Starting phenix.real_space_refine on Fri Jul 3 18:48:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7uzy_26922/07_2026/7uzy_26922.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uzy_26922/07_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_26922/07_2026/7uzy_26922.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uzy_26922/07_2026/7uzy_26922.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uzy_26922/07_2026/7uzy_26922.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uzy_26922/07_2026/7uzy_26922.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7uzy_26922/07_2026/7uzy_26922.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7uzy_26922/07_2026/7uzy_26922.cif" } 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-6108/lib/python3.11/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: 2.76, per 1000 atoms: 0.18 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: 1.28 Conformation dependent library (CDL) restraints added in 467.5 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: 1.57 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: 2.44 Time building geometry restraints manager: 1.58 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: 9194 34.94 - 69.87: 126 69.87 - 104.81: 11 104.81 - 139.74: 0 139.74 - 174.68: 3 Dihedral angle restraints: 9334 sinusoidal: 4174 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 9331 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: 5.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.290 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6304 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 : 12.941 174.677 6002 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/Z covalent geometry : bond 0.00506 / 0.30 (15688) covalent geometry : angle 0.75594 / 0.46 (21284) SS BOND : bond 0.09418 / 4.96 ( 2) SS BOND : angle 25.85717 / 13.61 ( 4) hydrogen bonds : bond 0.15918 / 10.56 ( 721) hydrogen bonds : angle 7.00594 / 4.77 ( 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 : 0.572 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: 0.1659 time to fit residues: 97.0137 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 : 0.565 ------------------------------------------------------------------------------- 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... F 5 ASN ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 50 ASN F 314 HIS 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.073460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.060690 restraints weight = 125495.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.062200 restraints weight = 88176.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.063271 restraints weight = 66719.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.064010 restraints weight = 53664.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.064392 restraints weight = 45553.258| |-----------------------------------------------------------------------------| r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15690 Z= 0.149 Angle : 0.636 9.822 21288 Z= 0.339 Chirality : 0.044 0.231 2379 Planarity : 0.004 0.054 2568 Dihedral : 12.467 177.270 2437 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.89 % Favored : 97.05 % Rotamer: Outliers : 0.06 % Allowed : 2.78 % Favored : 97.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.14 (0.19), residues: 1729 helix: 0.89 (0.18), residues: 775 sheet: 0.42 (0.29), residues: 286 loop : -1.50 (0.21), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 37 TYR 0.038 0.002 TYR I 80 PHE 0.042 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/Z covalent geometry : bond 0.00309 / 0.15 (15688) covalent geometry : angle 0.63522 / 0.34 (21284) SS BOND : bond 0.01261 / 0.65 ( 2) SS BOND : angle 2.30270 / 1.31 ( 4) hydrogen bonds : bond 0.04736 / 3.11 ( 721) hydrogen bonds : angle 5.31738 / 3.59 ( 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 : 0.498 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: 0.5834 (mmm) cc_final: 0.2380 (ttt) REVERT: F 33 HIS cc_start: 0.6493 (p-80) cc_final: 0.5851 (p-80) REVERT: F 163 MET cc_start: 0.4279 (ptt) cc_final: 0.3459 (ppp) REVERT: F 380 LEU cc_start: 0.9001 (tp) cc_final: 0.8780 (pp) REVERT: J 128 GLU cc_start: 0.7012 (tt0) cc_final: 0.6748 (tt0) REVERT: I 49 ARG cc_start: 0.9352 (pmt170) cc_final: 0.8927 (pmt170) REVERT: I 57 ARG cc_start: 0.9089 (mtm110) cc_final: 0.8781 (mtm110) REVERT: I 70 LEU cc_start: 0.7475 (mp) cc_final: 0.6863 (mp) REVERT: K 52 MET cc_start: 0.6798 (mmm) cc_final: 0.6453 (ptp) REVERT: K 85 PHE cc_start: 0.8987 (m-80) cc_final: 0.8785 (m-80) REVERT: C 100 ASP cc_start: 0.9003 (m-30) cc_final: 0.8485 (t0) REVERT: C 128 ASN cc_start: 0.8525 (t0) cc_final: 0.8297 (t0) REVERT: C 144 ARG cc_start: 0.8640 (mtp85) cc_final: 0.8018 (mtp85) REVERT: B 115 ASP cc_start: 0.8970 (m-30) cc_final: 0.8662 (m-30) REVERT: H 25 ASP cc_start: 0.8564 (t0) cc_final: 0.8112 (t0) outliers start: 1 outliers final: 1 residues processed: 261 average time/residue: 0.1431 time to fit residues: 52.8583 Evaluate side-chains 177 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 176 time to evaluate : 0.552 ------------------------------------------------------------------------------- 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: 0.0170 chunk 0 optimal weight: 9.9990 chunk 155 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 129 optimal weight: 0.9980 chunk 142 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 69 optimal weight: 8.9990 chunk 145 optimal weight: 8.9990 overall best weight: 0.9220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.072109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.059604 restraints weight = 133386.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.061103 restraints weight = 93342.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.061992 restraints weight = 70245.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.062848 restraints weight = 57359.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.063334 restraints weight = 48177.093| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.4495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 15690 Z= 0.131 Angle : 0.579 10.530 21288 Z= 0.307 Chirality : 0.042 0.309 2379 Planarity : 0.004 0.047 2568 Dihedral : 12.438 175.649 2437 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.95 % Favored : 96.99 % Rotamer: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.05 (0.19), residues: 1729 helix: 0.91 (0.18), residues: 780 sheet: 0.52 (0.29), residues: 295 loop : -1.43 (0.21), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 110 TYR 0.021 0.001 TYR I 86 PHE 0.029 0.002 PHE H 36 TRP 0.013 0.001 TRP H 52 HIS 0.006 0.001 HIS D 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (15688) covalent geometry : angle 0.57871 / 0.31 (21284) SS BOND : bond 0.00476 / 0.23 ( 2) SS BOND : angle 2.01153 / 1.16 ( 4) hydrogen bonds : bond 0.04101 / 2.68 ( 721) hydrogen bonds : angle 4.99940 / 3.39 ( 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 228 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.597 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: F 33 HIS cc_start: 0.6662 (p-80) cc_final: 0.6016 (p-80) REVERT: F 380 LEU cc_start: 0.9116 (tp) cc_final: 0.8754 (pp) REVERT: J 109 ASP cc_start: 0.9068 (t0) cc_final: 0.8562 (m-30) REVERT: J 112 ILE cc_start: 0.8087 (pt) cc_final: 0.7810 (pt) REVERT: I 41 ASN cc_start: 0.8922 (m-40) cc_final: 0.8623 (m-40) REVERT: I 49 ARG cc_start: 0.9382 (pmt170) cc_final: 0.9037 (pmt170) REVERT: I 70 LEU cc_start: 0.7390 (mp) cc_final: 0.6670 (mp) REVERT: I 85 PHE cc_start: 0.9659 (m-80) cc_final: 0.9157 (m-80) REVERT: I 91 ARG cc_start: 0.8569 (mmt90) cc_final: 0.8362 (mmm-85) REVERT: K 85 PHE cc_start: 0.8961 (m-80) cc_final: 0.8691 (m-80) REVERT: K 86 TYR cc_start: 0.8599 (m-10) cc_final: 0.8369 (m-10) REVERT: C 100 ASP cc_start: 0.9019 (m-30) cc_final: 0.8397 (t0) REVERT: C 128 ASN cc_start: 0.8551 (t0) cc_final: 0.8224 (t0) REVERT: A 144 ARG cc_start: 0.7637 (ptm-80) cc_final: 0.7100 (tmm-80) REVERT: B 115 ASP cc_start: 0.8964 (m-30) cc_final: 0.8635 (m-30) REVERT: H 22 ARG cc_start: 0.7579 (tpm170) cc_final: 0.7089 (mmm160) REVERT: H 25 ASP cc_start: 0.8631 (t0) cc_final: 0.8152 (t0) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.1375 time to fit residues: 45.0861 Evaluate side-chains 169 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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: 0.6980 chunk 96 optimal weight: 0.7980 chunk 169 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 136 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 chunk 122 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 118 optimal weight: 0.0980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 174 HIS ** 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 = 0.4079 r_free = 0.4079 target = 0.071525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.059347 restraints weight = 135334.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.060831 restraints weight = 94436.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.061785 restraints weight = 71007.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.062261 restraints weight = 57481.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.062986 restraints weight = 49938.199| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.4992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15690 Z= 0.114 Angle : 0.576 10.774 21288 Z= 0.298 Chirality : 0.042 0.292 2379 Planarity : 0.003 0.036 2568 Dihedral : 12.366 175.556 2437 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.83 % Favored : 97.11 % Rotamer: Outliers : 0.13 % Allowed : 2.21 % Favored : 97.66 % 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: 0.17 (0.19), residues: 1729 helix: 1.11 (0.18), residues: 786 sheet: 0.59 (0.29), residues: 303 loop : -1.39 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 57 TYR 0.022 0.001 TYR I 87 PHE 0.019 0.001 PHE H 36 TRP 0.012 0.001 TRP H 52 HIS 0.005 0.001 HIS D 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (15688) covalent geometry : angle 0.57553 / 0.30 (21284) SS BOND : bond 0.00341 / 0.16 ( 2) SS BOND : angle 1.83647 / 1.07 ( 4) hydrogen bonds : bond 0.03769 / 2.48 ( 721) hydrogen bonds : angle 4.75208 / 3.24 ( 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 212 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 210 time to evaluate : 0.563 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: 0.6302 (mmm) cc_final: 0.2590 (ttt) REVERT: F 7 LEU cc_start: 0.8271 (mt) cc_final: 0.7926 (mt) REVERT: F 33 HIS cc_start: 0.6755 (p-80) cc_final: 0.6105 (p-80) REVERT: F 288 MET cc_start: 0.9202 (mmp) cc_final: 0.8958 (mmm) REVERT: F 380 LEU cc_start: 0.9124 (tp) cc_final: 0.8804 (pp) REVERT: J 109 ASP cc_start: 0.9097 (t0) cc_final: 0.8639 (m-30) REVERT: J 112 ILE cc_start: 0.8045 (pt) cc_final: 0.7786 (pt) REVERT: I 41 ASN cc_start: 0.8939 (m-40) cc_final: 0.8653 (m-40) REVERT: I 49 ARG cc_start: 0.9221 (pmt170) cc_final: 0.8997 (pmt170) REVERT: I 68 ASP cc_start: 0.8652 (t70) cc_final: 0.8259 (t0) REVERT: I 70 LEU cc_start: 0.7449 (mp) cc_final: 0.6308 (mp) REVERT: I 85 PHE cc_start: 0.9691 (m-80) cc_final: 0.9294 (m-80) REVERT: I 86 TYR cc_start: 0.9162 (m-80) cc_final: 0.8548 (m-80) REVERT: K 85 PHE cc_start: 0.8946 (m-80) cc_final: 0.8616 (m-80) REVERT: D 69 GLN cc_start: 0.2859 (OUTLIER) cc_final: 0.1700 (pp30) REVERT: D 148 PHE cc_start: 0.4880 (m-80) cc_final: 0.4615 (m-10) REVERT: C 38 ASP cc_start: 0.8248 (t0) cc_final: 0.7427 (t70) REVERT: C 100 ASP cc_start: 0.9038 (m-30) cc_final: 0.8349 (t0) REVERT: C 128 ASN cc_start: 0.8542 (t0) cc_final: 0.8303 (t0) REVERT: A 144 ARG cc_start: 0.7620 (ptm-80) cc_final: 0.6851 (tmm-80) REVERT: A 193 GLN cc_start: 0.9300 (tt0) cc_final: 0.9075 (tm-30) REVERT: B 105 GLU cc_start: 0.9456 (mm-30) cc_final: 0.9072 (pm20) REVERT: B 115 ASP cc_start: 0.8881 (m-30) cc_final: 0.8557 (m-30) REVERT: H 22 ARG cc_start: 0.7599 (tpm170) cc_final: 0.7175 (mmm160) REVERT: H 25 ASP cc_start: 0.8736 (t0) cc_final: 0.8287 (t0) REVERT: H 258 MET cc_start: 0.7454 (pmm) cc_final: 0.7137 (mmt) outliers start: 2 outliers final: 0 residues processed: 212 average time/residue: 0.1367 time to fit residues: 42.2433 Evaluate side-chains 158 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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: 4.9990 chunk 115 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 104 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 79 optimal weight: 10.0000 chunk 93 optimal weight: 0.0670 overall best weight: 2.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 HIS F 83 ASN D 62 HIS ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 122 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.067026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.055296 restraints weight = 142730.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.056668 restraints weight = 98930.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.057583 restraints weight = 73998.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.058264 restraints weight = 59628.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.058746 restraints weight = 50575.323| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.5636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15690 Z= 0.191 Angle : 0.639 10.673 21288 Z= 0.332 Chirality : 0.043 0.256 2379 Planarity : 0.004 0.044 2568 Dihedral : 12.689 174.013 2437 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.47 % Favored : 96.47 % Rotamer: Outliers : 0.06 % Allowed : 2.15 % Favored : 97.79 % 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: -0.05 (0.19), residues: 1729 helix: 0.85 (0.18), residues: 794 sheet: 0.57 (0.29), residues: 297 loop : -1.44 (0.22), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 57 TYR 0.019 0.002 TYR K 86 PHE 0.027 0.002 PHE F 399 TRP 0.015 0.002 TRP F 373 HIS 0.012 0.001 HIS F 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.19 (15688) covalent geometry : angle 0.63909 / 0.33 (21284) SS BOND : bond 0.00849 / 0.43 ( 2) SS BOND : angle 1.32467 / 0.72 ( 4) hydrogen bonds : bond 0.04244 / 2.81 ( 721) hydrogen bonds : angle 4.91402 / 3.35 ( 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 196 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 195 time to evaluate : 0.620 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: 0.6509 (mmm) cc_final: 0.2764 (ttt) REVERT: F 33 HIS cc_start: 0.7284 (p-80) cc_final: 0.6605 (p-80) REVERT: F 47 PHE cc_start: 0.7595 (m-10) cc_final: 0.7374 (m-10) REVERT: F 258 ASP cc_start: 0.8975 (m-30) cc_final: 0.8711 (m-30) REVERT: F 452 MET cc_start: 0.3395 (mmp) cc_final: 0.2956 (mmm) REVERT: J 109 ASP cc_start: 0.9169 (t0) cc_final: 0.8733 (m-30) REVERT: J 112 ILE cc_start: 0.8191 (pt) cc_final: 0.7912 (pt) REVERT: J 127 PHE cc_start: 0.9461 (t80) cc_final: 0.9204 (t80) REVERT: J 128 GLU cc_start: 0.6940 (tt0) cc_final: 0.6455 (tt0) REVERT: I 41 ASN cc_start: 0.8902 (m-40) cc_final: 0.8638 (m-40) REVERT: I 49 ARG cc_start: 0.9238 (pmt170) cc_final: 0.8933 (pmt170) REVERT: I 85 PHE cc_start: 0.9683 (m-80) cc_final: 0.9282 (m-80) REVERT: I 86 TYR cc_start: 0.9133 (m-80) cc_final: 0.8572 (m-80) REVERT: K 104 MET cc_start: 0.8197 (ppp) cc_final: 0.7920 (ppp) REVERT: C 38 ASP cc_start: 0.8246 (t0) cc_final: 0.7647 (t0) REVERT: C 100 ASP cc_start: 0.8968 (m-30) cc_final: 0.8747 (m-30) REVERT: C 128 ASN cc_start: 0.8690 (t0) cc_final: 0.8318 (t0) REVERT: A 144 ARG cc_start: 0.8023 (ptm-80) cc_final: 0.7309 (tmm-80) REVERT: A 193 GLN cc_start: 0.9310 (tt0) cc_final: 0.9012 (tm-30) REVERT: B 47 PRO cc_start: 0.8885 (Cg_exo) cc_final: 0.8680 (Cg_endo) REVERT: B 168 ASN cc_start: 0.8682 (m110) cc_final: 0.8409 (m110) REVERT: B 181 LEU cc_start: 0.9537 (tp) cc_final: 0.9261 (tp) REVERT: H 22 ARG cc_start: 0.7577 (tpm170) cc_final: 0.7003 (mmm160) outliers start: 1 outliers final: 1 residues processed: 196 average time/residue: 0.1335 time to fit residues: 38.2727 Evaluate side-chains 145 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 144 time to evaluate : 0.631 ------------------------------------------------------------------------------- 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: 7.9990 chunk 81 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 78 optimal weight: 5.9990 chunk 168 optimal weight: 5.9990 chunk 19 optimal weight: 0.0030 chunk 135 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 153 optimal weight: 4.9990 overall best weight: 3.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 183 GLN F 263 GLN ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 57 ASN ** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.062525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.051144 restraints weight = 146479.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.052350 restraints weight = 106028.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.053127 restraints weight = 81135.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.053747 restraints weight = 66926.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.053992 restraints weight = 57580.018| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.6834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 15690 Z= 0.265 Angle : 0.760 11.689 21288 Z= 0.405 Chirality : 0.047 0.277 2379 Planarity : 0.005 0.053 2568 Dihedral : 13.336 174.526 2437 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 22.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.45 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % 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: -0.75 (0.19), residues: 1729 helix: 0.17 (0.17), residues: 789 sheet: 0.16 (0.29), residues: 294 loop : -1.59 (0.22), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 95 TYR 0.021 0.002 TYR I 87 PHE 0.032 0.003 PHE H 163 TRP 0.024 0.003 TRP F 373 HIS 0.007 0.002 HIS F 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.26 (15688) covalent geometry : angle 0.75981 / 0.40 (21284) SS BOND : bond 0.01033 / 0.52 ( 2) SS BOND : angle 1.42291 / 0.67 ( 4) hydrogen bonds : bond 0.05061 / 3.36 ( 721) hydrogen bonds : angle 5.53244 / 3.79 ( 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 177 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.592 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 1 MET cc_start: 0.6128 (mmm) cc_final: 0.2252 (ttt) REVERT: F 288 MET cc_start: 0.9085 (mmp) cc_final: 0.8836 (mmm) REVERT: J 104 MET cc_start: 0.8577 (mmp) cc_final: 0.8210 (mmm) REVERT: J 109 ASP cc_start: 0.9157 (t0) cc_final: 0.8690 (m-30) REVERT: J 127 PHE cc_start: 0.9458 (t80) cc_final: 0.9237 (t80) REVERT: I 41 ASN cc_start: 0.9009 (m-40) cc_final: 0.8769 (m-40) REVERT: I 85 PHE cc_start: 0.9665 (m-80) cc_final: 0.9377 (m-80) REVERT: I 128 GLU cc_start: 0.9077 (mt-10) cc_final: 0.8860 (mp0) REVERT: I 133 TYR cc_start: 0.9157 (m-80) cc_final: 0.8913 (m-80) REVERT: K 98 PHE cc_start: 0.8300 (t80) cc_final: 0.8097 (t80) REVERT: K 104 MET cc_start: 0.8193 (ppp) cc_final: 0.7748 (ppp) REVERT: D 82 LEU cc_start: 0.8331 (mt) cc_final: 0.8086 (mt) REVERT: D 90 ASN cc_start: 0.9016 (p0) cc_final: 0.8669 (p0) REVERT: C 128 ASN cc_start: 0.8763 (t0) cc_final: 0.8491 (t0) REVERT: A 193 GLN cc_start: 0.9235 (tt0) cc_final: 0.8934 (tm-30) REVERT: B 168 ASN cc_start: 0.8922 (m110) cc_final: 0.8649 (m110) REVERT: B 181 LEU cc_start: 0.9526 (tp) cc_final: 0.9247 (tp) REVERT: H 134 LEU cc_start: 0.8711 (mt) cc_final: 0.8448 (mp) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.1370 time to fit residues: 35.5589 Evaluate side-chains 133 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.594 ------------------------------------------------------------------------------- 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: 1.9990 chunk 44 optimal weight: 6.9990 chunk 164 optimal weight: 3.9990 chunk 23 optimal weight: 0.0470 chunk 159 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 114 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 overall best weight: 1.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 HIS ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 18 HIS ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.064094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.052681 restraints weight = 142982.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.053946 restraints weight = 100760.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.054759 restraints weight = 76023.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.055422 restraints weight = 62180.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.055901 restraints weight = 53158.655| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.7010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15690 Z= 0.146 Angle : 0.617 11.253 21288 Z= 0.324 Chirality : 0.042 0.245 2379 Planarity : 0.004 0.072 2568 Dihedral : 13.126 177.122 2437 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.41 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % 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: -0.42 (0.19), residues: 1729 helix: 0.50 (0.18), residues: 797 sheet: 0.26 (0.29), residues: 295 loop : -1.48 (0.23), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 93 TYR 0.030 0.001 TYR I 87 PHE 0.025 0.002 PHE H 163 TRP 0.014 0.002 TRP H 52 HIS 0.006 0.001 HIS D 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.15 (15688) covalent geometry : angle 0.61707 / 0.32 (21284) SS BOND : bond 0.00534 / 0.26 ( 2) SS BOND : angle 1.00621 / 0.55 ( 4) hydrogen bonds : bond 0.04077 / 2.67 ( 721) hydrogen bonds : angle 5.21095 / 3.56 ( 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 176 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.510 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 66 LYS cc_start: 0.8875 (mptt) cc_final: 0.8602 (mppt) REVERT: F 452 MET cc_start: 0.3276 (mmp) cc_final: 0.2851 (mmm) REVERT: J 109 ASP cc_start: 0.9126 (t0) cc_final: 0.8657 (m-30) REVERT: J 127 PHE cc_start: 0.9470 (t80) cc_final: 0.9223 (t80) REVERT: J 128 GLU cc_start: 0.7108 (tt0) cc_final: 0.6613 (tt0) REVERT: I 85 PHE cc_start: 0.9667 (m-80) cc_final: 0.9333 (m-80) REVERT: K 93 LYS cc_start: 0.8674 (pptt) cc_final: 0.8452 (tptt) REVERT: K 98 PHE cc_start: 0.8249 (t80) cc_final: 0.8048 (t80) REVERT: K 104 MET cc_start: 0.8208 (ppp) cc_final: 0.7775 (ppp) REVERT: D 82 LEU cc_start: 0.8286 (mt) cc_final: 0.8080 (mt) REVERT: C 55 MET cc_start: 0.5298 (tpt) cc_final: 0.5039 (tpt) REVERT: C 128 ASN cc_start: 0.8813 (t0) cc_final: 0.8563 (t0) REVERT: A 193 GLN cc_start: 0.9181 (tt0) cc_final: 0.8917 (tm-30) REVERT: B 115 ASP cc_start: 0.8323 (m-30) cc_final: 0.8096 (m-30) REVERT: B 168 ASN cc_start: 0.8869 (m110) cc_final: 0.8565 (m-40) REVERT: B 181 LEU cc_start: 0.9505 (tp) cc_final: 0.9228 (tp) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.1146 time to fit residues: 30.6593 Evaluate side-chains 137 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.508 ------------------------------------------------------------------------------- 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: 0.9980 chunk 44 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 146 optimal weight: 6.9990 chunk 73 optimal weight: 0.9980 chunk 66 optimal weight: 0.0270 chunk 52 optimal weight: 6.9990 chunk 129 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.7638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 18 HIS ** D 74 GLN ** 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 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.065134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.053868 restraints weight = 142712.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.055121 restraints weight = 98447.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.056019 restraints weight = 73808.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.056668 restraints weight = 59400.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.057133 restraints weight = 50320.108| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.7165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15690 Z= 0.119 Angle : 0.602 11.577 21288 Z= 0.313 Chirality : 0.043 0.335 2379 Planarity : 0.003 0.042 2568 Dihedral : 13.038 176.794 2437 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.30 % Favored : 96.65 % 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: -0.21 (0.19), residues: 1729 helix: 0.69 (0.18), residues: 794 sheet: 0.45 (0.30), residues: 291 loop : -1.43 (0.22), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 137 TYR 0.022 0.001 TYR J 136 PHE 0.034 0.002 PHE I 98 TRP 0.011 0.002 TRP H 52 HIS 0.006 0.001 HIS D 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 (15688) covalent geometry : angle 0.60180 / 0.31 (21284) SS BOND : bond 0.00296 / 0.15 ( 2) SS BOND : angle 1.13852 / 0.66 ( 4) hydrogen bonds : bond 0.03699 / 2.44 ( 721) hydrogen bonds : angle 5.00367 / 3.42 ( 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 179 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 178 time to evaluate : 0.622 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 1 MET cc_start: 0.6171 (mmm) cc_final: 0.2526 (ttt) REVERT: F 66 LYS cc_start: 0.8874 (mptt) cc_final: 0.8602 (mppt) REVERT: F 288 MET cc_start: 0.9147 (mmp) cc_final: 0.8891 (mmm) REVERT: F 452 MET cc_start: 0.3229 (mmp) cc_final: 0.2604 (mmm) REVERT: J 104 MET cc_start: 0.8654 (mmp) cc_final: 0.8308 (mmm) REVERT: J 109 ASP cc_start: 0.9140 (t0) cc_final: 0.8707 (m-30) REVERT: J 127 PHE cc_start: 0.9528 (t80) cc_final: 0.9268 (t80) REVERT: J 128 GLU cc_start: 0.6975 (tt0) cc_final: 0.6458 (tt0) REVERT: I 41 ASN cc_start: 0.9084 (m-40) cc_final: 0.8861 (m-40) REVERT: I 85 PHE cc_start: 0.9691 (m-80) cc_final: 0.9348 (m-80) REVERT: I 104 MET cc_start: 0.8930 (ppp) cc_final: 0.8627 (tmm) REVERT: I 133 TYR cc_start: 0.8261 (m-80) cc_final: 0.7915 (m-80) REVERT: K 86 TYR cc_start: 0.8833 (m-10) cc_final: 0.8488 (m-80) REVERT: K 98 PHE cc_start: 0.8118 (t80) cc_final: 0.7891 (t80) REVERT: D 82 LEU cc_start: 0.8254 (mt) cc_final: 0.8035 (mt) REVERT: C 128 ASN cc_start: 0.8819 (t0) cc_final: 0.8593 (t0) REVERT: A 178 ASN cc_start: 0.8039 (p0) cc_final: 0.7743 (p0) REVERT: B 115 ASP cc_start: 0.8344 (m-30) cc_final: 0.8128 (m-30) REVERT: B 168 ASN cc_start: 0.8814 (m110) cc_final: 0.8504 (m110) REVERT: B 181 LEU cc_start: 0.9593 (tp) cc_final: 0.9344 (tp) outliers start: 1 outliers final: 0 residues processed: 179 average time/residue: 0.1128 time to fit residues: 30.6058 Evaluate side-chains 136 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.636 ------------------------------------------------------------------------------- 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: 4.9990 chunk 15 optimal weight: 0.9980 chunk 141 optimal weight: 0.9990 chunk 30 optimal weight: 0.4980 chunk 107 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 22 optimal weight: 0.7980 chunk 81 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 GLN ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.065128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.054248 restraints weight = 146181.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.055574 restraints weight = 99252.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.056440 restraints weight = 73485.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.057100 restraints weight = 59132.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.057572 restraints weight = 50013.338| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.7334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15690 Z= 0.119 Angle : 0.599 12.669 21288 Z= 0.312 Chirality : 0.042 0.340 2379 Planarity : 0.003 0.042 2568 Dihedral : 12.944 176.198 2437 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.78 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % 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: -0.06 (0.20), residues: 1729 helix: 0.82 (0.18), residues: 795 sheet: 0.44 (0.30), residues: 291 loop : -1.32 (0.22), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 91 TYR 0.026 0.001 TYR I 87 PHE 0.019 0.001 PHE F 178 TRP 0.006 0.001 TRP H 52 HIS 0.006 0.001 HIS D 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 (15688) covalent geometry : angle 0.59842 / 0.31 (21284) SS BOND : bond 0.00309 / 0.15 ( 2) SS BOND : angle 1.11667 / 0.65 ( 4) hydrogen bonds : bond 0.03641 / 2.39 ( 721) hydrogen bonds : angle 4.94440 / 3.38 ( 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 174 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.626 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 1 MET cc_start: 0.6061 (mmm) cc_final: 0.2360 (ttt) REVERT: F 66 LYS cc_start: 0.8873 (mptt) cc_final: 0.8600 (mppt) REVERT: F 288 MET cc_start: 0.9147 (mmp) cc_final: 0.8868 (mmm) REVERT: F 452 MET cc_start: 0.3484 (mmp) cc_final: 0.2976 (mmm) REVERT: J 109 ASP cc_start: 0.9111 (t0) cc_final: 0.8639 (m-30) REVERT: J 112 ILE cc_start: 0.8616 (pt) cc_final: 0.8339 (pt) REVERT: I 85 PHE cc_start: 0.9696 (m-80) cc_final: 0.9324 (m-80) REVERT: I 133 TYR cc_start: 0.8079 (m-80) cc_final: 0.7701 (m-80) REVERT: K 86 TYR cc_start: 0.8857 (m-10) cc_final: 0.8544 (m-80) REVERT: K 98 PHE cc_start: 0.8111 (t80) cc_final: 0.7861 (t80) REVERT: K 104 MET cc_start: 0.8858 (ppp) cc_final: 0.8507 (ppp) REVERT: D 40 GLN cc_start: 0.9183 (mt0) cc_final: 0.8947 (mt0) REVERT: D 55 MET cc_start: 0.9193 (mtp) cc_final: 0.8981 (mtp) REVERT: D 82 LEU cc_start: 0.8242 (mt) cc_final: 0.7997 (mt) REVERT: C 128 ASN cc_start: 0.8887 (t0) cc_final: 0.8646 (t0) REVERT: B 115 ASP cc_start: 0.8354 (m-30) cc_final: 0.8131 (m-30) REVERT: B 168 ASN cc_start: 0.8794 (m110) cc_final: 0.8495 (m110) REVERT: B 181 LEU cc_start: 0.9627 (tp) cc_final: 0.9404 (tp) REVERT: H 121 PHE cc_start: 0.8995 (t80) cc_final: 0.8778 (t80) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.1132 time to fit residues: 30.1163 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 : 0.623 ------------------------------------------------------------------------------- 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: 1.9990 chunk 158 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 chunk 105 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 175 optimal weight: 7.9990 chunk 172 optimal weight: 5.9990 chunk 103 optimal weight: 0.0050 overall best weight: 2.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 HIS ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 ASN 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 = 0.3859 r_free = 0.3859 target = 0.061834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.050725 restraints weight = 147187.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.051875 restraints weight = 102899.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.052696 restraints weight = 78207.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.053219 restraints weight = 64406.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.053483 restraints weight = 55989.093| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.7907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15690 Z= 0.216 Angle : 0.713 12.220 21288 Z= 0.377 Chirality : 0.045 0.300 2379 Planarity : 0.004 0.050 2568 Dihedral : 13.295 174.289 2437 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 20.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % 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: -0.53 (0.19), residues: 1729 helix: 0.36 (0.18), residues: 797 sheet: 0.14 (0.30), residues: 295 loop : -1.43 (0.22), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 91 TYR 0.034 0.002 TYR I 87 PHE 0.024 0.002 PHE I 40 TRP 0.017 0.003 TRP F 373 HIS 0.008 0.001 HIS J 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.22 (15688) covalent geometry : angle 0.71269 / 0.38 (21284) SS BOND : bond 0.00704 / 0.35 ( 2) SS BOND : angle 1.33605 / 0.69 ( 4) hydrogen bonds : bond 0.04528 / 2.97 ( 721) hydrogen bonds : angle 5.35443 / 3.67 ( 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 154 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 452 MET cc_start: 0.4025 (mmp) cc_final: 0.3764 (mmm) REVERT: J 104 MET cc_start: 0.8491 (mmp) cc_final: 0.8273 (mmm) REVERT: J 109 ASP cc_start: 0.9168 (t0) cc_final: 0.8751 (m-30) REVERT: J 128 GLU cc_start: 0.7079 (tt0) cc_final: 0.6526 (tt0) REVERT: I 85 PHE cc_start: 0.9663 (m-80) cc_final: 0.9364 (m-80) REVERT: I 123 TYR cc_start: 0.9497 (t80) cc_final: 0.9238 (t80) REVERT: I 133 TYR cc_start: 0.8958 (m-80) cc_final: 0.8625 (m-80) REVERT: K 98 PHE cc_start: 0.8083 (t80) cc_final: 0.7833 (t80) REVERT: K 104 MET cc_start: 0.8793 (ppp) cc_final: 0.8484 (ppp) REVERT: D 40 GLN cc_start: 0.9233 (mt0) cc_final: 0.8933 (mt0) REVERT: D 55 MET cc_start: 0.9222 (mtp) cc_final: 0.8862 (mtp) REVERT: D 82 LEU cc_start: 0.8442 (mt) cc_final: 0.8196 (mt) REVERT: D 130 LEU cc_start: 0.8856 (mp) cc_final: 0.8463 (pp) REVERT: C 128 ASN cc_start: 0.8967 (t0) cc_final: 0.8717 (t0) REVERT: B 168 ASN cc_start: 0.8970 (m110) cc_final: 0.8701 (m110) REVERT: B 181 LEU cc_start: 0.9522 (tp) cc_final: 0.9124 (tt) REVERT: H 121 PHE cc_start: 0.8934 (t80) cc_final: 0.8719 (t80) REVERT: H 226 MET cc_start: 0.6145 (mmm) cc_final: 0.5454 (mmm) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.1104 time to fit residues: 26.2371 Evaluate side-chains 113 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.410 ------------------------------------------------------------------------------- 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: 0.7980 chunk 45 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 129 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 153 optimal weight: 0.0070 chunk 125 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 overall best weight: 0.8802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.063699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.052973 restraints weight = 148822.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.054239 restraints weight = 100965.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.055088 restraints weight = 75492.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.055707 restraints weight = 60933.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.056150 restraints weight = 51699.048| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.7936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15690 Z= 0.128 Angle : 0.625 12.275 21288 Z= 0.328 Chirality : 0.042 0.244 2379 Planarity : 0.004 0.042 2568 Dihedral : 13.083 176.963 2437 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % 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: -0.30 (0.19), residues: 1729 helix: 0.57 (0.18), residues: 797 sheet: 0.32 (0.30), residues: 292 loop : -1.37 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 91 TYR 0.022 0.001 TYR J 136 PHE 0.039 0.002 PHE J 85 TRP 0.009 0.001 TRP H 52 HIS 0.006 0.001 HIS D 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 (15688) covalent geometry : angle 0.62465 / 0.33 (21284) SS BOND : bond 0.00347 / 0.17 ( 2) SS BOND : angle 1.12420 / 0.65 ( 4) hydrogen bonds : bond 0.03861 / 2.56 ( 721) hydrogen bonds : angle 5.12536 / 3.51 ( 2084) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3075.48 seconds wall clock time: 54 minutes 0.96 seconds (3240.96 seconds total)