8.00 N 2599 7.00 C 9578 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS F 407 " - pdb=" SG CYS F 423 " distance=1.90 Simple disulfide: pdb=" SG CYS F 410 " - pdb=" SG CYS F 426 " distance=2.03 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=0, symmetry=0 Time building additional restraints: 1.40 Conformation dependent library (CDL) restraints added in 660.4 milliseconds 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3326 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 21 sheets defined 47.7% alpha, 17.0% beta 10 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'F' and resid 2 through 12 Processing helix chain 'F' and resid 13 through 15 No H-bonds generated for 'chain 'F' and resid 13 through 15' Processing helix chain 'F' and resid 16 through 22 removed outlier: 3.999A pdb=" N ILE F 20 " --> pdb=" O ILE F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 42 removed outlier: 3.539A pdb=" N LEU F 36 " --> pdb=" O THR F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 58 removed outlier: 3.770A pdb=" N LEU F 53 " --> pdb=" O ASP F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 66 removed outlier: 4.129A pdb=" N LYS F 66 " --> pdb=" O LYS F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 86 Processing helix chain 'F' and resid 153 through 170 Processing helix chain 'F' and resid 177 through 190 removed outlier: 3.887A pdb=" N GLN F 190 " --> pdb=" O GLU F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 227 Processing helix chain 'F' and resid 231 through 236 Processing helix chain 'F' and resid 244 through 249 Processing helix chain 'F' and resid 261 through 267 Processing helix chain 'F' and resid 273 through 300 Processing helix chain 'F' and resid 303 through 305 No H-bonds generated for 'chain 'F' and resid 303 through 305' Processing helix chain 'F' and resid 322 through 344 Processing helix chain 'F' and resid 358 through 363 removed outlier: 3.959A pdb=" N LEU F 362 " --> pdb=" O SER F 358 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N MET F 363 " --> pdb=" O GLY F 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 358 through 363' Processing helix chain 'F' and resid 367 through 384 removed outlier: 3.689A pdb=" N THR F 371 " --> pdb=" O GLY F 367 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS F 384 " --> pdb=" O LEU F 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 398 removed outlier: 3.538A pdb=" N HIS F 398 " --> pdb=" O LEU F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 419 through 421 No H-bonds generated for 'chain 'F' and resid 419 through 421' Processing helix chain 'F' and resid 424 through 437 removed outlier: 4.293A pdb=" N ARG F 437 " --> pdb=" O SER F 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 462 through 470 Processing helix chain 'F' and resid 552 through 566 Processing helix chain 'J' and resid 18 through 24 Processing helix chain 'J' and resid 44 through 47 Processing helix chain 'J' and resid 48 through 61 Processing helix chain 'J' and resid 75 through 92 removed outlier: 3.575A pdb=" N GLU J 92 " --> pdb=" O GLU J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 102 Processing helix chain 'J' and resid 103 through 115 Processing helix chain 'J' and resid 116 through 137 Processing helix chain 'I' and resid 15 through 24 removed outlier: 3.794A pdb=" N VAL I 20 " --> pdb=" O PHE I 16 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 47 Processing helix chain 'I' and resid 48 through 65 Processing helix chain 'I' and resid 71 through 92 Processing helix chain 'I' and resid 92 through 102 Processing helix chain 'I' and resid 103 through 115 Processing helix chain 'I' and resid 116 through 137 Processing helix chain 'K' and resid 44 through 47 Processing helix chain 'K' and resid 48 through 59 Processing helix chain 'K' and resid 73 through 92 Processing helix chain 'K' and resid 92 through 102 Processing helix chain 'K' and resid 103 through 112 Processing helix chain 'D' and resid 47 through 63 Processing helix chain 'D' and resid 66 through 73 Processing helix chain 'D' and resid 76 through 84 Processing helix chain 'D' and resid 104 through 114 Processing helix chain 'D' and resid 161 through 178 Processing helix chain 'C' and resid 47 through 63 removed outlier: 4.108A pdb=" N ILE C 51 " --> pdb=" O PRO C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 72 removed outlier: 4.301A pdb=" N HIS C 72 " --> pdb=" O LYS C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 84 Processing helix chain 'C' and resid 104 through 115 Processing helix chain 'C' and resid 158 through 160 No H-bonds generated for 'chain 'C' and resid 158 through 160' Processing helix chain 'C' and resid 161 through 178 removed outlier: 4.098A pdb=" N ASP C 165 " --> pdb=" O GLN C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 188 Processing helix chain 'A' and resid 47 through 63 removed outlier: 3.775A pdb=" N PHE A 63 " --> pdb=" O LEU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 73 removed outlier: 3.809A pdb=" N HIS A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN A 73 " --> pdb=" O GLN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 84 Processing helix chain 'A' and resid 104 through 115 Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 161 through 178 removed outlier: 3.585A pdb=" N ASN A 178 " --> pdb=" O HIS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 188 Processing helix chain 'B' and resid 47 through 63 removed outlier: 3.768A pdb=" N PHE B 63 " --> pdb=" O LEU B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 84 Processing helix chain 'B' and resid 104 through 115 Processing helix chain 'B' and resid 161 through 178 Processing helix chain 'H' and resid 31 through 47 Processing helix chain 'H' and resid 50 through 55 Processing helix chain 'H' and resid 100 through 106 Processing helix chain 'H' and resid 110 through 120 Processing helix chain 'H' and resid 168 through 183 Processing helix chain 'H' and resid 190 through 194 Processing helix chain 'H' and resid 205 through 213 Processing helix chain 'H' and resid 231 through 236 Processing sheet with id=AA1, first strand: chain 'F' and resid 307 through 311 removed outlier: 5.981A pdb=" N LEU F 307 " --> pdb=" O LEU F 318 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LEU F 318 " --> pdb=" O LEU F 307 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR F 309 " --> pdb=" O TYR F 316 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA F 315 " --> pdb=" O MET F 257 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 417 through 418 Processing sheet with id=AA3, first strand: chain 'F' and resid 450 through 452 removed outlier: 3.967A pdb=" N LYS F 456 " --> pdb=" O MET F 452 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE F 441 " --> pdb=" O ILE F 461 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 25 through 26 Processing sheet with id=AA5, first strand: chain 'D' and resid 96 through 103 removed outlier: 6.041A pdb=" N LEU D 96 " --> pdb=" O ASN D 155 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ASN D 155 " --> pdb=" O LEU D 96 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N ILE D 98 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ILE D 153 " --> pdb=" O ILE D 98 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ASP D 100 " --> pdb=" O VAL D 151 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL D 151 " --> pdb=" O ASP D 100 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY D 9 " --> pdb=" O PHE D 150 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER D 3 " --> pdb=" O VAL D 156 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N LYS D 4 " --> pdb=" O THR D 201 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N THR D 201 " --> pdb=" O LYS D 4 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LYS D 6 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ILE D 199 " --> pdb=" O LYS D 6 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N SER D 8 " --> pdb=" O THR D 197 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N THR D 197 " --> pdb=" O SER D 8 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 119 through 124 Processing sheet with id=AA7, first strand: chain 'C' and resid 45 through 46 removed outlier: 3.606A pdb=" N PHE C 102 " --> pdb=" O ASP C 149 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 45 through 46 removed outlier: 3.606A pdb=" N PHE C 102 " --> pdb=" O ASP C 149 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LYS C 4 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N THR C 10 " --> pdb=" O ASP C 196 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ASP C 196 " --> pdb=" O THR C 10 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N GLU C 12 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N PHE C 194 " --> pdb=" O GLU C 12 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 119 through 127 Processing sheet with id=AB1, first strand: chain 'A' and resid 45 through 46 removed outlier: 3.715A pdb=" N ALA A 101 " --> pdb=" O ILE A 46 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VAL A 151 " --> pdb=" O SER A 99 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA A 101 " --> pdb=" O ASP A 149 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ASP A 149 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N PHE A 103 " --> pdb=" O GLU A 147 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N GLU A 147 " --> pdb=" O PHE A 103 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LYS A 4 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR A 10 " --> pdb=" O ASP A 196 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ASP A 196 " --> pdb=" O THR A 10 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLU A 12 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N PHE A 194 " --> pdb=" O GLU A 12 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 119 through 126 removed outlier: 3.703A pdb=" N ASN A 135 " --> pdb=" O THR A 126 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.515A pdb=" N PHE B 102 " --> pdb=" O ASP B 149 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.728A pdb=" N SER B 3 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N LYS B 4 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N THR B 201 " --> pdb=" O LYS B 4 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LYS B 6 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ILE B 199 " --> pdb=" O LYS B 6 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N SER B 8 " --> pdb=" O THR B 197 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N THR B 197 " --> pdb=" O SER B 8 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 119 through 127 Processing sheet with id=AB6, first strand: chain 'H' and resid 63 through 65 removed outlier: 3.506A pdb=" N GLY H 160 " --> pdb=" O TYR H 65 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL H 7 " --> pdb=" O ILE H 203 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE H 203 " --> pdb=" O VAL H 7 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 58 through 59 Processing sheet with id=AB8, first strand: chain 'H' and resid 71 through 73 Processing sheet with id=AB9, first strand: chain 'H' and resid 125 through 131 Processing sheet with id=AC1, first strand: chain 'H' and resid 220 through 221 Processing sheet with id=AC2, first strand: chain 'H' and resid 243 through 248 removed outlier: 3.631A pdb=" N SER H 267 " --> pdb=" O THR H 244 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N GLY H 248 " --> pdb=" O SER H 263 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N SER H 263 " --> pdb=" O GLY H 248 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 283 through 284 704 hydrogen bonds defined for protein. 2040 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 22 hydrogen bonds 44 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 2.45 Time building geometry restraints manager: 1.90 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: 3599 1.33 - 1.45: 3653 1.45 - 1.57: 8282 1.57 - 1.70: 85 1.70 - 1.82: 69 Bond restraints: 15688 Sorted by residual: bond pdb=" O3' A G 13 " pdb=" P A G 14 " ideal model delta sigma weight residual 1.607 1.670 -0.063 1.50e-02 4.44e+03 1.78e+01 bond pdb=" N ILE F 415 " pdb=" CA ILE F 415 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.22e-02 6.72e+03 9.54e+00 bond pdb=" N GLU B 87 " pdb=" CA GLU B 87 " ideal model delta sigma weight residual 1.458 1.486 -0.028 9.00e-03 1.23e+04 9.47e+00 bond pdb=" N LEU A 130 " pdb=" CA LEU A 130 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.42e+00 bond pdb=" N VAL I 20 " pdb=" CA VAL I 20 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.19e-02 7.06e+03 9.34e+00 ... (remaining 15683 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 20974 2.52 - 5.03: 281 5.03 - 7.55: 27 7.55 - 10.07: 1 10.07 - 12.59: 1 Bond angle restraints: 21284 Sorted by residual: angle pdb=" C4' A G 14 " pdb=" C3' A G 14 " pdb=" O3' A G 14 " ideal model delta sigma weight residual 113.00 125.59 -12.59 1.50e+00 4.44e-01 7.04e+01 angle pdb=" O3' A G 14 " pdb=" C3' A G 14 " pdb=" C2' A G 14 " ideal model delta sigma weight residual 113.70 104.36 9.34 1.50e+00 4.44e-01 3.88e+01 angle pdb=" N GLU D 205 " pdb=" CA GLU D 205 " pdb=" C GLU D 205 " ideal model delta sigma weight residual 113.50 107.68 5.82 1.23e+00 6.61e-01 2.24e+01 angle pdb=" N GLU B 87 " pdb=" CA GLU B 87 " pdb=" C GLU B 87 " ideal model delta sigma weight residual 113.50 106.33 7.17 1.65e+00 3.67e-01 1.89e+01 angle pdb=" C4' A G 14 " pdb=" C3' A G 14 " pdb=" C2' A G 14 " ideal model delta sigma weight residual 102.60 98.27 4.33 1.00e+00 1.00e+00 1.87e+01 ... (remaining 21279 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.94: 9261 34.94 - 69.87: 172 69.87 - 104.81: 16 104.81 - 139.74: 0 139.74 - 174.68: 3 Dihedral angle restraints: 9452 sinusoidal: 4292 harmonic: 5160 Sorted by residual: dihedral pdb=" O4' C G 28 " pdb=" C1' C G 28 " pdb=" N1 C G 28 " pdb=" C2 C G 28 " ideal model delta sinusoidal sigma weight residual 200.00 43.39 156.61 1 1.50e+01 4.44e-03 8.18e+01 dihedral pdb=" O4' C G 2 " pdb=" C1' C G 2 " pdb=" N1 C G 2 " pdb=" C2 C G 2 " ideal model delta sinusoidal sigma weight residual -128.00 46.68 -174.68 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' C G 8 " pdb=" C1' C G 8 " pdb=" N1 C G 8 " pdb=" C2 C G 8 " ideal model delta sinusoidal sigma weight residual -160.00 -88.21 -71.79 1 1.50e+01 4.44e-03 2.93e+01 ... (remaining 9449 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1666 0.043 - 0.087: 542 0.087 - 0.130: 143 0.130 - 0.174: 22 0.174 - 0.217: 6 Chirality restraints: 2379 Sorted by residual: chirality pdb=" CB ILE F 415 " pdb=" CA ILE F 415 " pdb=" CG1 ILE F 415 " pdb=" CG2 ILE F 415 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" C1' U L 8 " pdb=" O4' U L 8 " pdb=" C2' U L 8 " pdb=" N1 U L 8 " both_signs ideal model delta sigma weight residual False 2.47 2.25 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA GLU B 87 " pdb=" N GLU B 87 " pdb=" C GLU B 87 " pdb=" CB GLU B 87 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.80e-01 ... (remaining 2376 not shown) Planarity restraints: 2568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A L 16 " -0.043 2.00e-02 2.50e+03 1.86e-02 9.50e+00 pdb=" N9 A L 16 " 0.040 2.00e-02 2.50e+03 pdb=" C8 A L 16 " 0.004 2.00e-02 2.50e+03 pdb=" N7 A L 16 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A L 16 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A L 16 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A L 16 " -0.013 2.00e-02 2.50e+03 pdb=" N1 A L 16 " -0.005 2.00e-02 2.50e+03 pdb=" C2 A L 16 " 0.003 2.00e-02 2.50e+03 pdb=" N3 A L 16 " 0.010 2.00e-02 2.50e+03 pdb=" C4 A L 16 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN J 54 " 0.014 2.00e-02 2.50e+03 2.88e-02 8.30e+00 pdb=" C GLN J 54 " -0.050 2.00e-02 2.50e+03 pdb=" O GLN J 54 " 0.019 2.00e-02 2.50e+03 pdb=" N VAL J 55 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG I 57 " -0.013 2.00e-02 2.50e+03 2.63e-02 6.90e+00 pdb=" C ARG I 57 " 0.045 2.00e-02 2.50e+03 pdb=" O ARG I 57 " -0.017 2.00e-02 2.50e+03 pdb=" N LEU I 58 " -0.015 2.00e-02 2.50e+03 ... (remaining 2565 not shown) Histogram of nonbonded interaction distances: 1.37 - 2.08: 4 2.08 - 2.78: 3498 2.78 - 3.49: 20574 3.49 - 4.19: 34226 4.19 - 4.90: 59731 Nonbonded interactions: 118033 Sorted by model distance: nonbonded pdb=" OD1 ASN C 57 " pdb=" NH1 ARG A 129 " model vdw 1.373 3.120 nonbonded pdb=" ND2 ASN B 57 " pdb=" O2 C G 8 " model vdw 1.819 3.120 nonbonded pdb=" OD1 ASN C 57 " pdb=" CZ ARG A 129 " model vdw 1.957 3.270 nonbonded pdb=" OG1 THR C 126 " pdb=" O2' U G 25 " model vdw 2.066 3.040 nonbonded pdb=" ND2 ASN C 57 " pdb=" N7 G G 20 " model vdw 2.117 3.200 ... (remaining 118028 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 2 through 23 or resid 33 through 63 or resid 76 through 20 \ 7)) selection = (chain 'B' and resid 2 through 207) selection = (chain 'C' and (resid 2 through 23 or resid 33 through 63 or resid 76 through 20 \ 7)) selection = (chain 'D' and (resid 2 through 23 or resid 33 through 63 or resid 76 through 20 \ 7)) } ncs_group { reference = (chain 'I' and (resid 17 through 61 or resid 74 through 137)) selection = (chain 'J' and (resid 17 through 24 or resid 39 through 137)) } 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 group one per residue 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: 7.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.500 Find NCS groups from input model: 0.170 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: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6425 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.133 15690 Z= 0.304 Angle : 0.835 51.639 21288 Z= 0.491 Chirality : 0.046 0.217 2379 Planarity : 0.005 0.057 2568 Dihedral : 13.953 174.677 6120 Min Nonbonded Distance : 1.373 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.74 % Favored : 95.20 % Rotamer: Outliers : 0.38 % Allowed : 4.04 % Favored : 95.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.19), residues: 1729 helix: 0.42 (0.18), residues: 764 sheet: 0.09 (0.29), residues: 292 loop : -1.58 (0.21), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 91 TYR 0.020 0.002 TYR H 200 PHE 0.016 0.002 PHE A 148 TRP 0.006 0.001 TRP F 184 HIS 0.008 0.001 HIS F 14 Details of bonding type rmsd covalent geometry : bond 0.00506 (15688) covalent geometry : angle 0.75594 (21284) SS BOND : bond 0.09418 ( 2) SS BOND : angle 25.85717 ( 4) hydrogen bonds : bond 0.15918 ( 721) hydrogen bonds : angle 7.00594 ( 2084) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 431 time to evaluate : 0.568 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: F 380 LEU cc_start: 0.8314 (tp) cc_final: 0.7670 (pp) REVERT: J 53 GLU cc_start: 0.9093 (mm-30) cc_final: 0.8781 (mm-30) REVERT: I 51 LEU cc_start: 0.9205 (mt) cc_final: 0.8557 (mt) outliers start: 6 outliers final: 0 residues processed: 435 average time/residue: 0.1722 time to fit residues: 99.9330 Evaluate side-chains 201 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.1980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.8980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 5 ASN ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 50 ASN F 83 ASN F 183 GLN F 397 ASN D 69 GLN ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 114 ASN D 189 ASN ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 GLN C 110 HIS A 69 GLN A 97 GLN ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.073458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.060662 restraints weight = 125519.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.062149 restraints weight = 88937.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.063174 restraints weight = 67504.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.063935 restraints weight = 54532.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.064513 restraints weight = 46303.371| |-----------------------------------------------------------------------------| r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 15690 Z= 0.147 Angle : 0.638 10.298 21288 Z= 0.339 Chirality : 0.043 0.211 2379 Planarity : 0.004 0.058 2568 Dihedral : 14.775 177.574 2555 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.89 % Favored : 97.05 % Rotamer: Outliers : 0.06 % Allowed : 2.71 % Favored : 97.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.19), residues: 1729 helix: 0.88 (0.18), residues: 775 sheet: 0.43 (0.29), residues: 286 loop : -1.50 (0.21), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 37 TYR 0.027 0.002 TYR I 80 PHE 0.045 0.002 PHE K 85 TRP 0.011 0.002 TRP H 52 HIS 0.014 0.001 HIS C 110 Details of bonding type rmsd covalent geometry : bond 0.00303 (15688) covalent geometry : angle 0.63690 (21284) SS BOND : bond 0.01394 ( 2) SS BOND : angle 2.35606 ( 4) hydrogen bonds : bond 0.04704 ( 721) hydrogen bonds : angle 5.30814 ( 2084) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 261 time to evaluate : 0.587 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: F 1 MET cc_start: 0.5853 (mmm) cc_final: 0.2405 (ttt) REVERT: F 33 HIS cc_start: 0.6497 (p-80) cc_final: 0.5852 (p-80) REVERT: F 163 MET cc_start: 0.4273 (ptt) cc_final: 0.3450 (ppp) REVERT: F 380 LEU cc_start: 0.9013 (tp) cc_final: 0.8780 (pp) REVERT: J 128 GLU cc_start: 0.7004 (tt0) cc_final: 0.6751 (tt0) REVERT: I 49 ARG cc_start: 0.9355 (pmt170) cc_final: 0.8928 (pmt170) REVERT: I 57 ARG cc_start: 0.9090 (mtm110) cc_final: 0.8800 (mtm110) REVERT: I 70 LEU cc_start: 0.7457 (mp) cc_final: 0.6836 (mp) REVERT: K 52 MET cc_start: 0.6770 (mmm) cc_final: 0.6415 (ptp) REVERT: C 100 ASP cc_start: 0.9000 (m-30) cc_final: 0.8485 (t0) REVERT: C 128 ASN cc_start: 0.8556 (t0) cc_final: 0.8329 (t0) REVERT: C 144 ARG cc_start: 0.8641 (mtp85) cc_final: 0.8014 (mtp85) REVERT: B 115 ASP cc_start: 0.8973 (m-30) cc_final: 0.8652 (m-30) REVERT: H 25 ASP cc_start: 0.8569 (t0) cc_final: 0.8114 (t0) outliers start: 1 outliers final: 1 residues processed: 261 average time/residue: 0.1503 time to fit residues: 54.9959 Evaluate side-chains 176 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 175 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 91 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 155 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 129 optimal weight: 0.8980 chunk 142 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 145 optimal weight: 8.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 GLN ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.071692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.059295 restraints weight = 133537.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.060783 restraints weight = 91685.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.061810 restraints weight = 68831.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.062509 restraints weight = 55303.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.063029 restraints weight = 47028.333| |-----------------------------------------------------------------------------| r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.4491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15690 Z= 0.141 Angle : 0.596 10.978 21288 Z= 0.316 Chirality : 0.043 0.311 2379 Planarity : 0.004 0.054 2568 Dihedral : 14.768 175.975 2555 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.07 % Favored : 96.88 % Rotamer: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.19), residues: 1729 helix: 0.89 (0.18), residues: 777 sheet: 0.54 (0.29), residues: 295 loop : -1.43 (0.22), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 110 TYR 0.024 0.001 TYR I 86 PHE 0.031 0.002 PHE K 85 TRP 0.013 0.002 TRP H 52 HIS 0.006 0.001 HIS H 174 Details of bonding type rmsd covalent geometry : bond 0.00291 (15688) covalent geometry : angle 0.59533 (21284) SS BOND : bond 0.00478 ( 2) SS BOND : angle 1.93546 ( 4) hydrogen bonds : bond 0.04265 ( 721) hydrogen bonds : angle 5.04999 ( 2084) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.403 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: F 7 LEU cc_start: 0.8217 (mt) cc_final: 0.8013 (mt) REVERT: F 33 HIS cc_start: 0.6701 (p-80) cc_final: 0.6056 (p-80) REVERT: F 380 LEU cc_start: 0.9102 (tp) cc_final: 0.8767 (pp) REVERT: J 109 ASP cc_start: 0.9045 (t0) cc_final: 0.8555 (m-30) REVERT: J 112 ILE cc_start: 0.8031 (pt) cc_final: 0.7744 (pt) REVERT: I 41 ASN cc_start: 0.8921 (m-40) cc_final: 0.8628 (m-40) REVERT: I 49 ARG cc_start: 0.9383 (pmt170) cc_final: 0.9023 (pmt170) REVERT: I 70 LEU cc_start: 0.7373 (mp) cc_final: 0.6665 (mp) REVERT: I 85 PHE cc_start: 0.9646 (m-80) cc_final: 0.9238 (m-80) REVERT: I 86 TYR cc_start: 0.9172 (m-80) cc_final: 0.8677 (m-80) REVERT: K 85 PHE cc_start: 0.8946 (m-80) cc_final: 0.8739 (m-80) REVERT: K 104 MET cc_start: 0.7926 (ppp) cc_final: 0.7466 (ppp) REVERT: C 100 ASP cc_start: 0.9055 (m-30) cc_final: 0.8435 (t0) REVERT: C 128 ASN cc_start: 0.8576 (t0) cc_final: 0.8240 (t0) REVERT: A 144 ARG cc_start: 0.7664 (ptm-80) cc_final: 0.7140 (tmm-80) REVERT: A 178 ASN cc_start: 0.9025 (t0) cc_final: 0.8678 (t0) REVERT: A 198 ASN cc_start: 0.7877 (t0) cc_final: 0.7643 (m110) REVERT: B 115 ASP cc_start: 0.8962 (m-30) cc_final: 0.8637 (m-30) REVERT: H 22 ARG cc_start: 0.7607 (tpm170) cc_final: 0.7092 (mmm160) REVERT: H 25 ASP cc_start: 0.8645 (t0) cc_final: 0.8169 (t0) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.1371 time to fit residues: 44.1910 Evaluate side-chains 164 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 56 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 169 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 136 optimal weight: 0.5980 chunk 37 optimal weight: 8.9990 chunk 33 optimal weight: 7.9990 chunk 8 optimal weight: 7.9990 chunk 122 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 ASN J 18 HIS D 69 GLN ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 161 GLN ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.067777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.055925 restraints weight = 141109.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.057309 restraints weight = 97989.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.058201 restraints weight = 73966.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.058863 restraints weight = 60159.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.059360 restraints weight = 51155.065| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.5321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15690 Z= 0.173 Angle : 0.630 11.782 21288 Z= 0.333 Chirality : 0.043 0.173 2379 Planarity : 0.004 0.044 2568 Dihedral : 14.945 174.739 2555 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.47 % Favored : 96.47 % Rotamer: Outliers : 0.13 % Allowed : 2.78 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.19), residues: 1729 helix: 0.81 (0.18), residues: 789 sheet: 0.61 (0.30), residues: 292 loop : -1.51 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG I 57 TYR 0.036 0.002 TYR I 87 PHE 0.022 0.002 PHE K 85 TRP 0.019 0.002 TRP H 52 HIS 0.005 0.001 HIS D 110 Details of bonding type rmsd covalent geometry : bond 0.00356 (15688) covalent geometry : angle 0.62963 (21284) SS BOND : bond 0.00658 ( 2) SS BOND : angle 1.38987 ( 4) hydrogen bonds : bond 0.04349 ( 721) hydrogen bonds : angle 4.99577 ( 2084) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 200 time to evaluate : 0.501 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: F 1 MET cc_start: 0.6338 (mmm) cc_final: 0.3077 (ttt) REVERT: F 7 LEU cc_start: 0.8216 (mt) cc_final: 0.7959 (mt) REVERT: F 33 HIS cc_start: 0.7135 (p-80) cc_final: 0.6477 (p-80) REVERT: J 109 ASP cc_start: 0.9084 (t0) cc_final: 0.8632 (m-30) REVERT: J 112 ILE cc_start: 0.8096 (pt) cc_final: 0.7818 (pt) REVERT: I 41 ASN cc_start: 0.8909 (m-40) cc_final: 0.8640 (m-40) REVERT: I 70 LEU cc_start: 0.7514 (mp) cc_final: 0.6563 (mp) REVERT: I 85 PHE cc_start: 0.9614 (m-80) cc_final: 0.9084 (m-80) REVERT: K 85 PHE cc_start: 0.9044 (m-80) cc_final: 0.8774 (m-80) REVERT: K 86 TYR cc_start: 0.8344 (m-10) cc_final: 0.8116 (m-10) REVERT: D 55 MET cc_start: 0.9042 (mtp) cc_final: 0.8796 (mtp) REVERT: D 69 GLN cc_start: 0.2950 (OUTLIER) cc_final: 0.1714 (pp30) REVERT: C 38 ASP cc_start: 0.8326 (t0) cc_final: 0.7734 (t0) REVERT: C 100 ASP cc_start: 0.9008 (m-30) cc_final: 0.8736 (m-30) REVERT: C 128 ASN cc_start: 0.8734 (t0) cc_final: 0.8387 (t0) REVERT: A 144 ARG cc_start: 0.7904 (ptm-80) cc_final: 0.7237 (tmm-80) REVERT: A 178 ASN cc_start: 0.9106 (t0) cc_final: 0.8869 (t0) REVERT: A 193 GLN cc_start: 0.9333 (tt0) cc_final: 0.9113 (tm-30) REVERT: A 198 ASN cc_start: 0.8091 (t0) cc_final: 0.7874 (m110) REVERT: B 105 GLU cc_start: 0.9442 (mm-30) cc_final: 0.9060 (pm20) REVERT: H 22 ARG cc_start: 0.7825 (tpm170) cc_final: 0.7121 (mmm160) REVERT: H 121 PHE cc_start: 0.8431 (t80) cc_final: 0.8214 (t80) outliers start: 2 outliers final: 0 residues processed: 202 average time/residue: 0.1266 time to fit residues: 37.4591 Evaluate side-chains 152 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 151 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 129 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 chunk 104 optimal weight: 7.9990 chunk 134 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 HIS F 263 GLN ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 HIS ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN B 113 GLN ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 GLN H 87 HIS ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.063400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.051697 restraints weight = 144553.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.053010 restraints weight = 104165.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.053866 restraints weight = 78913.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.054357 restraints weight = 64547.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.054870 restraints weight = 56405.653| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.6460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 15690 Z= 0.245 Angle : 0.725 10.894 21288 Z= 0.383 Chirality : 0.045 0.296 2379 Planarity : 0.005 0.067 2568 Dihedral : 15.406 174.578 2555 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 21.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.11 % Favored : 95.84 % Rotamer: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.19), residues: 1729 helix: 0.26 (0.17), residues: 801 sheet: 0.25 (0.30), residues: 290 loop : -1.59 (0.22), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 93 TYR 0.024 0.002 TYR I 87 PHE 0.033 0.002 PHE F 399 TRP 0.024 0.003 TRP H 52 HIS 0.011 0.002 HIS A 174 Details of bonding type rmsd covalent geometry : bond 0.00502 (15688) covalent geometry : angle 0.72465 (21284) SS BOND : bond 0.00942 ( 2) SS BOND : angle 1.21357 ( 4) hydrogen bonds : bond 0.04918 ( 721) hydrogen bonds : angle 5.35464 ( 2084) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.619 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: F 1 MET cc_start: 0.6064 (mmm) cc_final: 0.2242 (ttt) REVERT: F 163 MET cc_start: 0.5883 (ppp) cc_final: 0.5680 (ppp) REVERT: F 288 MET cc_start: 0.9186 (mmp) cc_final: 0.8930 (mmm) REVERT: F 452 MET cc_start: 0.3293 (mmp) cc_final: 0.2771 (mmm) REVERT: J 109 ASP cc_start: 0.9118 (t0) cc_final: 0.8676 (m-30) REVERT: J 112 ILE cc_start: 0.8233 (pt) cc_final: 0.7908 (pt) REVERT: I 41 ASN cc_start: 0.9026 (m-40) cc_final: 0.8757 (m-40) REVERT: I 49 ARG cc_start: 0.9254 (pmt170) cc_final: 0.8845 (pmt170) REVERT: I 85 PHE cc_start: 0.9682 (m-80) cc_final: 0.9400 (m-80) REVERT: I 91 ARG cc_start: 0.8811 (mmm-85) cc_final: 0.8428 (mmm-85) REVERT: I 133 TYR cc_start: 0.9143 (m-80) cc_final: 0.8907 (m-80) REVERT: D 55 MET cc_start: 0.9132 (mtp) cc_final: 0.8751 (mtp) REVERT: D 82 LEU cc_start: 0.8345 (mt) cc_final: 0.8142 (mt) REVERT: D 90 ASN cc_start: 0.8888 (p0) cc_final: 0.8499 (p0) REVERT: C 128 ASN cc_start: 0.8632 (t0) cc_final: 0.8310 (t0) REVERT: A 193 GLN cc_start: 0.9285 (tt0) cc_final: 0.8974 (tm-30) REVERT: B 105 GLU cc_start: 0.9346 (mm-30) cc_final: 0.9122 (tp30) REVERT: B 168 ASN cc_start: 0.8877 (m110) cc_final: 0.8611 (m110) REVERT: B 181 LEU cc_start: 0.9569 (tp) cc_final: 0.9303 (tp) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.1304 time to fit residues: 36.8986 Evaluate side-chains 138 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 124 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 168 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 135 optimal weight: 0.8980 chunk 107 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 130 optimal weight: 0.8980 chunk 153 optimal weight: 0.0010 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 18 HIS D 74 GLN ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN A 174 HIS ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 HIS ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.065897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.054236 restraints weight = 141824.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.055596 restraints weight = 98627.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.056440 restraints weight = 74397.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.057157 restraints weight = 61194.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.057427 restraints weight = 51809.293| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.6597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15690 Z= 0.123 Angle : 0.610 14.043 21288 Z= 0.314 Chirality : 0.043 0.366 2379 Planarity : 0.004 0.070 2568 Dihedral : 15.228 178.178 2555 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.95 % Favored : 96.99 % Rotamer: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.19), residues: 1729 helix: 0.68 (0.18), residues: 807 sheet: 0.32 (0.29), residues: 297 loop : -1.48 (0.23), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 81 TYR 0.015 0.001 TYR F 284 PHE 0.023 0.002 PHE F 40 TRP 0.015 0.002 TRP H 52 HIS 0.007 0.001 HIS J 18 Details of bonding type rmsd covalent geometry : bond 0.00255 (15688) covalent geometry : angle 0.61028 (21284) SS BOND : bond 0.00429 ( 2) SS BOND : angle 1.30629 ( 4) hydrogen bonds : bond 0.03818 ( 721) hydrogen bonds : angle 5.04059 ( 2084) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.599 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: F 288 MET cc_start: 0.9225 (mmp) cc_final: 0.8975 (mmm) REVERT: J 109 ASP cc_start: 0.9130 (t0) cc_final: 0.8682 (m-30) REVERT: J 123 TYR cc_start: 0.9238 (t80) cc_final: 0.9014 (t80) REVERT: I 41 ASN cc_start: 0.8884 (m-40) cc_final: 0.8621 (m-40) REVERT: I 68 ASP cc_start: 0.8458 (t70) cc_final: 0.7841 (t0) REVERT: I 85 PHE cc_start: 0.9646 (m-80) cc_final: 0.9336 (m-80) REVERT: I 91 ARG cc_start: 0.8756 (mmm-85) cc_final: 0.8400 (mmm-85) REVERT: I 133 TYR cc_start: 0.9057 (m-80) cc_final: 0.8788 (m-80) REVERT: K 98 PHE cc_start: 0.8332 (t80) cc_final: 0.8131 (t80) REVERT: K 104 MET cc_start: 0.8910 (ppp) cc_final: 0.8540 (ppp) REVERT: D 55 MET cc_start: 0.9095 (mtp) cc_final: 0.8742 (mtp) REVERT: C 128 ASN cc_start: 0.8782 (t0) cc_final: 0.8566 (t0) REVERT: A 198 ASN cc_start: 0.8190 (t0) cc_final: 0.7953 (m110) REVERT: B 47 PRO cc_start: 0.8901 (Cg_exo) cc_final: 0.8652 (Cg_endo) REVERT: B 105 GLU cc_start: 0.9437 (mm-30) cc_final: 0.9129 (tp30) REVERT: B 115 ASP cc_start: 0.8367 (m-30) cc_final: 0.8164 (m-30) REVERT: B 168 ASN cc_start: 0.8779 (m110) cc_final: 0.8453 (m110) REVERT: B 181 LEU cc_start: 0.9628 (tp) cc_final: 0.9363 (tp) REVERT: H 258 MET cc_start: 0.7849 (mpp) cc_final: 0.7543 (pmm) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.1189 time to fit residues: 34.5296 Evaluate side-chains 140 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 73 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 164 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 159 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 71 optimal weight: 9.9990 chunk 114 optimal weight: 9.9990 chunk 24 optimal weight: 0.8980 chunk 127 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 ASN ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN A 57 ASN ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.060786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.050312 restraints weight = 155792.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.051334 restraints weight = 109669.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.052041 restraints weight = 84984.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.052576 restraints weight = 70511.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.052922 restraints weight = 61145.127| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.7177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15690 Z= 0.199 Angle : 0.664 11.844 21288 Z= 0.347 Chirality : 0.043 0.220 2379 Planarity : 0.004 0.056 2568 Dihedral : 15.436 173.762 2555 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.99 % Favored : 95.95 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.19), residues: 1729 helix: 0.54 (0.18), residues: 796 sheet: 0.26 (0.30), residues: 287 loop : -1.50 (0.22), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 129 TYR 0.019 0.002 TYR J 133 PHE 0.024 0.002 PHE F 40 TRP 0.016 0.002 TRP H 52 HIS 0.006 0.001 HIS D 110 Details of bonding type rmsd covalent geometry : bond 0.00412 (15688) covalent geometry : angle 0.66351 (21284) SS BOND : bond 0.00823 ( 2) SS BOND : angle 1.42096 ( 4) hydrogen bonds : bond 0.04421 ( 721) hydrogen bonds : angle 5.21799 ( 2084) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.564 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: F 7 LEU cc_start: 0.8233 (mt) cc_final: 0.8024 (mt) REVERT: F 288 MET cc_start: 0.9093 (mmp) cc_final: 0.8806 (mmm) REVERT: F 452 MET cc_start: 0.3616 (mmp) cc_final: 0.2433 (mmm) REVERT: J 109 ASP cc_start: 0.9157 (t0) cc_final: 0.8684 (m-30) REVERT: I 41 ASN cc_start: 0.8892 (m-40) cc_final: 0.8634 (m-40) REVERT: I 85 PHE cc_start: 0.9668 (m-80) cc_final: 0.9401 (m-80) REVERT: I 91 ARG cc_start: 0.8868 (mmm-85) cc_final: 0.8558 (mmm-85) REVERT: K 86 TYR cc_start: 0.8574 (m-80) cc_final: 0.8307 (m-80) REVERT: D 55 MET cc_start: 0.9190 (mtp) cc_final: 0.8788 (mtp) REVERT: C 128 ASN cc_start: 0.8914 (t0) cc_final: 0.8631 (t0) REVERT: A 116 ILE cc_start: 0.7439 (mt) cc_final: 0.6606 (mt) REVERT: B 105 GLU cc_start: 0.9322 (mm-30) cc_final: 0.9069 (tp30) REVERT: B 168 ASN cc_start: 0.8883 (m110) cc_final: 0.8609 (m110) REVERT: B 181 LEU cc_start: 0.9502 (tp) cc_final: 0.9236 (tp) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.1189 time to fit residues: 30.4033 Evaluate side-chains 128 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 76 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 146 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 52 optimal weight: 20.0000 chunk 129 optimal weight: 0.0970 chunk 96 optimal weight: 3.9990 chunk 158 optimal weight: 0.0970 chunk 53 optimal weight: 4.9990 overall best weight: 0.5376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 26 HIS ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 GLN A 57 ASN ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 214 GLN ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.065651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.054529 restraints weight = 146826.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.055877 restraints weight = 98414.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.056780 restraints weight = 73285.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.057435 restraints weight = 59021.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.057888 restraints weight = 50156.111| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 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 : 0.002 0.032 15690 Z= 0.112 Angle : 0.602 13.494 21288 Z= 0.308 Chirality : 0.041 0.191 2379 Planarity : 0.004 0.056 2568 Dihedral : 15.283 178.307 2555 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.89 % Favored : 97.05 % Rotamer: Outliers : 0.06 % Allowed : 0.82 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.19), residues: 1729 helix: 0.83 (0.18), residues: 793 sheet: 0.35 (0.29), residues: 291 loop : -1.36 (0.22), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 93 TYR 0.015 0.001 TYR I 137 PHE 0.027 0.001 PHE J 85 TRP 0.009 0.001 TRP H 52 HIS 0.006 0.001 HIS D 110 Details of bonding type rmsd covalent geometry : bond 0.00233 (15688) covalent geometry : angle 0.60161 (21284) SS BOND : bond 0.00246 ( 2) SS BOND : angle 1.18259 ( 4) hydrogen bonds : bond 0.03593 ( 721) hydrogen bonds : angle 4.94613 ( 2084) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 185 time to evaluate : 0.614 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: F 288 MET cc_start: 0.9228 (mmp) cc_final: 0.8976 (mmm) REVERT: F 452 MET cc_start: 0.3132 (mmp) cc_final: 0.2498 (mmm) REVERT: J 109 ASP cc_start: 0.9183 (t0) cc_final: 0.8715 (m-30) REVERT: J 112 ILE cc_start: 0.8062 (pt) cc_final: 0.7683 (pt) REVERT: J 127 PHE cc_start: 0.9480 (t80) cc_final: 0.9143 (t80) REVERT: J 128 GLU cc_start: 0.7169 (tt0) cc_final: 0.6656 (tt0) REVERT: I 41 ASN cc_start: 0.8861 (m-40) cc_final: 0.8604 (m-40) REVERT: I 85 PHE cc_start: 0.9662 (m-80) cc_final: 0.9382 (m-80) REVERT: I 91 ARG cc_start: 0.8847 (mmm-85) cc_final: 0.8501 (mmm-85) REVERT: I 133 TYR cc_start: 0.9090 (m-80) cc_final: 0.8714 (m-80) REVERT: D 40 GLN cc_start: 0.9168 (mt0) cc_final: 0.8927 (mt0) REVERT: D 55 MET cc_start: 0.9091 (mtp) cc_final: 0.8730 (mtp) REVERT: D 83 PHE cc_start: 0.8009 (m-10) cc_final: 0.7708 (m-10) REVERT: D 97 GLN cc_start: 0.8265 (mp10) cc_final: 0.7994 (mp10) REVERT: C 128 ASN cc_start: 0.8881 (t0) cc_final: 0.8637 (t0) REVERT: A 116 ILE cc_start: 0.7448 (mt) cc_final: 0.6635 (mt) REVERT: B 115 ASP cc_start: 0.8347 (m-30) cc_final: 0.8116 (m-30) REVERT: B 168 ASN cc_start: 0.8793 (m110) cc_final: 0.8470 (m110) REVERT: B 181 LEU cc_start: 0.9638 (tp) cc_final: 0.9398 (tp) outliers start: 1 outliers final: 0 residues processed: 186 average time/residue: 0.1295 time to fit residues: 35.8519 Evaluate side-chains 129 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 47 optimal weight: 0.9990 chunk 119 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 22 optimal weight: 0.1980 chunk 81 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 218 HIS ** 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 = 0.3962 r_free = 0.3962 target = 0.065159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.054142 restraints weight = 146182.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.055451 restraints weight = 98171.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.056349 restraints weight = 73385.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.056964 restraints weight = 59224.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.057420 restraints weight = 50764.128| |-----------------------------------------------------------------------------| r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.7353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15690 Z= 0.120 Angle : 0.609 14.571 21288 Z= 0.314 Chirality : 0.041 0.160 2379 Planarity : 0.004 0.043 2568 Dihedral : 15.259 176.203 2555 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.20), residues: 1729 helix: 0.94 (0.18), residues: 792 sheet: 0.41 (0.30), residues: 291 loop : -1.29 (0.22), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 57 TYR 0.014 0.001 TYR H 184 PHE 0.028 0.002 PHE F 178 TRP 0.009 0.001 TRP H 52 HIS 0.006 0.001 HIS D 110 Details of bonding type rmsd covalent geometry : bond 0.00254 (15688) covalent geometry : angle 0.60851 (21284) SS BOND : bond 0.00340 ( 2) SS BOND : angle 1.20206 ( 4) hydrogen bonds : bond 0.03699 ( 721) hydrogen bonds : angle 4.96080 ( 2084) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.567 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: F 1 MET cc_start: 0.6566 (mmt) cc_final: 0.1645 (ttt) REVERT: F 452 MET cc_start: 0.3384 (mmp) cc_final: 0.2893 (mmm) REVERT: J 109 ASP cc_start: 0.9120 (t0) cc_final: 0.8675 (m-30) REVERT: J 112 ILE cc_start: 0.8170 (pt) cc_final: 0.7795 (pt) REVERT: J 123 TYR cc_start: 0.8978 (t80) cc_final: 0.8658 (t80) REVERT: J 127 PHE cc_start: 0.9501 (t80) cc_final: 0.9142 (t80) REVERT: J 128 GLU cc_start: 0.7198 (tt0) cc_final: 0.6686 (tt0) REVERT: I 41 ASN cc_start: 0.8839 (m-40) cc_final: 0.8591 (m-40) REVERT: I 85 PHE cc_start: 0.9660 (m-80) cc_final: 0.9414 (m-80) REVERT: I 91 ARG cc_start: 0.8681 (mmm-85) cc_final: 0.8425 (mmm-85) REVERT: I 128 GLU cc_start: 0.8938 (mt-10) cc_final: 0.8694 (mm-30) REVERT: K 86 TYR cc_start: 0.8662 (m-10) cc_final: 0.8423 (m-80) REVERT: K 104 MET cc_start: 0.8825 (ppp) cc_final: 0.8493 (ppp) REVERT: D 40 GLN cc_start: 0.9169 (mt0) cc_final: 0.8919 (mt0) REVERT: D 55 MET cc_start: 0.9095 (mtp) cc_final: 0.8741 (mtp) REVERT: C 128 ASN cc_start: 0.8908 (t0) cc_final: 0.8659 (t0) REVERT: B 115 ASP cc_start: 0.8381 (m-30) cc_final: 0.8170 (m-30) REVERT: B 164 ASP cc_start: 0.9005 (m-30) cc_final: 0.8419 (p0) REVERT: B 168 ASN cc_start: 0.8786 (m110) cc_final: 0.8472 (m110) REVERT: B 181 LEU cc_start: 0.9608 (tp) cc_final: 0.9376 (tp) REVERT: H 121 PHE cc_start: 0.8942 (t80) cc_final: 0.8730 (t80) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.1254 time to fit residues: 33.3343 Evaluate side-chains 131 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 134 optimal weight: 3.9990 chunk 158 optimal weight: 8.9990 chunk 53 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 13 optimal weight: 0.4980 chunk 90 optimal weight: 9.9990 chunk 69 optimal weight: 8.9990 chunk 175 optimal weight: 7.9990 chunk 172 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 251 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 = 0.3930 r_free = 0.3930 target = 0.063989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.053033 restraints weight = 149722.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.054300 restraints weight = 102640.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.055244 restraints weight = 76718.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.055862 restraints weight = 61177.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.056274 restraints weight = 51925.977| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.7621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15690 Z= 0.145 Angle : 0.620 12.438 21288 Z= 0.321 Chirality : 0.041 0.245 2379 Planarity : 0.004 0.044 2568 Dihedral : 15.358 175.497 2555 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.20), residues: 1729 helix: 0.90 (0.18), residues: 794 sheet: 0.32 (0.30), residues: 296 loop : -1.28 (0.23), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 57 TYR 0.022 0.001 TYR H 184 PHE 0.024 0.001 PHE H 40 TRP 0.010 0.001 TRP H 52 HIS 0.007 0.001 HIS D 110 Details of bonding type rmsd covalent geometry : bond 0.00303 (15688) covalent geometry : angle 0.61952 (21284) SS BOND : bond 0.00502 ( 2) SS BOND : angle 1.21343 ( 4) hydrogen bonds : bond 0.03829 ( 721) hydrogen bonds : angle 5.00868 ( 2084) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.516 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: F 288 MET cc_start: 0.9118 (mmp) cc_final: 0.8905 (mmm) REVERT: F 452 MET cc_start: 0.3090 (mmp) cc_final: 0.2618 (mmm) REVERT: J 109 ASP cc_start: 0.9128 (t0) cc_final: 0.8691 (m-30) REVERT: J 123 TYR cc_start: 0.8913 (t80) cc_final: 0.8592 (t80) REVERT: J 127 PHE cc_start: 0.9511 (t80) cc_final: 0.9198 (t80) REVERT: I 41 ASN cc_start: 0.8850 (m-40) cc_final: 0.8587 (m-40) REVERT: I 85 PHE cc_start: 0.9672 (m-80) cc_final: 0.9416 (m-80) REVERT: I 91 ARG cc_start: 0.8871 (mmm-85) cc_final: 0.8509 (mmm-85) REVERT: I 123 TYR cc_start: 0.9453 (t80) cc_final: 0.9232 (t80) REVERT: I 128 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8686 (mm-30) REVERT: K 104 MET cc_start: 0.8857 (ppp) cc_final: 0.8528 (ppp) REVERT: D 40 GLN cc_start: 0.9192 (mt0) cc_final: 0.8940 (mt0) REVERT: D 55 MET cc_start: 0.9117 (mtp) cc_final: 0.8758 (mtp) REVERT: D 82 LEU cc_start: 0.8299 (mt) cc_final: 0.8078 (mt) REVERT: D 97 GLN cc_start: 0.8334 (mp10) cc_final: 0.8124 (pm20) REVERT: C 128 ASN cc_start: 0.9044 (t0) cc_final: 0.8803 (t0) REVERT: A 207 ASP cc_start: 0.9164 (m-30) cc_final: 0.8340 (p0) REVERT: B 115 ASP cc_start: 0.8237 (m-30) cc_final: 0.8019 (m-30) REVERT: B 168 ASN cc_start: 0.8921 (m110) cc_final: 0.8653 (m110) REVERT: B 181 LEU cc_start: 0.9596 (tp) cc_final: 0.9215 (tt) REVERT: H 52 TRP cc_start: 0.7244 (m-90) cc_final: 0.5894 (m-90) REVERT: H 121 PHE cc_start: 0.8946 (t80) cc_final: 0.8688 (t80) REVERT: H 179 MET cc_start: 0.4974 (ttp) cc_final: 0.4588 (ttt) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.1190 time to fit residues: 29.9207 Evaluate side-chains 125 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 10 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 46 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 129 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 153 optimal weight: 0.6980 chunk 125 optimal weight: 0.9990 chunk 57 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 218 HIS ** 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 = 0.3961 r_free = 0.3961 target = 0.065062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.054298 restraints weight = 147212.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.055620 restraints weight = 98587.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.056536 restraints weight = 73225.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.057152 restraints weight = 58674.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.057608 restraints weight = 49828.610| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.7711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15690 Z= 0.112 Angle : 0.595 13.012 21288 Z= 0.306 Chirality : 0.041 0.206 2379 Planarity : 0.003 0.042 2568 Dihedral : 15.279 177.194 2555 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.20), residues: 1729 helix: 0.98 (0.18), residues: 794 sheet: 0.41 (0.30), residues: 296 loop : -1.24 (0.23), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 37 TYR 0.018 0.001 TYR H 184 PHE 0.023 0.001 PHE H 40 TRP 0.007 0.001 TRP H 52 HIS 0.007 0.001 HIS D 110 Details of bonding type rmsd covalent geometry : bond 0.00235 (15688) covalent geometry : angle 0.59508 (21284) SS BOND : bond 0.00266 ( 2) SS BOND : angle 1.30956 ( 4) hydrogen bonds : bond 0.03488 ( 721) hydrogen bonds : angle 4.88659 ( 2084) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3245.35 seconds wall clock time: 56 minutes 41.70 seconds (3401.70 seconds total)