Starting phenix.real_space_refine on Sat Sep 12 11:47:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7uzy_26922/09_2026/7uzy_26922.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uzy_26922/09_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_26922/09_2026/7uzy_26922.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uzy_26922/09_2026/7uzy_26922.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uzy_26922/09_2026/7uzy_26922.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uzy_26922/09_2026/7uzy_26922.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7uzy_26922/09_2026/7uzy_26922.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7uzy_26922/09_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-2.2.1-6174/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: {'RNAv2': 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: {'RNAv2': 14} Modifications used: {'rna2p_pur': 3, 'rna3p_pur': 6, 'rna3p_pyr': 5} Link IDs: {'rna2p': 3, 'rna3p': 10} Chain breaks: 1 Time building chain proxies: 3.10, per 1000 atoms: 0.20 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: 1.32 Conformation dependent library (CDL) restraints added in 564.1 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: 1.68 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: 2.54 Time building geometry restraints manager: 1.76 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 1.20e-02 6.94e+03 2.78e+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 - 2.62: 20918 2.62 - 5.23: 332 5.23 - 7.85: 31 7.85 - 10.47: 2 10.47 - 13.09: 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 112.50 125.59 -13.09 2.00e+00 2.50e-01 4.28e+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=" O3' A G 14 " pdb=" C3' A G 14 " pdb=" C2' A G 14 " ideal model delta sigma weight residual 113.80 104.36 9.44 2.00e+00 2.50e-01 2.23e+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=" C3' A G 13 " pdb=" O3' A G 13 " pdb=" P A G 14 " ideal model delta sigma weight residual 119.70 124.86 -5.16 1.20e+00 6.94e-01 1.85e+01 ... (remaining 21279 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 8596 17.46 - 34.91: 533 34.91 - 52.37: 117 52.37 - 69.83: 72 69.83 - 87.28: 16 Dihedral angle restraints: 9334 sinusoidal: 4174 harmonic: 5160 Sorted by residual: dihedral pdb=" C4' A L 12 " pdb=" C3' A L 12 " pdb=" C2' A L 12 " pdb=" C1' A L 12 " ideal model delta sinusoidal sigma weight residual 36.34 -40.69 77.03 1 3.10e+00 1.04e-01 7.75e+02 dihedral pdb=" C4' U G 9 " pdb=" C3' U G 9 " pdb=" C2' U G 9 " pdb=" C1' U G 9 " ideal model delta sinusoidal sigma weight residual 36.34 -39.75 76.10 1 3.10e+00 1.04e-01 7.59e+02 dihedral pdb=" C4' G G 27 " pdb=" C3' G G 27 " pdb=" C2' G G 27 " pdb=" C1' G G 27 " ideal model delta sinusoidal sigma weight residual 36.34 -38.88 75.23 1 3.10e+00 1.04e-01 7.44e+02 ... (remaining 9331 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1998 0.069 - 0.137: 290 0.137 - 0.205: 32 0.205 - 0.274: 47 0.274 - 0.342: 12 Chirality restraints: 2379 Sorted by residual: chirality pdb=" P A L 19 " pdb=" OP1 A L 19 " pdb=" OP2 A L 19 " pdb=" O5' A L 19 " both_signs ideal model delta sigma weight residual True 2.17 -2.52 -0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" P A G 14 " pdb=" OP1 A G 14 " pdb=" OP2 A G 14 " pdb=" O5' A G 14 " both_signs ideal model delta sigma weight residual True 2.17 -2.50 -0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" C3' G G 27 " pdb=" C4' G G 27 " pdb=" O3' G G 27 " pdb=" C2' G G 27 " both_signs ideal model delta sigma weight residual False -2.50 -2.82 0.32 2.00e-01 2.50e+01 2.64e+00 ... (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: 6.410 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: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.460 Find NCS groups from input model: 0.140 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.730 ------------------------------------------------------------------------------- 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 : 0.884 51.639 21288 Z= 0.493 Chirality : 0.062 0.342 2379 Planarity : 0.005 0.057 2568 Dihedral : 13.635 87.284 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 0.00511 / 0.30 (15688) covalent geometry : angle 0.80939 / 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 : 0.673 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: 0.1715 time to fit residues: 100.7540 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 : 0.513 ------------------------------------------------------------------------------- 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 83 ASN F 183 GLN F 397 ASN D 69 GLN ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 114 ASN D 189 ASN ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 GLN C 110 HIS A 69 GLN A 97 GLN ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.073519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.060918 restraints weight = 125697.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.062389 restraints weight = 88030.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.063375 restraints weight = 67101.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.064126 restraints weight = 54492.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.064642 restraints weight = 46284.414| |-----------------------------------------------------------------------------| r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15690 Z= 0.174 Angle : 0.915 25.951 21288 Z= 0.415 Chirality : 0.081 1.449 2379 Planarity : 0.004 0.058 2568 Dihedral : 12.602 150.922 2437 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.89 % Favored : 97.05 % Rotamer: Outliers : 0.06 % Allowed : 2.46 % Favored : 97.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.19), residues: 1729 helix: 0.90 (0.18), residues: 774 sheet: 0.39 (0.29), residues: 290 loop : -1.51 (0.21), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 37 TYR 0.028 0.002 TYR I 80 PHE 0.038 0.002 PHE K 85 TRP 0.013 0.002 TRP H 52 HIS 0.013 0.001 HIS C 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.17 (15688) covalent geometry : angle 0.91445 / 0.42 (21284) SS BOND : bond 0.00540 / 0.26 ( 2) SS BOND : angle 2.64507 / 1.51 ( 4) hydrogen bonds : bond 0.04862 / 3.17 ( 721) hydrogen bonds : angle 5.30597 / 3.58 ( 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 : 0.682 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: F 1 MET cc_start: 0.5839 (mmm) cc_final: 0.2381 (ttt) REVERT: F 33 HIS cc_start: 0.6491 (p-80) cc_final: 0.5847 (p-80) REVERT: F 163 MET cc_start: 0.4449 (ptt) cc_final: 0.3606 (ppp) REVERT: F 380 LEU cc_start: 0.9005 (tp) cc_final: 0.8773 (pp) REVERT: I 49 ARG cc_start: 0.9350 (pmt170) cc_final: 0.8927 (pmt170) REVERT: I 57 ARG cc_start: 0.9092 (mtm110) cc_final: 0.8792 (mtm110) REVERT: I 70 LEU cc_start: 0.7467 (mp) cc_final: 0.6846 (mp) REVERT: C 128 ASN cc_start: 0.8531 (t0) cc_final: 0.8307 (t0) REVERT: C 144 ARG cc_start: 0.8636 (mtp85) cc_final: 0.8011 (mtp85) REVERT: B 115 ASP cc_start: 0.8974 (m-30) cc_final: 0.8657 (m-30) REVERT: H 25 ASP cc_start: 0.8567 (t0) cc_final: 0.8110 (t0) outliers start: 1 outliers final: 1 residues processed: 261 average time/residue: 0.1445 time to fit residues: 53.3410 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 : 0.533 ------------------------------------------------------------------------------- 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: 0.0770 chunk 0 optimal weight: 10.0000 chunk 155 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 84 optimal weight: 8.9990 chunk 20 optimal weight: 0.6980 chunk 129 optimal weight: 0.6980 chunk 142 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 145 optimal weight: 9.9990 overall best weight: 1.0942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 161 GLN ** 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 = 0.4086 r_free = 0.4086 target = 0.071702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.059176 restraints weight = 132913.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.060660 restraints weight = 91812.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.061719 restraints weight = 69237.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.062204 restraints weight = 55432.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.062873 restraints weight = 48302.863| |-----------------------------------------------------------------------------| r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.4724 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= 0.150 Angle : 0.779 23.352 21288 Z= 0.363 Chirality : 0.066 1.130 2379 Planarity : 0.004 0.068 2568 Dihedral : 12.388 142.954 2437 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.07 % Favored : 96.88 % Rotamer: Outliers : 0.06 % Allowed : 2.90 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.19), residues: 1729 helix: 0.89 (0.18), residues: 779 sheet: 0.50 (0.29), residues: 297 loop : -1.43 (0.22), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 93 TYR 0.021 0.002 TYR I 86 PHE 0.031 0.002 PHE K 85 TRP 0.015 0.002 TRP H 52 HIS 0.006 0.001 HIS H 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 (15688) covalent geometry : angle 0.77867 / 0.36 (21284) SS BOND : bond 0.00491 / 0.24 ( 2) SS BOND : angle 1.88219 / 1.09 ( 4) hydrogen bonds : bond 0.04380 / 2.86 ( 721) hydrogen bonds : angle 5.03528 / 3.42 ( 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: 1 poor density : 227 time to evaluate : 0.595 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: F 7 LEU cc_start: 0.8150 (mt) cc_final: 0.7943 (mt) REVERT: F 33 HIS cc_start: 0.6721 (p-80) cc_final: 0.6073 (p-80) REVERT: F 163 MET cc_start: 0.3845 (ptt) cc_final: 0.3609 (ppp) REVERT: F 380 LEU cc_start: 0.9121 (tp) cc_final: 0.8757 (pp) REVERT: J 109 ASP cc_start: 0.9058 (t0) cc_final: 0.8563 (m-30) REVERT: J 112 ILE cc_start: 0.8048 (pt) cc_final: 0.7767 (pt) REVERT: I 41 ASN cc_start: 0.8916 (m-40) cc_final: 0.8621 (m-40) REVERT: I 49 ARG cc_start: 0.9392 (pmt170) cc_final: 0.9111 (pmt170) REVERT: I 70 LEU cc_start: 0.7369 (mp) cc_final: 0.6702 (mp) REVERT: I 85 PHE cc_start: 0.9680 (m-80) cc_final: 0.9142 (m-80) REVERT: I 86 TYR cc_start: 0.9149 (m-80) cc_final: 0.8624 (m-80) REVERT: I 91 ARG cc_start: 0.8559 (mmt90) cc_final: 0.8353 (mmm-85) REVERT: I 133 TYR cc_start: 0.8488 (m-80) cc_final: 0.8282 (m-80) REVERT: K 104 MET cc_start: 0.8010 (ppp) cc_final: 0.7573 (ppp) REVERT: D 82 LEU cc_start: 0.8231 (mt) cc_final: 0.8029 (mt) REVERT: C 100 ASP cc_start: 0.9026 (m-30) cc_final: 0.8417 (t0) REVERT: C 128 ASN cc_start: 0.8527 (t0) cc_final: 0.8217 (t0) REVERT: A 144 ARG cc_start: 0.7673 (ptm-80) cc_final: 0.7153 (tmm-80) REVERT: B 115 ASP cc_start: 0.8893 (m-30) cc_final: 0.8567 (m-30) REVERT: H 22 ARG cc_start: 0.7730 (tpm170) cc_final: 0.7129 (mmm160) REVERT: H 25 ASP cc_start: 0.8642 (t0) cc_final: 0.8164 (t0) REVERT: H 28 MET cc_start: 0.7829 (mtp) cc_final: 0.7574 (tpt) outliers start: 1 outliers final: 0 residues processed: 228 average time/residue: 0.1394 time to fit residues: 46.1221 Evaluate side-chains 160 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.593 ------------------------------------------------------------------------------- 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: 0.7980 chunk 96 optimal weight: 4.9990 chunk 169 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 136 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 122 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 118 optimal weight: 6.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 HIS F 83 ASN J 18 HIS D 62 HIS D 69 GLN ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 ASN ** 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 45 GLN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.066818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.055095 restraints weight = 142175.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.056423 restraints weight = 98928.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.057293 restraints weight = 74925.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.057998 restraints weight = 60960.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.058482 restraints weight = 51775.974| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.5652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 15690 Z= 0.222 Angle : 0.821 13.035 21288 Z= 0.392 Chirality : 0.061 0.868 2379 Planarity : 0.004 0.048 2568 Dihedral : 12.325 143.039 2437 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.76 % Favored : 96.18 % Rotamer: Outliers : 0.13 % Allowed : 2.97 % Favored : 96.91 % 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: -0.29 (0.19), residues: 1729 helix: 0.60 (0.17), residues: 795 sheet: 0.52 (0.29), residues: 293 loop : -1.51 (0.22), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 57 TYR 0.030 0.002 TYR K 86 PHE 0.030 0.002 PHE K 85 TRP 0.019 0.002 TRP H 52 HIS 0.005 0.001 HIS F 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.22 (15688) covalent geometry : angle 0.82088 / 0.39 (21284) SS BOND : bond 0.00787 / 0.38 ( 2) SS BOND : angle 1.35715 / 0.74 ( 4) hydrogen bonds : bond 0.04785 / 3.15 ( 721) hydrogen bonds : angle 5.17109 / 3.53 ( 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 198 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 196 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 1 MET cc_start: 0.6236 (mmm) cc_final: 0.2779 (ttt) REVERT: F 7 LEU cc_start: 0.8203 (mt) cc_final: 0.7917 (mt) REVERT: F 33 HIS cc_start: 0.7335 (p-80) cc_final: 0.6658 (p-80) REVERT: F 163 MET cc_start: 0.4597 (ptt) cc_final: 0.3952 (ppp) REVERT: F 288 MET cc_start: 0.9151 (mmp) cc_final: 0.8930 (mmm) REVERT: J 109 ASP cc_start: 0.9136 (t0) cc_final: 0.8704 (m-30) REVERT: J 112 ILE cc_start: 0.8236 (pt) cc_final: 0.7951 (pt) REVERT: J 128 GLU cc_start: 0.7054 (tt0) cc_final: 0.6532 (tt0) REVERT: I 41 ASN cc_start: 0.8936 (m-40) cc_final: 0.8667 (m-40) REVERT: I 70 LEU cc_start: 0.7530 (mp) cc_final: 0.6610 (mp) REVERT: I 85 PHE cc_start: 0.9697 (m-80) cc_final: 0.9403 (m-80) REVERT: I 91 ARG cc_start: 0.8742 (mmt90) cc_final: 0.8540 (mmm-85) REVERT: K 85 PHE cc_start: 0.9089 (m-80) cc_final: 0.8744 (m-80) REVERT: D 54 LYS cc_start: 0.8417 (tppt) cc_final: 0.8146 (tppt) REVERT: D 69 GLN cc_start: 0.3058 (OUTLIER) cc_final: 0.1811 (pp30) REVERT: D 82 LEU cc_start: 0.8394 (mt) cc_final: 0.8166 (mt) REVERT: C 100 ASP cc_start: 0.8977 (m-30) cc_final: 0.8705 (m-30) REVERT: C 128 ASN cc_start: 0.8611 (t0) cc_final: 0.8265 (t0) REVERT: A 144 ARG cc_start: 0.7997 (ptm-80) cc_final: 0.7317 (tmm-80) REVERT: A 193 GLN cc_start: 0.9337 (tt0) cc_final: 0.9017 (tm-30) REVERT: B 168 ASN cc_start: 0.8770 (m110) cc_final: 0.8505 (m110) REVERT: H 22 ARG cc_start: 0.7788 (tpm170) cc_final: 0.7134 (mmm160) outliers start: 2 outliers final: 1 residues processed: 198 average time/residue: 0.1355 time to fit residues: 39.0793 Evaluate side-chains 154 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 152 time to evaluate : 0.563 ------------------------------------------------------------------------------- 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: 0.0170 chunk 115 optimal weight: 3.9990 chunk 65 optimal weight: 9.9990 chunk 119 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 99 optimal weight: 8.9990 chunk 104 optimal weight: 6.9990 chunk 134 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 overall best weight: 2.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 18 HIS ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 ASN ** 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 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 = 0.3950 r_free = 0.3950 target = 0.065298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.053641 restraints weight = 142812.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.054912 restraints weight = 100461.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.055774 restraints weight = 75733.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.056430 restraints weight = 62140.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.056933 restraints weight = 52929.194| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.6337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15690 Z= 0.189 Angle : 0.758 12.286 21288 Z= 0.360 Chirality : 0.058 0.876 2379 Planarity : 0.004 0.044 2568 Dihedral : 12.158 137.961 2437 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.35 % Favored : 96.59 % 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: -0.30 (0.19), residues: 1729 helix: 0.64 (0.18), residues: 798 sheet: 0.29 (0.29), residues: 302 loop : -1.48 (0.23), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 191 TYR 0.021 0.002 TYR I 87 PHE 0.030 0.002 PHE H 8 TRP 0.022 0.002 TRP H 52 HIS 0.009 0.001 HIS A 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.19 (15688) covalent geometry : angle 0.75771 / 0.36 (21284) SS BOND : bond 0.00629 / 0.31 ( 2) SS BOND : angle 1.12488 / 0.60 ( 4) hydrogen bonds : bond 0.04345 / 2.88 ( 721) hydrogen bonds : angle 5.13368 / 3.49 ( 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 193 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.638 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 288 MET cc_start: 0.9283 (mmp) cc_final: 0.9010 (mmm) REVERT: F 452 MET cc_start: 0.3343 (mmp) cc_final: 0.2766 (mmm) REVERT: J 128 GLU cc_start: 0.7164 (tt0) cc_final: 0.6719 (tt0) REVERT: I 41 ASN cc_start: 0.8923 (m-40) cc_final: 0.8660 (m-40) REVERT: I 49 ARG cc_start: 0.9176 (pmt170) cc_final: 0.8961 (pmt170) REVERT: I 70 LEU cc_start: 0.7531 (mp) cc_final: 0.6683 (mp) REVERT: I 85 PHE cc_start: 0.9686 (m-80) cc_final: 0.9348 (m-80) REVERT: I 91 ARG cc_start: 0.8805 (mmt90) cc_final: 0.8489 (mmm-85) REVERT: I 133 TYR cc_start: 0.8968 (m-80) cc_final: 0.8659 (m-80) REVERT: D 54 LYS cc_start: 0.8338 (tppt) cc_final: 0.8062 (tppt) REVERT: D 82 LEU cc_start: 0.8500 (mt) cc_final: 0.8266 (mt) REVERT: C 128 ASN cc_start: 0.8637 (t0) cc_final: 0.8410 (t0) REVERT: A 144 ARG cc_start: 0.7987 (ptm-80) cc_final: 0.7280 (tmm-80) REVERT: B 115 ASP cc_start: 0.8385 (m-30) cc_final: 0.8166 (m-30) REVERT: B 168 ASN cc_start: 0.8781 (m110) cc_final: 0.8481 (m110) REVERT: B 181 LEU cc_start: 0.9585 (tp) cc_final: 0.9324 (tp) REVERT: H 121 PHE cc_start: 0.8593 (t80) cc_final: 0.8341 (t80) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.1271 time to fit residues: 35.7956 Evaluate side-chains 146 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.595 ------------------------------------------------------------------------------- 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: 6.9990 chunk 81 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 168 optimal weight: 8.9990 chunk 19 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 153 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 263 GLN J 18 HIS ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 57 ASN ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 GLN ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 87 HIS ** H 137 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.059942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.049607 restraints weight = 157365.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.050612 restraints weight = 110931.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.051293 restraints weight = 86234.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.051786 restraints weight = 71762.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.052146 restraints weight = 62396.876| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.7136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 15690 Z= 0.269 Angle : 0.854 13.177 21288 Z= 0.414 Chirality : 0.060 0.728 2379 Planarity : 0.004 0.052 2568 Dihedral : 12.220 141.496 2437 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 22.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.80 % Favored : 95.14 % 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: -0.75 (0.19), residues: 1729 helix: 0.23 (0.18), residues: 785 sheet: 0.16 (0.29), residues: 294 loop : -1.65 (0.22), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 246 TYR 0.023 0.002 TYR I 133 PHE 0.024 0.002 PHE C 166 TRP 0.023 0.003 TRP H 52 HIS 0.007 0.001 HIS F 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.27 (15688) covalent geometry : angle 0.85405 / 0.41 (21284) SS BOND : bond 0.00721 / 0.36 ( 2) SS BOND : angle 1.73546 / 0.83 ( 4) hydrogen bonds : bond 0.05065 / 3.37 ( 721) hydrogen bonds : angle 5.53646 / 3.78 ( 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 178 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.555 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 1 MET cc_start: 0.5809 (mmm) cc_final: 0.1976 (ttt) REVERT: F 33 HIS cc_start: 0.7326 (p-80) cc_final: 0.6639 (p90) REVERT: F 363 MET cc_start: -0.2974 (tpt) cc_final: -0.3198 (tpt) REVERT: F 452 MET cc_start: 0.3671 (mmp) cc_final: 0.3283 (mmm) REVERT: J 109 ASP cc_start: 0.9165 (t0) cc_final: 0.8679 (m-30) REVERT: J 128 GLU cc_start: 0.7531 (tt0) cc_final: 0.7091 (tt0) REVERT: I 41 ASN cc_start: 0.8963 (m-40) cc_final: 0.8697 (m-40) REVERT: I 49 ARG cc_start: 0.9151 (pmt170) cc_final: 0.8783 (pmt170) REVERT: I 85 PHE cc_start: 0.9702 (m-80) cc_final: 0.9345 (m-80) REVERT: I 128 GLU cc_start: 0.9085 (mt-10) cc_final: 0.8865 (mm-30) REVERT: D 54 LYS cc_start: 0.8508 (tppt) cc_final: 0.8085 (tppt) REVERT: D 82 LEU cc_start: 0.8469 (mt) cc_final: 0.8215 (mt) REVERT: D 90 ASN cc_start: 0.8971 (p0) cc_final: 0.8490 (p0) REVERT: C 128 ASN cc_start: 0.8825 (t0) cc_final: 0.8562 (t0) REVERT: A 116 ILE cc_start: 0.7275 (mt) cc_final: 0.6894 (mt) REVERT: B 168 ASN cc_start: 0.8941 (m110) cc_final: 0.8668 (m110) REVERT: B 181 LEU cc_start: 0.9457 (tp) cc_final: 0.9193 (tp) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.1347 time to fit residues: 35.3755 Evaluate side-chains 138 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 73 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 164 optimal weight: 2.9990 chunk 23 optimal weight: 0.0010 chunk 159 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 114 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 overall best weight: 1.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 57 ASN ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.064105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.052783 restraints weight = 140201.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.054030 restraints weight = 98055.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.054845 restraints weight = 74058.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.055490 restraints weight = 60442.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.055965 restraints weight = 51583.062| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.7266 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= 0.138 Angle : 0.728 12.997 21288 Z= 0.344 Chirality : 0.055 0.649 2379 Planarity : 0.004 0.068 2568 Dihedral : 11.897 137.660 2437 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.35 % Favored : 96.59 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % 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: -0.33 (0.19), residues: 1729 helix: 0.63 (0.18), residues: 795 sheet: 0.34 (0.29), residues: 291 loop : -1.53 (0.22), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 93 TYR 0.017 0.001 TYR H 184 PHE 0.028 0.002 PHE F 332 TRP 0.015 0.002 TRP H 52 HIS 0.006 0.001 HIS D 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (15688) covalent geometry : angle 0.72776 / 0.34 (21284) SS BOND : bond 0.00487 / 0.24 ( 2) SS BOND : angle 1.20356 / 0.65 ( 4) hydrogen bonds : bond 0.04045 / 2.66 ( 721) hydrogen bonds : angle 5.23615 / 3.57 ( 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 191 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.610 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 288 MET cc_start: 0.9247 (mmp) cc_final: 0.8994 (mmm) REVERT: J 104 MET cc_start: 0.8493 (mmp) cc_final: 0.8178 (mmm) REVERT: J 109 ASP cc_start: 0.9098 (t0) cc_final: 0.8653 (m-30) REVERT: J 128 GLU cc_start: 0.7141 (tt0) cc_final: 0.6608 (tt0) REVERT: I 41 ASN cc_start: 0.8881 (m-40) cc_final: 0.8633 (m-40) REVERT: I 85 PHE cc_start: 0.9674 (m-80) cc_final: 0.9434 (m-80) REVERT: I 133 TYR cc_start: 0.8279 (m-80) cc_final: 0.7882 (m-80) REVERT: K 86 TYR cc_start: 0.8692 (m-10) cc_final: 0.8206 (m-80) REVERT: K 98 PHE cc_start: 0.7894 (t80) cc_final: 0.7625 (t80) REVERT: D 54 LYS cc_start: 0.8379 (tppt) cc_final: 0.8086 (tppt) REVERT: D 55 MET cc_start: 0.8776 (mtm) cc_final: 0.8556 (mtp) REVERT: A 116 ILE cc_start: 0.7065 (mt) cc_final: 0.5973 (mt) REVERT: B 115 ASP cc_start: 0.8384 (m-30) cc_final: 0.8178 (m-30) REVERT: B 168 ASN cc_start: 0.8849 (m110) cc_final: 0.8562 (m110) REVERT: B 181 LEU cc_start: 0.9592 (tp) cc_final: 0.9330 (tp) REVERT: H 121 PHE cc_start: 0.8934 (t80) cc_final: 0.8690 (t80) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.1389 time to fit residues: 39.1715 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 : 0.628 ------------------------------------------------------------------------------- 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: 1.9990 chunk 44 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 66 optimal weight: 0.2980 chunk 52 optimal weight: 9.9990 chunk 129 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 158 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.064451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.053574 restraints weight = 149038.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.054833 restraints weight = 100620.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.055710 restraints weight = 75149.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.056389 restraints weight = 60487.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.056830 restraints weight = 51128.950| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.7452 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= 0.134 Angle : 0.717 12.671 21288 Z= 0.340 Chirality : 0.054 0.613 2379 Planarity : 0.004 0.045 2568 Dihedral : 11.749 137.637 2437 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.35 % Favored : 96.59 % 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: -0.16 (0.19), residues: 1729 helix: 0.75 (0.18), residues: 796 sheet: 0.42 (0.30), residues: 291 loop : -1.41 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 57 TYR 0.020 0.001 TYR I 133 PHE 0.027 0.002 PHE H 8 TRP 0.013 0.001 TRP H 52 HIS 0.007 0.001 HIS D 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (15688) covalent geometry : angle 0.71653 / 0.34 (21284) SS BOND : bond 0.00422 / 0.21 ( 2) SS BOND : angle 1.20039 / 0.68 ( 4) hydrogen bonds : bond 0.03968 / 2.64 ( 721) hydrogen bonds : angle 5.11560 / 3.48 ( 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 182 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.663 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 452 MET cc_start: 0.3398 (mmp) cc_final: 0.2954 (mmm) REVERT: J 109 ASP cc_start: 0.9097 (t0) cc_final: 0.8646 (m-30) REVERT: J 128 GLU cc_start: 0.7328 (tt0) cc_final: 0.6865 (tt0) REVERT: I 41 ASN cc_start: 0.8806 (m-40) cc_final: 0.8551 (m-40) REVERT: I 49 ARG cc_start: 0.9196 (pmt170) cc_final: 0.8873 (pmt170) REVERT: I 85 PHE cc_start: 0.9670 (m-80) cc_final: 0.9235 (m-80) REVERT: K 86 TYR cc_start: 0.8580 (m-10) cc_final: 0.8289 (m-80) REVERT: K 98 PHE cc_start: 0.7880 (t80) cc_final: 0.7592 (t80) REVERT: D 54 LYS cc_start: 0.8427 (tppt) cc_final: 0.8055 (tppt) REVERT: D 55 MET cc_start: 0.8762 (mtm) cc_final: 0.8550 (mtp) REVERT: D 82 LEU cc_start: 0.8548 (mt) cc_final: 0.8341 (mt) REVERT: A 116 ILE cc_start: 0.7136 (mt) cc_final: 0.6055 (mt) REVERT: B 115 ASP cc_start: 0.8357 (m-30) cc_final: 0.8140 (m-30) REVERT: B 168 ASN cc_start: 0.8834 (m110) cc_final: 0.8538 (m110) REVERT: B 181 LEU cc_start: 0.9595 (tp) cc_final: 0.9198 (tt) REVERT: H 25 ASP cc_start: 0.8874 (t0) cc_final: 0.8422 (t0) REVERT: H 121 PHE cc_start: 0.8937 (t80) cc_final: 0.8661 (t80) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.1382 time to fit residues: 37.7566 Evaluate side-chains 135 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.620 ------------------------------------------------------------------------------- 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: 0.6980 chunk 119 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 141 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 chunk 100 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 22 optimal weight: 0.4980 chunk 81 optimal weight: 7.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 26 HIS ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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** ** A 174 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.065148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.054372 restraints weight = 146020.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.055653 restraints weight = 99903.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.056601 restraints weight = 74290.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.057042 restraints weight = 58770.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.057640 restraints weight = 51047.869| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.7586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15690 Z= 0.125 Angle : 0.720 13.026 21288 Z= 0.346 Chirality : 0.054 0.594 2379 Planarity : 0.003 0.043 2568 Dihedral : 11.622 136.724 2437 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.19), residues: 1729 helix: 0.81 (0.18), residues: 796 sheet: 0.55 (0.30), residues: 291 loop : -1.36 (0.22), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 91 TYR 0.028 0.001 TYR I 87 PHE 0.026 0.001 PHE H 8 TRP 0.010 0.001 TRP H 52 HIS 0.006 0.001 HIS D 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 (15688) covalent geometry : angle 0.71968 / 0.35 (21284) SS BOND : bond 0.00283 / 0.14 ( 2) SS BOND : angle 1.26877 / 0.74 ( 4) hydrogen bonds : bond 0.03898 / 2.58 ( 721) hydrogen bonds : angle 5.07378 / 3.47 ( 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 180 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 1 MET cc_start: 0.6005 (mmt) cc_final: 0.1066 (ttt) REVERT: J 104 MET cc_start: 0.8609 (mmp) cc_final: 0.8194 (mmm) REVERT: J 109 ASP cc_start: 0.9092 (t0) cc_final: 0.8654 (m-30) REVERT: J 128 GLU cc_start: 0.7202 (tt0) cc_final: 0.6738 (tt0) REVERT: I 41 ASN cc_start: 0.8819 (m-40) cc_final: 0.8576 (m-40) REVERT: I 51 LEU cc_start: 0.9771 (mt) cc_final: 0.9541 (mt) REVERT: I 85 PHE cc_start: 0.9652 (m-80) cc_final: 0.9238 (m-80) REVERT: I 133 TYR cc_start: 0.8978 (m-80) cc_final: 0.8478 (m-80) REVERT: K 98 PHE cc_start: 0.7798 (t80) cc_final: 0.7496 (t80) REVERT: K 104 MET cc_start: 0.8103 (ppp) cc_final: 0.7879 (ppp) REVERT: D 55 MET cc_start: 0.8749 (mtm) cc_final: 0.8526 (mtp) REVERT: D 82 LEU cc_start: 0.8265 (mt) cc_final: 0.7991 (mt) REVERT: A 116 ILE cc_start: 0.7101 (mt) cc_final: 0.5937 (mt) REVERT: B 115 ASP cc_start: 0.8345 (m-30) cc_final: 0.8133 (m-30) REVERT: B 168 ASN cc_start: 0.8791 (m110) cc_final: 0.8504 (m110) REVERT: B 181 LEU cc_start: 0.9603 (tp) cc_final: 0.9370 (tp) REVERT: H 25 ASP cc_start: 0.8907 (t0) cc_final: 0.8442 (t0) REVERT: H 121 PHE cc_start: 0.8955 (t80) cc_final: 0.8644 (t80) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.1314 time to fit residues: 35.5622 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 : 0.630 ------------------------------------------------------------------------------- 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: 3.9990 chunk 53 optimal weight: 0.9980 chunk 105 optimal weight: 0.0370 chunk 56 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 69 optimal weight: 8.9990 chunk 175 optimal weight: 5.9990 chunk 172 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 overall best weight: 1.2062 ------------------------------------------------------------------------------- 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** ** J 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 ASN D 193 GLN ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.064647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.053671 restraints weight = 147633.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.054998 restraints weight = 100005.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.055910 restraints weight = 74561.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.056504 restraints weight = 59894.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.056951 restraints weight = 51197.607| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.7776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15690 Z= 0.141 Angle : 0.731 12.520 21288 Z= 0.352 Chirality : 0.053 0.587 2379 Planarity : 0.004 0.097 2568 Dihedral : 11.624 137.133 2437 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.06 % Allowed : 0.32 % 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: -0.07 (0.20), residues: 1729 helix: 0.79 (0.18), residues: 794 sheet: 0.55 (0.30), residues: 291 loop : -1.36 (0.22), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 57 TYR 0.023 0.001 TYR H 184 PHE 0.034 0.002 PHE H 40 TRP 0.010 0.001 TRP H 52 HIS 0.006 0.001 HIS D 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (15688) covalent geometry : angle 0.73114 / 0.35 (21284) SS BOND : bond 0.00413 / 0.20 ( 2) SS BOND : angle 1.21792 / 0.69 ( 4) hydrogen bonds : bond 0.03964 / 2.65 ( 721) hydrogen bonds : angle 5.09171 / 3.49 ( 2084) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 167 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 1 MET cc_start: 0.6160 (mmt) cc_final: 0.1100 (ttt) REVERT: J 109 ASP cc_start: 0.9097 (t0) cc_final: 0.8663 (m-30) REVERT: J 128 GLU cc_start: 0.7271 (tt0) cc_final: 0.6815 (tt0) REVERT: I 14 MET cc_start: 0.5830 (tpp) cc_final: 0.4890 (tmm) REVERT: I 41 ASN cc_start: 0.8854 (m-40) cc_final: 0.8608 (m-40) REVERT: I 85 PHE cc_start: 0.9657 (m-80) cc_final: 0.9247 (m-80) REVERT: I 133 TYR cc_start: 0.9098 (m-80) cc_final: 0.8651 (m-80) REVERT: K 98 PHE cc_start: 0.7598 (t80) cc_final: 0.7262 (t80) REVERT: D 40 GLN cc_start: 0.9175 (mt0) cc_final: 0.8928 (mt0) REVERT: D 82 LEU cc_start: 0.8299 (mt) cc_final: 0.8088 (mt) REVERT: A 116 ILE cc_start: 0.7031 (mt) cc_final: 0.5973 (mt) REVERT: A 207 ASP cc_start: 0.9172 (m-30) cc_final: 0.8341 (p0) REVERT: B 115 ASP cc_start: 0.8222 (m-30) cc_final: 0.8008 (m-30) REVERT: B 168 ASN cc_start: 0.8900 (m110) cc_final: 0.8629 (m110) REVERT: B 181 LEU cc_start: 0.9603 (tp) cc_final: 0.9380 (tp) REVERT: H 25 ASP cc_start: 0.8873 (t0) cc_final: 0.8397 (t0) REVERT: H 52 TRP cc_start: 0.7088 (m-90) cc_final: 0.5786 (m-90) REVERT: H 121 PHE cc_start: 0.8911 (t80) cc_final: 0.8625 (t80) outliers start: 1 outliers final: 0 residues processed: 168 average time/residue: 0.1195 time to fit residues: 31.3047 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 : 0.618 ------------------------------------------------------------------------------- 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: 9.9990 chunk 45 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 153 optimal weight: 6.9990 chunk 125 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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** J 138 GLN ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 HIS ** 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 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 = 0.3933 r_free = 0.3933 target = 0.064202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.053492 restraints weight = 149050.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.054793 restraints weight = 100937.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.055627 restraints weight = 74702.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.056243 restraints weight = 60286.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.056718 restraints weight = 51106.112| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.7976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15690 Z= 0.147 Angle : 0.737 12.415 21288 Z= 0.355 Chirality : 0.053 0.576 2379 Planarity : 0.004 0.064 2568 Dihedral : 11.606 137.209 2437 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % 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: -0.08 (0.20), residues: 1729 helix: 0.73 (0.18), residues: 794 sheet: 0.61 (0.30), residues: 289 loop : -1.31 (0.23), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 56 TYR 0.032 0.002 TYR I 87 PHE 0.029 0.002 PHE H 40 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 0.00311 / 0.15 (15688) covalent geometry : angle 0.73653 / 0.36 (21284) SS BOND : bond 0.00443 / 0.22 ( 2) SS BOND : angle 1.22035 / 0.69 ( 4) hydrogen bonds : bond 0.03970 / 2.68 ( 721) hydrogen bonds : angle 5.19150 / 3.56 ( 2084) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3311.69 seconds wall clock time: 58 minutes 11.66 seconds (3491.66 seconds total)