Starting phenix.real_space_refine on Sat Jun 14 01:25:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uzy_26922/06_2025/7uzy_26922.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uzy_26922/06_2025/7uzy_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7uzy_26922/06_2025/7uzy_26922.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uzy_26922/06_2025/7uzy_26922.map" model { file = "/net/cci-nas-00/data/ceres_data/7uzy_26922/06_2025/7uzy_26922.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uzy_26922/06_2025/7uzy_26922.cif" } resolution = 4.05 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15332 Number of models: 1 Model: "" Number of chains: 11 Chain: "F" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3353 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 3, 'TRANS': 410} Chain breaks: 7 Chain: "J" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 871 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 1, 'TRANS': 100} Chain breaks: 2 Chain: "I" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 937 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 1, 'TRANS': 108} Chain breaks: 1 Chain: "K" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 505 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 1, 'TRANS': 57} Chain breaks: 1 Chain: "D" Number of atoms: 1572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1572 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 4, 'TRANS': 193} Chain breaks: 1 Chain: "C" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1628 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 200} Chain breaks: 1 Chain: "A" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1628 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 200} Chain breaks: 1 Chain: "B" Number of atoms: 1523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1523 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 187} Chain breaks: 2 Chain: "H" Number of atoms: 2378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2378 Classifications: {'peptide': 296} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 286} Chain breaks: 1 Chain: "G" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 637 Classifications: {'RNA': 30} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 5, 'rna3p_pur': 11, 'rna3p_pyr': 9} Link IDs: {'rna2p': 10, 'rna3p': 19} Chain: "L" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 300 Classifications: {'RNA': 14} Modifications used: {'rna2p_pur': 3, 'rna3p_pur': 6, 'rna3p_pyr': 5} Link IDs: {'rna2p': 3, 'rna3p': 10} Chain breaks: 1 Time building chain proxies: 10.82, per 1000 atoms: 0.71 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: 4.36 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 5.08 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: 5.56 Time building geometry restraints manager: 5.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3599 1.33 - 1.45: 3653 1.45 - 1.57: 8282 1.57 - 1.70: 85 1.70 - 1.82: 69 Bond restraints: 15688 Sorted by residual: bond pdb=" O3' A G 13 " pdb=" P A G 14 " ideal model delta sigma weight residual 1.607 1.670 -0.063 1.50e-02 4.44e+03 1.78e+01 bond pdb=" N ILE F 415 " pdb=" CA ILE F 415 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.22e-02 6.72e+03 9.54e+00 bond pdb=" N GLU B 87 " pdb=" CA GLU B 87 " ideal model delta sigma weight residual 1.458 1.486 -0.028 9.00e-03 1.23e+04 9.47e+00 bond pdb=" N LEU A 130 " pdb=" CA LEU A 130 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.42e+00 bond pdb=" N VAL I 20 " pdb=" CA VAL I 20 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.19e-02 7.06e+03 9.34e+00 ... (remaining 15683 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 20974 2.52 - 5.03: 281 5.03 - 7.55: 27 7.55 - 10.07: 1 10.07 - 12.59: 1 Bond angle restraints: 21284 Sorted by residual: angle pdb=" C4' A G 14 " pdb=" C3' A G 14 " pdb=" O3' A G 14 " ideal model delta sigma weight residual 113.00 125.59 -12.59 1.50e+00 4.44e-01 7.04e+01 angle pdb=" O3' A G 14 " pdb=" C3' A G 14 " pdb=" C2' A G 14 " ideal model delta sigma weight residual 113.70 104.36 9.34 1.50e+00 4.44e-01 3.88e+01 angle pdb=" N GLU D 205 " pdb=" CA GLU D 205 " pdb=" C GLU D 205 " ideal model delta sigma weight residual 113.50 107.68 5.82 1.23e+00 6.61e-01 2.24e+01 angle pdb=" N GLU B 87 " pdb=" CA GLU B 87 " pdb=" C GLU B 87 " ideal model delta sigma weight residual 113.50 106.33 7.17 1.65e+00 3.67e-01 1.89e+01 angle pdb=" C4' A G 14 " pdb=" C3' A G 14 " pdb=" C2' A G 14 " ideal model delta sigma weight residual 102.60 98.27 4.33 1.00e+00 1.00e+00 1.87e+01 ... (remaining 21279 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.94: 9261 34.94 - 69.87: 172 69.87 - 104.81: 16 104.81 - 139.74: 0 139.74 - 174.68: 3 Dihedral angle restraints: 9452 sinusoidal: 4292 harmonic: 5160 Sorted by residual: dihedral pdb=" O4' C G 28 " pdb=" C1' C G 28 " pdb=" N1 C G 28 " pdb=" C2 C G 28 " ideal model delta sinusoidal sigma weight residual 200.00 43.39 156.61 1 1.50e+01 4.44e-03 8.18e+01 dihedral pdb=" O4' C G 2 " pdb=" C1' C G 2 " pdb=" N1 C G 2 " pdb=" C2 C G 2 " ideal model delta sinusoidal sigma weight residual -128.00 46.68 -174.68 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' C G 8 " pdb=" C1' C G 8 " pdb=" N1 C G 8 " pdb=" C2 C G 8 " ideal model delta sinusoidal sigma weight residual -160.00 -88.21 -71.79 1 1.50e+01 4.44e-03 2.93e+01 ... (remaining 9449 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1666 0.043 - 0.087: 542 0.087 - 0.130: 143 0.130 - 0.174: 22 0.174 - 0.217: 6 Chirality restraints: 2379 Sorted by residual: chirality pdb=" CB ILE F 415 " pdb=" CA ILE F 415 " pdb=" CG1 ILE F 415 " pdb=" CG2 ILE F 415 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" C1' U L 8 " pdb=" O4' U L 8 " pdb=" C2' U L 8 " pdb=" N1 U L 8 " both_signs ideal model delta sigma weight residual False 2.47 2.25 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA GLU B 87 " pdb=" N GLU B 87 " pdb=" C GLU B 87 " pdb=" CB GLU B 87 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.80e-01 ... (remaining 2376 not shown) Planarity restraints: 2568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A L 16 " -0.043 2.00e-02 2.50e+03 1.86e-02 9.50e+00 pdb=" N9 A L 16 " 0.040 2.00e-02 2.50e+03 pdb=" C8 A L 16 " 0.004 2.00e-02 2.50e+03 pdb=" N7 A L 16 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A L 16 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A L 16 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A L 16 " -0.013 2.00e-02 2.50e+03 pdb=" N1 A L 16 " -0.005 2.00e-02 2.50e+03 pdb=" C2 A L 16 " 0.003 2.00e-02 2.50e+03 pdb=" N3 A L 16 " 0.010 2.00e-02 2.50e+03 pdb=" C4 A L 16 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN J 54 " 0.014 2.00e-02 2.50e+03 2.88e-02 8.30e+00 pdb=" C GLN J 54 " -0.050 2.00e-02 2.50e+03 pdb=" O GLN J 54 " 0.019 2.00e-02 2.50e+03 pdb=" N VAL J 55 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG I 57 " -0.013 2.00e-02 2.50e+03 2.63e-02 6.90e+00 pdb=" C ARG I 57 " 0.045 2.00e-02 2.50e+03 pdb=" O ARG I 57 " -0.017 2.00e-02 2.50e+03 pdb=" N LEU I 58 " -0.015 2.00e-02 2.50e+03 ... (remaining 2565 not shown) Histogram of nonbonded interaction distances: 1.37 - 2.08: 4 2.08 - 2.78: 3498 2.78 - 3.49: 20574 3.49 - 4.19: 34226 4.19 - 4.90: 59731 Nonbonded interactions: 118033 Sorted by model distance: nonbonded pdb=" OD1 ASN C 57 " pdb=" NH1 ARG A 129 " model vdw 1.373 3.120 nonbonded pdb=" ND2 ASN B 57 " pdb=" O2 C G 8 " model vdw 1.819 3.120 nonbonded pdb=" OD1 ASN C 57 " pdb=" CZ ARG A 129 " model vdw 1.957 3.270 nonbonded pdb=" OG1 THR C 126 " pdb=" O2' U G 25 " model vdw 2.066 3.040 nonbonded pdb=" ND2 ASN C 57 " pdb=" N7 G G 20 " model vdw 2.117 3.200 ... (remaining 118028 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 23 or resid 33 through 63 or resid 76 through 20 \ 7)) selection = (chain 'B' and resid 2 through 207) selection = (chain 'C' and (resid 2 through 23 or resid 33 through 63 or resid 76 through 20 \ 7)) selection = (chain 'D' and (resid 2 through 23 or resid 33 through 63 or resid 76 through 20 \ 7)) } ncs_group { reference = (chain 'I' and (resid 17 through 61 or resid 74 through 137)) selection = (chain 'J' and (resid 17 through 24 or resid 39 through 137)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.350 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: 0.680 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 43.690 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6425 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.133 15690 Z= 0.304 Angle : 0.835 51.639 21288 Z= 0.491 Chirality : 0.046 0.217 2379 Planarity : 0.005 0.057 2568 Dihedral : 13.953 174.677 6120 Min Nonbonded Distance : 1.373 Molprobity Statistics. All-atom Clashscore : 14.50 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (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 TRP 0.006 0.001 TRP F 184 HIS 0.008 0.001 HIS F 14 PHE 0.016 0.002 PHE A 148 TYR 0.020 0.002 TYR H 200 ARG 0.009 0.001 ARG K 91 Details of bonding type rmsd hydrogen bonds : bond 0.15918 ( 721) hydrogen bonds : angle 7.00594 ( 2084) SS BOND : bond 0.09418 ( 2) SS BOND : angle 25.85717 ( 4) covalent geometry : bond 0.00506 (15688) covalent geometry : angle 0.75594 (21284) *********************** 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 : 1.857 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: 0.3795 time to fit residues: 219.7345 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 : 1.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 7.9990 chunk 134 optimal weight: 5.9990 chunk 74 optimal weight: 0.0980 chunk 46 optimal weight: 8.9990 chunk 91 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 139 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 5 ASN ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 50 ASN F 83 ASN F 183 GLN F 314 HIS F 397 ASN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4077 r_free = 0.4077 target = 0.071565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.058915 restraints weight = 128509.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.060330 restraints weight = 90646.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.061362 restraints weight = 68693.530| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15690 Z= 0.170 Angle : 0.658 8.969 21288 Z= 0.351 Chirality : 0.044 0.207 2379 Planarity : 0.004 0.073 2568 Dihedral : 14.869 177.254 2555 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.89 % Favored : 97.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.19), residues: 1729 helix: 0.75 (0.18), residues: 789 sheet: 0.31 (0.29), residues: 298 loop : -1.54 (0.22), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 52 HIS 0.013 0.001 HIS C 110 PHE 0.040 0.002 PHE K 85 TYR 0.040 0.002 TYR I 80 ARG 0.007 0.001 ARG D 78 Details of bonding type rmsd hydrogen bonds : bond 0.04800 ( 721) hydrogen bonds : angle 5.34959 ( 2084) SS BOND : bond 0.00933 ( 2) SS BOND : angle 2.28938 ( 4) covalent geometry : bond 0.00351 (15688) covalent geometry : angle 0.65715 (21284) *********************** 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 255 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 254 time to evaluate : 1.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 33 HIS cc_start: 0.6740 (p-80) cc_final: 0.6078 (p-80) REVERT: F 163 MET cc_start: 0.4571 (ptt) cc_final: 0.3693 (ppp) REVERT: F 380 LEU cc_start: 0.9040 (tp) cc_final: 0.8784 (pp) REVERT: J 128 GLU cc_start: 0.7124 (tt0) cc_final: 0.6868 (tt0) REVERT: I 49 ARG cc_start: 0.9362 (pmt170) cc_final: 0.8865 (pmt170) REVERT: I 70 LEU cc_start: 0.7520 (mp) cc_final: 0.6965 (mp) REVERT: I 85 PHE cc_start: 0.9371 (m-10) cc_final: 0.8929 (m-80) REVERT: I 86 TYR cc_start: 0.9071 (m-80) cc_final: 0.8711 (m-80) REVERT: D 82 LEU cc_start: 0.8185 (mt) cc_final: 0.7975 (mt) REVERT: C 100 ASP cc_start: 0.9073 (m-30) cc_final: 0.8534 (t0) REVERT: C 128 ASN cc_start: 0.8654 (t0) cc_final: 0.8449 (t0) REVERT: C 144 ARG cc_start: 0.8714 (mtp85) cc_final: 0.8031 (mtp85) REVERT: A 178 ASN cc_start: 0.8766 (t0) cc_final: 0.8400 (t0) REVERT: B 115 ASP cc_start: 0.8997 (m-30) cc_final: 0.8710 (m-30) outliers start: 1 outliers final: 1 residues processed: 254 average time/residue: 0.3348 time to fit residues: 118.5926 Evaluate side-chains 178 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 177 time to evaluate : 1.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 28 optimal weight: 10.0000 chunk 137 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 132 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 18 HIS ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 GLN ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.069436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.056935 restraints weight = 136260.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.058367 restraints weight = 95721.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.059361 restraints weight = 72919.520| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.4782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15690 Z= 0.167 Angle : 0.612 10.369 21288 Z= 0.327 Chirality : 0.042 0.318 2379 Planarity : 0.004 0.038 2568 Dihedral : 14.889 175.735 2555 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.18 % Favored : 96.76 % Rotamer: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.19), residues: 1729 helix: 0.68 (0.17), residues: 780 sheet: 0.34 (0.29), residues: 300 loop : -1.47 (0.22), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 52 HIS 0.006 0.001 HIS D 110 PHE 0.031 0.002 PHE K 85 TYR 0.030 0.002 TYR I 87 ARG 0.022 0.001 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.04523 ( 721) hydrogen bonds : angle 5.14361 ( 2084) SS BOND : bond 0.00607 ( 2) SS BOND : angle 1.59142 ( 4) covalent geometry : bond 0.00339 (15688) covalent geometry : angle 0.61149 (21284) *********************** 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 218 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 1.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 33 HIS cc_start: 0.6891 (p-80) cc_final: 0.6251 (p-80) REVERT: F 163 MET cc_start: 0.4099 (ptt) cc_final: 0.3778 (ppp) REVERT: F 212 ILE cc_start: 0.8940 (mm) cc_final: 0.8648 (pt) REVERT: F 380 LEU cc_start: 0.9081 (tp) cc_final: 0.8671 (pp) REVERT: J 109 ASP cc_start: 0.9095 (t0) cc_final: 0.8615 (m-30) REVERT: J 112 ILE cc_start: 0.8137 (pt) cc_final: 0.7863 (pt) REVERT: J 128 GLU cc_start: 0.6908 (tt0) cc_final: 0.6539 (tt0) REVERT: I 41 ASN cc_start: 0.8923 (m-40) cc_final: 0.8637 (m-40) REVERT: I 49 ARG cc_start: 0.9384 (pmt170) cc_final: 0.8934 (pmt170) REVERT: I 70 LEU cc_start: 0.7450 (mp) cc_final: 0.6473 (mp) REVERT: I 133 TYR cc_start: 0.8701 (m-80) cc_final: 0.8276 (m-80) REVERT: K 104 MET cc_start: 0.8029 (ppp) cc_final: 0.7748 (ppp) REVERT: D 82 LEU cc_start: 0.8269 (mt) cc_final: 0.7957 (mt) REVERT: C 100 ASP cc_start: 0.9121 (m-30) cc_final: 0.8433 (t0) REVERT: C 128 ASN cc_start: 0.8659 (t0) cc_final: 0.8266 (t0) REVERT: A 144 ARG cc_start: 0.7849 (ptm-80) cc_final: 0.7228 (tmm-80) REVERT: A 178 ASN cc_start: 0.8773 (t0) cc_final: 0.8530 (t0) REVERT: B 115 ASP cc_start: 0.8897 (m-30) cc_final: 0.8614 (m-30) REVERT: B 181 LEU cc_start: 0.9507 (tp) cc_final: 0.9248 (tp) REVERT: H 22 ARG cc_start: 0.7698 (tpm170) cc_final: 0.7152 (mmm160) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.3277 time to fit residues: 103.3188 Evaluate side-chains 161 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 1.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 140 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 145 optimal weight: 6.9990 chunk 129 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 172 optimal weight: 0.0040 chunk 159 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 171 optimal weight: 6.9990 overall best weight: 1.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 18 HIS D 62 HIS ** D 74 GLN ** 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** A 174 HIS B 174 HIS ** H 214 GLN ** 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 = 0.3994 r_free = 0.3994 target = 0.067977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.055819 restraints weight = 138282.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.057211 restraints weight = 97544.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.058076 restraints weight = 74109.443| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.5377 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= 0.151 Angle : 0.598 11.893 21288 Z= 0.313 Chirality : 0.041 0.166 2379 Planarity : 0.004 0.044 2568 Dihedral : 14.936 176.087 2555 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.35 % Favored : 96.59 % Rotamer: Outliers : 0.06 % Allowed : 2.59 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.19), residues: 1729 helix: 0.73 (0.17), residues: 794 sheet: 0.35 (0.29), residues: 298 loop : -1.52 (0.22), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 52 HIS 0.006 0.001 HIS F 314 PHE 0.028 0.002 PHE K 85 TYR 0.028 0.002 TYR K 86 ARG 0.005 0.000 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.04090 ( 721) hydrogen bonds : angle 4.99996 ( 2084) SS BOND : bond 0.00966 ( 2) SS BOND : angle 1.57138 ( 4) covalent geometry : bond 0.00314 (15688) covalent geometry : angle 0.59737 (21284) *********************** 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 203 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 202 time to evaluate : 4.112 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: F 1 MET cc_start: 0.6331 (mmm) cc_final: 0.3080 (ttt) REVERT: F 33 HIS cc_start: 0.7215 (p-80) cc_final: 0.6540 (p-80) REVERT: F 163 MET cc_start: 0.4525 (ptt) cc_final: 0.3939 (ppp) REVERT: F 258 ASP cc_start: 0.8867 (m-30) cc_final: 0.8501 (m-30) REVERT: F 288 MET cc_start: 0.9221 (mmp) cc_final: 0.8974 (mmm) REVERT: J 109 ASP cc_start: 0.9101 (t0) cc_final: 0.8653 (m-30) REVERT: J 112 ILE cc_start: 0.8065 (pt) cc_final: 0.7808 (pt) REVERT: J 128 GLU cc_start: 0.7083 (tt0) cc_final: 0.6656 (tt0) REVERT: I 41 ASN cc_start: 0.8901 (m-40) cc_final: 0.8627 (m-40) REVERT: I 49 ARG cc_start: 0.9320 (pmt170) cc_final: 0.8821 (pmt170) REVERT: I 70 LEU cc_start: 0.7623 (mp) cc_final: 0.6822 (mp) REVERT: I 133 TYR cc_start: 0.8713 (m-80) cc_final: 0.8266 (m-80) REVERT: K 85 PHE cc_start: 0.9083 (m-80) cc_final: 0.8737 (m-80) REVERT: D 55 MET cc_start: 0.9117 (mtp) cc_final: 0.8896 (mtp) REVERT: D 82 LEU cc_start: 0.8211 (mt) cc_final: 0.7915 (mt) REVERT: C 100 ASP cc_start: 0.9134 (m-30) cc_final: 0.8420 (t0) REVERT: C 128 ASN cc_start: 0.8567 (t0) cc_final: 0.8347 (t0) REVERT: A 55 MET cc_start: 0.4971 (mmm) cc_final: 0.4732 (mmt) REVERT: A 144 ARG cc_start: 0.7900 (ptm-80) cc_final: 0.7246 (tmm-80) REVERT: A 178 ASN cc_start: 0.8664 (t0) cc_final: 0.8419 (t0) REVERT: A 193 GLN cc_start: 0.9344 (tt0) cc_final: 0.9124 (tm-30) REVERT: B 115 ASP cc_start: 0.8883 (m-30) cc_final: 0.8646 (m-30) REVERT: B 168 ASN cc_start: 0.8648 (m110) cc_final: 0.8367 (m110) REVERT: B 181 LEU cc_start: 0.9600 (tp) cc_final: 0.9340 (tp) REVERT: H 22 ARG cc_start: 0.7767 (tpm170) cc_final: 0.7085 (mmm160) outliers start: 1 outliers final: 0 residues processed: 203 average time/residue: 0.3846 time to fit residues: 114.6652 Evaluate side-chains 149 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 1.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 35 optimal weight: 7.9990 chunk 164 optimal weight: 5.9990 chunk 52 optimal weight: 20.0000 chunk 88 optimal weight: 6.9990 chunk 81 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 5 ASN F 38 HIS F 59 HIS ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 ASN F 263 GLN ** F 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 18 HIS D 18 HIS ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 57 ASN B 113 GLN ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 GLN H 87 HIS H 122 ASN H 129 GLN H 192 ASN ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.056906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.046111 restraints weight = 150566.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.046934 restraints weight = 116653.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.047471 restraints weight = 93837.421| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.7296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.081 15690 Z= 0.393 Angle : 0.968 11.563 21288 Z= 0.511 Chirality : 0.053 0.460 2379 Planarity : 0.007 0.074 2568 Dihedral : 16.038 173.275 2555 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 31.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.38 % Favored : 94.56 % Rotamer: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.18), residues: 1729 helix: -0.81 (0.16), residues: 782 sheet: -0.42 (0.29), residues: 287 loop : -1.92 (0.21), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP F 373 HIS 0.012 0.003 HIS F 169 PHE 0.034 0.004 PHE H 18 TYR 0.036 0.003 TYR I 87 ARG 0.009 0.001 ARG H 240 Details of bonding type rmsd hydrogen bonds : bond 0.06690 ( 721) hydrogen bonds : angle 6.20026 ( 2084) SS BOND : bond 0.01577 ( 2) SS BOND : angle 2.60420 ( 4) covalent geometry : bond 0.00805 (15688) covalent geometry : angle 0.96744 (21284) *********************** 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 172 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 2.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 1 MET cc_start: 0.6175 (mmm) cc_final: 0.2838 (ttm) REVERT: F 33 HIS cc_start: 0.7879 (p-80) cc_final: 0.7204 (p90) REVERT: F 288 MET cc_start: 0.9170 (mmp) cc_final: 0.8842 (mmm) REVERT: F 452 MET cc_start: 0.3976 (mmp) cc_final: 0.2833 (mmm) REVERT: J 109 ASP cc_start: 0.9128 (t0) cc_final: 0.8654 (m-30) REVERT: I 41 ASN cc_start: 0.9029 (m-40) cc_final: 0.8732 (m-40) REVERT: I 70 LEU cc_start: 0.7812 (mp) cc_final: 0.7516 (mp) REVERT: I 85 PHE cc_start: 0.9614 (m-10) cc_final: 0.9288 (m-80) REVERT: I 91 ARG cc_start: 0.8881 (mmm-85) cc_final: 0.8459 (mmm-85) REVERT: D 55 MET cc_start: 0.9207 (mtp) cc_final: 0.8717 (mtp) REVERT: D 82 LEU cc_start: 0.8531 (mt) cc_final: 0.8291 (mt) REVERT: C 38 ASP cc_start: 0.8507 (t0) cc_final: 0.7840 (t70) REVERT: C 41 THR cc_start: 0.8504 (p) cc_final: 0.8255 (p) REVERT: C 128 ASN cc_start: 0.8796 (t0) cc_final: 0.8569 (t0) REVERT: A 116 ILE cc_start: 0.7282 (mt) cc_final: 0.6719 (mt) REVERT: A 178 ASN cc_start: 0.8656 (t0) cc_final: 0.8338 (t0) REVERT: A 193 GLN cc_start: 0.9249 (tt0) cc_final: 0.8917 (tm-30) REVERT: B 168 ASN cc_start: 0.9085 (m110) cc_final: 0.8865 (m110) REVERT: B 181 LEU cc_start: 0.9550 (tp) cc_final: 0.9157 (tt) REVERT: H 226 MET cc_start: 0.7620 (mmm) cc_final: 0.7142 (mmm) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.3941 time to fit residues: 100.3789 Evaluate side-chains 126 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 3.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 151 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 165 optimal weight: 7.9990 chunk 115 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 chunk 26 optimal weight: 0.7980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 5 ASN ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 375 ASN D 113 GLN ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 18 HIS ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.061403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.050047 restraints weight = 148265.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.051244 restraints weight = 106115.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.052106 restraints weight = 81398.282| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.7390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15690 Z= 0.185 Angle : 0.671 13.640 21288 Z= 0.355 Chirality : 0.044 0.177 2379 Planarity : 0.004 0.048 2568 Dihedral : 15.770 178.148 2555 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 20.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.99 % Favored : 95.95 % Rotamer: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.19), residues: 1729 helix: -0.19 (0.17), residues: 796 sheet: -0.11 (0.29), residues: 280 loop : -1.79 (0.22), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP H 52 HIS 0.007 0.001 HIS D 110 PHE 0.026 0.002 PHE J 85 TYR 0.030 0.002 TYR J 133 ARG 0.010 0.001 ARG F 370 Details of bonding type rmsd hydrogen bonds : bond 0.04663 ( 721) hydrogen bonds : angle 5.57382 ( 2084) SS BOND : bond 0.00816 ( 2) SS BOND : angle 1.09815 ( 4) covalent geometry : bond 0.00384 (15688) covalent geometry : angle 0.67049 (21284) *********************** 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 176 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 1.964 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: F 33 HIS cc_start: 0.7152 (p-80) cc_final: 0.6421 (p90) REVERT: F 288 MET cc_start: 0.9199 (mmp) cc_final: 0.8954 (mmm) REVERT: J 109 ASP cc_start: 0.9139 (t0) cc_final: 0.8669 (m-30) REVERT: I 41 ASN cc_start: 0.8981 (m-40) cc_final: 0.8684 (m-40) REVERT: I 70 LEU cc_start: 0.7666 (mp) cc_final: 0.7116 (mp) REVERT: I 85 PHE cc_start: 0.9628 (m-10) cc_final: 0.9263 (m-80) REVERT: I 91 ARG cc_start: 0.8815 (mmm-85) cc_final: 0.8555 (mmm-85) REVERT: I 127 PHE cc_start: 0.9739 (t80) cc_final: 0.9455 (t80) REVERT: K 93 LYS cc_start: 0.8729 (pptt) cc_final: 0.8497 (tptt) REVERT: D 55 MET cc_start: 0.9198 (mtp) cc_final: 0.8740 (mtp) REVERT: D 82 LEU cc_start: 0.8360 (mt) cc_final: 0.8151 (mt) REVERT: C 128 ASN cc_start: 0.8843 (t0) cc_final: 0.8576 (t0) REVERT: A 178 ASN cc_start: 0.8578 (t0) cc_final: 0.8312 (t0) REVERT: A 193 GLN cc_start: 0.9160 (tt0) cc_final: 0.8910 (tm-30) REVERT: B 47 PRO cc_start: 0.8731 (Cg_exo) cc_final: 0.8435 (Cg_endo) REVERT: B 115 ASP cc_start: 0.8224 (m-30) cc_final: 0.8002 (m-30) REVERT: B 168 ASN cc_start: 0.9023 (m110) cc_final: 0.8752 (m-40) REVERT: B 181 LEU cc_start: 0.9563 (tp) cc_final: 0.9324 (tp) REVERT: H 226 MET cc_start: 0.7497 (mmm) cc_final: 0.7042 (mmm) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.3600 time to fit residues: 94.7027 Evaluate side-chains 132 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 1.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 115 optimal weight: 4.9990 chunk 145 optimal weight: 6.9990 chunk 102 optimal weight: 6.9990 chunk 19 optimal weight: 0.6980 chunk 15 optimal weight: 8.9990 chunk 132 optimal weight: 0.0980 chunk 33 optimal weight: 0.0570 chunk 104 optimal weight: 2.9990 chunk 153 optimal weight: 0.0020 chunk 0 optimal weight: 9.9990 chunk 167 optimal weight: 1.9990 overall best weight: 0.5708 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 375 ASN ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 57 ASN ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 HIS ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.063820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.053009 restraints weight = 151108.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.054247 restraints weight = 103802.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.055136 restraints weight = 76518.316| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.7403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15690 Z= 0.118 Angle : 0.599 9.582 21288 Z= 0.313 Chirality : 0.042 0.157 2379 Planarity : 0.004 0.048 2568 Dihedral : 15.558 177.467 2555 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.35 % Favored : 96.59 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.19), residues: 1729 helix: 0.51 (0.18), residues: 790 sheet: 0.20 (0.29), residues: 287 loop : -1.56 (0.22), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 52 HIS 0.008 0.001 HIS D 110 PHE 0.026 0.002 PHE J 85 TYR 0.015 0.001 TYR K 86 ARG 0.011 0.001 ARG K 91 Details of bonding type rmsd hydrogen bonds : bond 0.03854 ( 721) hydrogen bonds : angle 5.14279 ( 2084) SS BOND : bond 0.00364 ( 2) SS BOND : angle 1.08950 ( 4) covalent geometry : bond 0.00242 (15688) covalent geometry : angle 0.59909 (21284) *********************** 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 184 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 1.717 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: J 109 ASP cc_start: 0.9118 (t0) cc_final: 0.8631 (m-30) REVERT: J 112 ILE cc_start: 0.8545 (pt) cc_final: 0.8206 (pt) REVERT: J 123 TYR cc_start: 0.8909 (t80) cc_final: 0.8705 (t80) REVERT: J 127 PHE cc_start: 0.9485 (t80) cc_final: 0.9234 (t80) REVERT: I 41 ASN cc_start: 0.8837 (m-40) cc_final: 0.8577 (m-40) REVERT: I 85 PHE cc_start: 0.9607 (m-10) cc_final: 0.9211 (m-80) REVERT: I 91 ARG cc_start: 0.8894 (mmm-85) cc_final: 0.8555 (mmm-85) REVERT: I 127 PHE cc_start: 0.9696 (t80) cc_final: 0.9474 (t80) REVERT: I 133 TYR cc_start: 0.8720 (m-80) cc_final: 0.8231 (m-80) REVERT: K 86 TYR cc_start: 0.8619 (m-80) cc_final: 0.8386 (m-80) REVERT: K 93 LYS cc_start: 0.8760 (pptt) cc_final: 0.8560 (tptt) REVERT: D 55 MET cc_start: 0.9102 (mtp) cc_final: 0.8703 (mtp) REVERT: D 82 LEU cc_start: 0.8275 (mt) cc_final: 0.8069 (mt) REVERT: D 97 GLN cc_start: 0.8240 (mp10) cc_final: 0.7972 (mp10) REVERT: C 128 ASN cc_start: 0.8928 (t0) cc_final: 0.8659 (t0) REVERT: A 55 MET cc_start: 0.5002 (mmm) cc_final: 0.4796 (mmm) REVERT: A 178 ASN cc_start: 0.8868 (t0) cc_final: 0.8512 (t0) REVERT: A 193 GLN cc_start: 0.9177 (tt0) cc_final: 0.8932 (tm-30) REVERT: B 47 PRO cc_start: 0.8922 (Cg_exo) cc_final: 0.8630 (Cg_endo) REVERT: B 115 ASP cc_start: 0.8174 (m-30) cc_final: 0.7969 (m-30) REVERT: B 168 ASN cc_start: 0.8924 (m110) cc_final: 0.8633 (m-40) REVERT: B 181 LEU cc_start: 0.9643 (tp) cc_final: 0.9421 (tp) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.2689 time to fit residues: 74.3855 Evaluate side-chains 143 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 1.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 162 optimal weight: 0.0170 chunk 71 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 chunk 81 optimal weight: 0.1980 chunk 66 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 159 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 166 optimal weight: 9.9990 chunk 109 optimal weight: 3.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 26 HIS ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 214 GLN ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.064179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.053503 restraints weight = 147913.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.054788 restraints weight = 98838.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.055676 restraints weight = 73215.423| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.7500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15690 Z= 0.114 Angle : 0.598 11.925 21288 Z= 0.309 Chirality : 0.042 0.158 2379 Planarity : 0.003 0.039 2568 Dihedral : 15.495 176.751 2555 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.07 % Favored : 96.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.19), residues: 1729 helix: 0.71 (0.18), residues: 791 sheet: 0.19 (0.29), residues: 293 loop : -1.44 (0.22), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 52 HIS 0.007 0.001 HIS D 110 PHE 0.025 0.001 PHE F 178 TYR 0.014 0.001 TYR H 184 ARG 0.005 0.000 ARG F 370 Details of bonding type rmsd hydrogen bonds : bond 0.03689 ( 721) hydrogen bonds : angle 5.01461 ( 2084) SS BOND : bond 0.00336 ( 2) SS BOND : angle 1.16816 ( 4) covalent geometry : bond 0.00235 (15688) covalent geometry : angle 0.59816 (21284) *********************** 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 : 4.555 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: J 109 ASP cc_start: 0.9103 (t0) cc_final: 0.8653 (m-30) REVERT: J 112 ILE cc_start: 0.8480 (pt) cc_final: 0.8145 (pt) REVERT: J 123 TYR cc_start: 0.9034 (t80) cc_final: 0.8701 (t80) REVERT: J 127 PHE cc_start: 0.9506 (t80) cc_final: 0.9248 (t80) REVERT: I 41 ASN cc_start: 0.8817 (m-40) cc_final: 0.8574 (m-40) REVERT: I 85 PHE cc_start: 0.9596 (m-10) cc_final: 0.9219 (m-80) REVERT: I 91 ARG cc_start: 0.8933 (mmm-85) cc_final: 0.8559 (mmm-85) REVERT: I 133 TYR cc_start: 0.8665 (m-80) cc_final: 0.8341 (m-80) REVERT: K 98 PHE cc_start: 0.7843 (t80) cc_final: 0.7595 (t80) REVERT: D 55 MET cc_start: 0.9113 (mtp) cc_final: 0.8773 (mtp) REVERT: D 82 LEU cc_start: 0.8218 (mt) cc_final: 0.8015 (mt) REVERT: C 128 ASN cc_start: 0.8921 (t0) cc_final: 0.8644 (t0) REVERT: A 178 ASN cc_start: 0.8802 (t0) cc_final: 0.8452 (t0) REVERT: A 193 GLN cc_start: 0.9188 (tt0) cc_final: 0.8963 (tm-30) REVERT: B 47 PRO cc_start: 0.8958 (Cg_exo) cc_final: 0.8675 (Cg_endo) REVERT: B 115 ASP cc_start: 0.8168 (m-30) cc_final: 0.7959 (m-30) REVERT: B 168 ASN cc_start: 0.8929 (m110) cc_final: 0.8664 (m110) REVERT: B 181 LEU cc_start: 0.9659 (tp) cc_final: 0.9448 (tp) REVERT: H 134 LEU cc_start: 0.8549 (mt) cc_final: 0.8313 (mp) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.3525 time to fit residues: 97.4775 Evaluate side-chains 130 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 71 optimal weight: 0.3980 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 0.8980 chunk 79 optimal weight: 8.9990 chunk 137 optimal weight: 4.9990 chunk 33 optimal weight: 0.0050 chunk 120 optimal weight: 10.0000 chunk 47 optimal weight: 0.2980 chunk 134 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 172 optimal weight: 5.9990 overall best weight: 0.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 ASN ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 ASN ** 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 = 0.3925 r_free = 0.3925 target = 0.063971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.052427 restraints weight = 141213.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.053660 restraints weight = 100024.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.054556 restraints weight = 76134.902| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.7672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15690 Z= 0.122 Angle : 0.601 12.406 21288 Z= 0.315 Chirality : 0.042 0.196 2379 Planarity : 0.003 0.040 2568 Dihedral : 15.423 176.755 2555 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.19), residues: 1729 helix: 0.70 (0.18), residues: 788 sheet: 0.32 (0.30), residues: 291 loop : -1.37 (0.22), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 52 HIS 0.006 0.001 HIS D 110 PHE 0.022 0.001 PHE F 178 TYR 0.014 0.001 TYR H 184 ARG 0.005 0.000 ARG F 370 Details of bonding type rmsd hydrogen bonds : bond 0.03783 ( 721) hydrogen bonds : angle 5.01668 ( 2084) SS BOND : bond 0.00385 ( 2) SS BOND : angle 1.15867 ( 4) covalent geometry : bond 0.00254 (15688) covalent geometry : angle 0.60058 (21284) *********************** 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 178 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 2.095 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: 0.6007 (mmt) cc_final: 0.1161 (ttt) REVERT: J 109 ASP cc_start: 0.9065 (t0) cc_final: 0.8635 (m-30) REVERT: J 123 TYR cc_start: 0.9040 (t80) cc_final: 0.8704 (t80) REVERT: J 127 PHE cc_start: 0.9572 (t80) cc_final: 0.9277 (t80) REVERT: I 41 ASN cc_start: 0.8848 (m-40) cc_final: 0.8608 (m-40) REVERT: I 70 LEU cc_start: 0.7490 (mp) cc_final: 0.7276 (mp) REVERT: I 85 PHE cc_start: 0.9627 (m-10) cc_final: 0.9266 (m-80) REVERT: I 91 ARG cc_start: 0.8635 (mmm-85) cc_final: 0.8287 (mmm-85) REVERT: I 133 TYR cc_start: 0.8554 (m-80) cc_final: 0.8154 (m-80) REVERT: K 98 PHE cc_start: 0.7885 (t80) cc_final: 0.7609 (t80) REVERT: K 104 MET cc_start: 0.8220 (ppp) cc_final: 0.7792 (ppp) REVERT: D 55 MET cc_start: 0.9098 (mtp) cc_final: 0.8766 (mtp) REVERT: D 82 LEU cc_start: 0.8370 (mt) cc_final: 0.8089 (mt) REVERT: A 178 ASN cc_start: 0.8825 (t0) cc_final: 0.8452 (t0) REVERT: A 193 GLN cc_start: 0.9195 (tt0) cc_final: 0.8969 (tm-30) REVERT: B 168 ASN cc_start: 0.8933 (m110) cc_final: 0.8686 (m110) REVERT: B 181 LEU cc_start: 0.9624 (tp) cc_final: 0.9276 (tt) REVERT: H 52 TRP cc_start: 0.7463 (m-90) cc_final: 0.6065 (m-90) REVERT: H 121 PHE cc_start: 0.9039 (t80) cc_final: 0.8791 (t80) REVERT: H 134 LEU cc_start: 0.8509 (mt) cc_final: 0.8287 (mp) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.2852 time to fit residues: 78.0590 Evaluate side-chains 127 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 1.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 164 optimal weight: 8.9990 chunk 165 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 162 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 158 optimal weight: 3.9990 chunk 177 optimal weight: 10.0000 chunk 125 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 60 HIS ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 GLN ** 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 = 0.3919 r_free = 0.3919 target = 0.063745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.052230 restraints weight = 142373.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.053504 restraints weight = 100267.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.054281 restraints weight = 75510.603| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.7841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15690 Z= 0.126 Angle : 0.606 12.389 21288 Z= 0.316 Chirality : 0.041 0.169 2379 Planarity : 0.004 0.041 2568 Dihedral : 15.318 176.292 2555 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.20), residues: 1729 helix: 0.74 (0.18), residues: 794 sheet: 0.30 (0.30), residues: 292 loop : -1.29 (0.23), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 52 HIS 0.006 0.001 HIS D 110 PHE 0.019 0.001 PHE C 103 TYR 0.022 0.001 TYR H 184 ARG 0.005 0.000 ARG F 370 Details of bonding type rmsd hydrogen bonds : bond 0.03802 ( 721) hydrogen bonds : angle 4.98771 ( 2084) SS BOND : bond 0.00407 ( 2) SS BOND : angle 1.12824 ( 4) covalent geometry : bond 0.00263 (15688) covalent geometry : angle 0.60561 (21284) ********************** 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 170 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 169 time to evaluate : 1.728 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: F 1 MET cc_start: 0.5984 (mmt) cc_final: 0.1156 (ttt) REVERT: J 109 ASP cc_start: 0.9061 (t0) cc_final: 0.8632 (m-30) REVERT: J 123 TYR cc_start: 0.9057 (t80) cc_final: 0.8694 (t80) REVERT: J 127 PHE cc_start: 0.9574 (t80) cc_final: 0.9253 (t80) REVERT: I 41 ASN cc_start: 0.8825 (m-40) cc_final: 0.8594 (m-40) REVERT: I 85 PHE cc_start: 0.9619 (m-10) cc_final: 0.9251 (m-80) REVERT: I 91 ARG cc_start: 0.8611 (mmm-85) cc_final: 0.8238 (mmm-85) REVERT: I 133 TYR cc_start: 0.8342 (m-80) cc_final: 0.8028 (m-80) REVERT: K 86 TYR cc_start: 0.8841 (m-10) cc_final: 0.8628 (m-80) REVERT: K 98 PHE cc_start: 0.7900 (t80) cc_final: 0.7624 (t80) REVERT: K 104 MET cc_start: 0.8848 (ppp) cc_final: 0.8557 (ppp) REVERT: D 55 MET cc_start: 0.9095 (mtp) cc_final: 0.8769 (mtp) REVERT: D 82 LEU cc_start: 0.8366 (mt) cc_final: 0.8059 (mt) REVERT: D 97 GLN cc_start: 0.8438 (mp10) cc_final: 0.8179 (pm20) REVERT: A 178 ASN cc_start: 0.8868 (t0) cc_final: 0.8525 (t0) REVERT: B 115 ASP cc_start: 0.8013 (m-30) cc_final: 0.7702 (m-30) REVERT: B 168 ASN cc_start: 0.8931 (m110) cc_final: 0.8685 (m110) REVERT: B 181 LEU cc_start: 0.9629 (tp) cc_final: 0.9280 (tt) REVERT: H 28 MET cc_start: 0.8124 (tpp) cc_final: 0.7877 (tpt) REVERT: H 50 THR cc_start: 0.8264 (p) cc_final: 0.8058 (p) REVERT: H 52 TRP cc_start: 0.7453 (m-90) cc_final: 0.6134 (m-90) REVERT: H 121 PHE cc_start: 0.9056 (t80) cc_final: 0.8758 (t80) REVERT: H 134 LEU cc_start: 0.8501 (mt) cc_final: 0.8296 (mp) REVERT: H 179 MET cc_start: 0.2947 (ttt) cc_final: 0.2372 (mmm) outliers start: 1 outliers final: 0 residues processed: 170 average time/residue: 0.2605 time to fit residues: 67.6284 Evaluate side-chains 130 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 1.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 70 optimal weight: 0.0020 chunk 74 optimal weight: 0.7980 chunk 153 optimal weight: 0.5980 chunk 152 optimal weight: 0.9990 chunk 156 optimal weight: 7.9990 chunk 95 optimal weight: 0.6980 chunk 117 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 52 optimal weight: 0.0040 overall best weight: 0.4200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.065110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.054442 restraints weight = 148935.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.055752 restraints weight = 98580.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.056643 restraints weight = 72953.576| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.7908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15690 Z= 0.108 Angle : 0.593 13.211 21288 Z= 0.307 Chirality : 0.041 0.163 2379 Planarity : 0.003 0.043 2568 Dihedral : 15.180 177.442 2555 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.20), residues: 1729 helix: 0.83 (0.18), residues: 793 sheet: 0.36 (0.30), residues: 300 loop : -1.25 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 339 HIS 0.006 0.001 HIS D 110 PHE 0.029 0.001 PHE F 178 TYR 0.017 0.001 TYR H 184 ARG 0.005 0.000 ARG A 191 Details of bonding type rmsd hydrogen bonds : bond 0.03536 ( 721) hydrogen bonds : angle 4.83776 ( 2084) SS BOND : bond 0.00194 ( 2) SS BOND : angle 1.30519 ( 4) covalent geometry : bond 0.00223 (15688) covalent geometry : angle 0.59309 (21284) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6631.58 seconds wall clock time: 119 minutes 37.58 seconds (7177.58 seconds total)