Starting phenix.real_space_refine on Thu Jan 15 21:45:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i8b_35246/01_2026/8i8b_35246.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i8b_35246/01_2026/8i8b_35246.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8i8b_35246/01_2026/8i8b_35246.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i8b_35246/01_2026/8i8b_35246.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8i8b_35246/01_2026/8i8b_35246.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i8b_35246/01_2026/8i8b_35246.map" } resolution = 4.31 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.028 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: 4 Type Number sf(0) Gaussians S 194 5.16 5 C 19219 2.51 5 N 5042 2.21 5 O 5560 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30015 Number of models: 1 Model: "" Number of chains: 14 Chain: "W" Number of atoms: 2187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2187 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 11, 'TRANS': 259} Chain breaks: 1 Chain: "X" Number of atoms: 2187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2187 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 11, 'TRANS': 259} Chain breaks: 1 Chain: "Y" Number of atoms: 2187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2187 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 11, 'TRANS': 259} Chain breaks: 1 Chain: "Z" Number of atoms: 2187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2187 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 11, 'TRANS': 259} Chain breaks: 1 Chain: "A" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1565 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 5, 'TRANS': 182} Chain breaks: 1 Chain: "B" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1565 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 5, 'TRANS': 182} Chain breaks: 1 Chain: "C" Number of atoms: 1919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1919 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 223} Chain: "D" Number of atoms: 2817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2817 Classifications: {'peptide': 346} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 321} Chain breaks: 2 Chain: "E" Number of atoms: 3888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3888 Classifications: {'peptide': 474} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 448} Chain: "F" Number of atoms: 1853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1853 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain: "G" Number of atoms: 1853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1853 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain: "H" Number of atoms: 1854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1854 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 5, 'TRANS': 222} Chain breaks: 1 Chain: "I" Number of atoms: 1294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1294 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain breaks: 1 Chain: "J" Number of atoms: 2659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2659 Classifications: {'peptide': 316} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 302} Time building chain proxies: 6.18, per 1000 atoms: 0.21 Number of scatterers: 30015 At special positions: 0 Unit cell: (151.2, 182.25, 207.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 194 16.00 O 5560 8.00 N 5042 7.00 C 19219 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS W 36 " - pdb=" SG CYS W 49 " distance=2.03 Simple disulfide: pdb=" SG CYS W 229 " - pdb=" SG CYS X 229 " distance=2.03 Simple disulfide: pdb=" SG CYS X 36 " - pdb=" SG CYS X 49 " distance=2.03 Simple disulfide: pdb=" SG CYS X 169 " - pdb=" SG CYS D 187 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 36 " - pdb=" SG CYS Y 49 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 229 " - pdb=" SG CYS Z 229 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 36 " - pdb=" SG CYS Z 49 " distance=2.03 Simple disulfide: pdb=" SG CYS A 512 " - pdb=" SG CYS A 514 " distance=2.04 Simple disulfide: pdb=" SG CYS B 512 " - pdb=" SG CYS B 514 " distance=2.03 Simple disulfide: pdb=" SG CYS C 512 " - pdb=" SG CYS C 514 " distance=2.03 Simple disulfide: pdb=" SG CYS D 3 " - pdb=" SG CYS D 116 " distance=2.03 Simple disulfide: pdb=" SG CYS D 128 " - pdb=" SG CYS D 250 " 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: 2.58 Conformation dependent library (CDL) restraints added in 1.2 seconds 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7120 Finding SS restraints... Secondary structure from input PDB file: 139 helices and 27 sheets defined 46.7% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'W' and resid 18 through 23 removed outlier: 3.720A pdb=" N SER W 22 " --> pdb=" O ILE W 19 " (cutoff:3.500A) Processing helix chain 'W' and resid 37 through 42 Processing helix chain 'W' and resid 49 through 57 Processing helix chain 'W' and resid 88 through 91 removed outlier: 3.521A pdb=" N LYS W 91 " --> pdb=" O ARG W 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 88 through 91' Processing helix chain 'W' and resid 111 through 122 Processing helix chain 'W' and resid 124 through 136 Processing helix chain 'W' and resid 140 through 164 removed outlier: 4.251A pdb=" N ASN W 144 " --> pdb=" O GLY W 140 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N GLN W 146 " --> pdb=" O THR W 142 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ARG W 147 " --> pdb=" O SER W 143 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N THR W 162 " --> pdb=" O SER W 158 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N THR W 163 " --> pdb=" O ILE W 159 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN W 164 " --> pdb=" O LEU W 160 " (cutoff:3.500A) Processing helix chain 'W' and resid 189 through 193 removed outlier: 3.508A pdb=" N ALA W 192 " --> pdb=" O ARG W 189 " (cutoff:3.500A) Processing helix chain 'W' and resid 201 through 212 Processing helix chain 'W' and resid 280 through 285 Processing helix chain 'X' and resid 19 through 23 Processing helix chain 'X' and resid 37 through 42 Processing helix chain 'X' and resid 49 through 57 Processing helix chain 'X' and resid 88 through 91 Processing helix chain 'X' and resid 101 through 106 Processing helix chain 'X' and resid 107 through 110 Processing helix chain 'X' and resid 111 through 123 Processing helix chain 'X' and resid 124 through 136 Processing helix chain 'X' and resid 144 through 171 removed outlier: 4.696A pdb=" N THR X 162 " --> pdb=" O SER X 158 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N THR X 163 " --> pdb=" O ILE X 159 " (cutoff:3.500A) Proline residue: X 165 - end of helix Processing helix chain 'X' and resid 193 through 200 Processing helix chain 'X' and resid 201 through 212 Processing helix chain 'X' and resid 280 through 285 Processing helix chain 'Y' and resid 18 through 23 removed outlier: 3.975A pdb=" N SER Y 22 " --> pdb=" O ILE Y 19 " (cutoff:3.500A) Processing helix chain 'Y' and resid 37 through 42 removed outlier: 3.549A pdb=" N TYR Y 41 " --> pdb=" O PRO Y 38 " (cutoff:3.500A) Processing helix chain 'Y' and resid 49 through 57 Processing helix chain 'Y' and resid 88 through 91 removed outlier: 3.665A pdb=" N LYS Y 91 " --> pdb=" O ARG Y 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 88 through 91' Processing helix chain 'Y' and resid 111 through 122 Processing helix chain 'Y' and resid 124 through 137 removed outlier: 3.653A pdb=" N TYR Y 137 " --> pdb=" O ASP Y 133 " (cutoff:3.500A) Processing helix chain 'Y' and resid 140 through 164 removed outlier: 3.904A pdb=" N ASN Y 144 " --> pdb=" O GLY Y 140 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N GLN Y 146 " --> pdb=" O THR Y 142 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N ARG Y 147 " --> pdb=" O SER Y 143 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR Y 162 " --> pdb=" O SER Y 158 " (cutoff:3.500A) Processing helix chain 'Y' and resid 189 through 194 Processing helix chain 'Y' and resid 201 through 212 Processing helix chain 'Y' and resid 280 through 285 Processing helix chain 'Z' and resid 19 through 23 removed outlier: 3.605A pdb=" N SER Z 22 " --> pdb=" O ILE Z 19 " (cutoff:3.500A) Processing helix chain 'Z' and resid 37 through 42 Processing helix chain 'Z' and resid 49 through 57 Processing helix chain 'Z' and resid 111 through 122 Processing helix chain 'Z' and resid 124 through 138 removed outlier: 3.872A pdb=" N TYR Z 137 " --> pdb=" O ASP Z 133 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR Z 138 " --> pdb=" O ASN Z 134 " (cutoff:3.500A) Processing helix chain 'Z' and resid 144 through 164 removed outlier: 4.166A pdb=" N THR Z 162 " --> pdb=" O SER Z 158 " (cutoff:3.500A) Processing helix chain 'Z' and resid 189 through 194 removed outlier: 4.124A pdb=" N ASP Z 194 " --> pdb=" O GLY Z 190 " (cutoff:3.500A) Processing helix chain 'Z' and resid 201 through 212 Processing helix chain 'Z' and resid 280 through 285 Processing helix chain 'A' and resid 491 through 509 removed outlier: 3.868A pdb=" N TYR A 509 " --> pdb=" O MET A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 526 Processing helix chain 'A' and resid 527 through 535 Processing helix chain 'A' and resid 547 through 553 Processing helix chain 'A' and resid 554 through 557 Processing helix chain 'A' and resid 566 through 589 Processing helix chain 'A' and resid 589 through 599 removed outlier: 3.551A pdb=" N MET A 593 " --> pdb=" O ASN A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 629 Processing helix chain 'A' and resid 639 through 660 removed outlier: 3.554A pdb=" N LEU A 660 " --> pdb=" O ALA A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 685 Processing helix chain 'B' and resid 491 through 509 Processing helix chain 'B' and resid 523 through 526 Processing helix chain 'B' and resid 527 through 535 Processing helix chain 'B' and resid 547 through 557 Proline residue: B 554 - end of helix removed outlier: 3.936A pdb=" N LEU B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 589 Processing helix chain 'B' and resid 589 through 600 removed outlier: 3.575A pdb=" N MET B 593 " --> pdb=" O ASN B 589 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE B 600 " --> pdb=" O THR B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 629 Processing helix chain 'B' and resid 639 through 659 Processing helix chain 'B' and resid 674 through 685 Processing helix chain 'C' and resid 466 through 485 removed outlier: 4.422A pdb=" N GLU C 485 " --> pdb=" O LEU C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 510 Processing helix chain 'C' and resid 523 through 526 Processing helix chain 'C' and resid 527 through 535 Processing helix chain 'C' and resid 547 through 553 Processing helix chain 'C' and resid 554 through 559 removed outlier: 3.904A pdb=" N ASN C 559 " --> pdb=" O THR C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 589 Processing helix chain 'C' and resid 589 through 600 removed outlier: 4.125A pdb=" N PHE C 600 " --> pdb=" O THR C 596 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 627 Processing helix chain 'C' and resid 639 through 659 removed outlier: 3.766A pdb=" N ASN C 659 " --> pdb=" O LEU C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 674 through 685 Processing helix chain 'D' and resid 14 through 16 No H-bonds generated for 'chain 'D' and resid 14 through 16' Processing helix chain 'D' and resid 19 through 23 Processing helix chain 'D' and resid 43 through 50 removed outlier: 3.606A pdb=" N ILE D 50 " --> pdb=" O ARG D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 173 Processing helix chain 'D' and resid 174 through 181 Processing helix chain 'D' and resid 193 through 211 Processing helix chain 'D' and resid 222 through 243 Processing helix chain 'D' and resid 254 through 269 Processing helix chain 'D' and resid 275 through 292 removed outlier: 4.685A pdb=" N ILE D 287 " --> pdb=" O MET D 283 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N PHE D 289 " --> pdb=" O GLN D 285 " (cutoff:3.500A) Proline residue: D 290 - end of helix Processing helix chain 'D' and resid 295 through 302 removed outlier: 3.533A pdb=" N ILE D 299 " --> pdb=" O PRO D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 358 removed outlier: 3.983A pdb=" N ASN D 358 " --> pdb=" O SER D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 374 removed outlier: 3.561A pdb=" N ILE D 362 " --> pdb=" O ASN D 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 13 No H-bonds generated for 'chain 'E' and resid 11 through 13' Processing helix chain 'E' and resid 14 through 24 removed outlier: 3.948A pdb=" N PHE E 24 " --> pdb=" O LEU E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 45 removed outlier: 3.951A pdb=" N PHE E 39 " --> pdb=" O GLU E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 51 removed outlier: 3.549A pdb=" N LEU E 50 " --> pdb=" O THR E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 66 removed outlier: 3.577A pdb=" N LEU E 56 " --> pdb=" O ASP E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 82 removed outlier: 3.594A pdb=" N LYS E 81 " --> pdb=" O THR E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 138 removed outlier: 3.805A pdb=" N MET E 126 " --> pdb=" O ASN E 122 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ALA E 128 " --> pdb=" O ARG E 124 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N PHE E 129 " --> pdb=" O LYS E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 201 Processing helix chain 'E' and resid 250 through 265 removed outlier: 4.165A pdb=" N ILE E 254 " --> pdb=" O LYS E 250 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN E 265 " --> pdb=" O GLU E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 279 removed outlier: 4.368A pdb=" N PHE E 278 " --> pdb=" O ASP E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 291 Processing helix chain 'E' and resid 398 through 402 removed outlier: 3.527A pdb=" N LEU E 401 " --> pdb=" O HIS E 398 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 459 removed outlier: 3.649A pdb=" N ASP E 458 " --> pdb=" O SER E 455 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU E 459 " --> pdb=" O LEU E 456 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 455 through 459' Processing helix chain 'E' and resid 460 through 472 removed outlier: 3.613A pdb=" N GLN E 464 " --> pdb=" O ASN E 460 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE E 472 " --> pdb=" O LEU E 468 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 133 Processing helix chain 'F' and resid 141 through 155 removed outlier: 3.623A pdb=" N VAL F 145 " --> pdb=" O LYS F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 168 removed outlier: 3.504A pdb=" N THR F 168 " --> pdb=" O LEU F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 195 Processing helix chain 'F' and resid 203 through 219 Processing helix chain 'F' and resid 242 through 255 removed outlier: 3.723A pdb=" N LEU F 246 " --> pdb=" O THR F 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 286 Processing helix chain 'F' and resid 289 through 312 removed outlier: 3.619A pdb=" N MET F 293 " --> pdb=" O PRO F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 320 through 333 Processing helix chain 'G' and resid 115 through 131 Processing helix chain 'G' and resid 141 through 155 removed outlier: 3.589A pdb=" N VAL G 145 " --> pdb=" O LYS G 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 158 through 168 removed outlier: 3.630A pdb=" N THR G 168 " --> pdb=" O LEU G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 195 Processing helix chain 'G' and resid 203 through 218 Processing helix chain 'G' and resid 242 through 255 removed outlier: 3.573A pdb=" N LYS G 253 " --> pdb=" O GLU G 249 " (cutoff:3.500A) Processing helix chain 'G' and resid 275 through 286 removed outlier: 3.782A pdb=" N LEU G 281 " --> pdb=" O PHE G 277 " (cutoff:3.500A) Processing helix chain 'G' and resid 289 through 313 Processing helix chain 'G' and resid 320 through 335 Processing helix chain 'H' and resid 28 through 61 Processing helix chain 'H' and resid 66 through 73 Processing helix chain 'H' and resid 77 through 96 Processing helix chain 'H' and resid 138 through 146 Processing helix chain 'H' and resid 202 through 229 removed outlier: 4.049A pdb=" N GLN H 208 " --> pdb=" O VAL H 204 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 239 removed outlier: 3.629A pdb=" N THR H 239 " --> pdb=" O CYS H 235 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 60 Processing helix chain 'I' and resid 66 through 73 removed outlier: 3.678A pdb=" N PHE I 71 " --> pdb=" O LEU I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 76 through 96 removed outlier: 3.642A pdb=" N ILE I 80 " --> pdb=" O ASP I 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 137 through 146 Processing helix chain 'I' and resid 203 through 230 Processing helix chain 'I' and resid 232 through 240 Processing helix chain 'I' and resid 241 through 245 removed outlier: 3.975A pdb=" N PHE I 244 " --> pdb=" O HIS I 241 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 30 No H-bonds generated for 'chain 'J' and resid 28 through 30' Processing helix chain 'J' and resid 31 through 36 removed outlier: 3.967A pdb=" N LEU J 35 " --> pdb=" O ASP J 31 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 63 removed outlier: 3.706A pdb=" N ASN J 63 " --> pdb=" O ILE J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 90 Processing helix chain 'J' and resid 107 through 111 Processing helix chain 'J' and resid 119 through 124 Processing helix chain 'J' and resid 157 through 170 removed outlier: 4.062A pdb=" N ASP J 161 " --> pdb=" O PRO J 157 " (cutoff:3.500A) Processing helix chain 'J' and resid 180 through 192 Processing helix chain 'J' and resid 252 through 263 removed outlier: 3.947A pdb=" N VAL J 256 " --> pdb=" O SER J 252 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS J 263 " --> pdb=" O TYR J 259 " (cutoff:3.500A) Processing helix chain 'J' and resid 277 through 281 Processing helix chain 'J' and resid 299 through 319 removed outlier: 4.227A pdb=" N TYR J 303 " --> pdb=" O ASP J 299 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'W' and resid 62 through 66 removed outlier: 3.507A pdb=" N PHE W 74 " --> pdb=" O ILE W 66 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'W' and resid 93 through 95 removed outlier: 6.633A pdb=" N LEU W 239 " --> pdb=" O LEU W 94 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'W' and resid 176 through 178 removed outlier: 6.914A pdb=" N TYR W 216 " --> pdb=" O GLN W 302 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N ILE W 304 " --> pdb=" O TYR W 216 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLN W 218 " --> pdb=" O ILE W 304 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'X' and resid 62 through 65 Processing sheet with id=AA5, first strand: chain 'X' and resid 93 through 95 removed outlier: 6.561A pdb=" N LEU X 239 " --> pdb=" O LEU X 94 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'X' and resid 216 through 219 Processing sheet with id=AA7, first strand: chain 'Y' and resid 62 through 66 Processing sheet with id=AA8, first strand: chain 'Y' and resid 93 through 95 removed outlier: 3.654A pdb=" N ASP Y 235 " --> pdb=" O GLY Y 238 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL Y 240 " --> pdb=" O ILE Y 233 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE Y 233 " --> pdb=" O VAL Y 240 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'Y' and resid 176 through 178 removed outlier: 6.536A pdb=" N TYR Y 216 " --> pdb=" O GLN Y 302 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N ILE Y 304 " --> pdb=" O TYR Y 216 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLN Y 218 " --> pdb=" O ILE Y 304 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE Y 219 " --> pdb=" O GLU Y 222 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Z' and resid 62 through 66 Processing sheet with id=AB2, first strand: chain 'Z' and resid 93 through 96 removed outlier: 3.762A pdb=" N ILE Z 233 " --> pdb=" O VAL Z 240 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Z' and resid 176 through 178 removed outlier: 6.443A pdb=" N TYR Z 216 " --> pdb=" O GLN Z 302 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N ILE Z 304 " --> pdb=" O TYR Z 216 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N GLN Z 218 " --> pdb=" O ILE Z 304 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 60 through 65 removed outlier: 3.643A pdb=" N TRP D 88 " --> pdb=" O TYR D 40 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ARG D 103 " --> pdb=" O ILE D 85 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER D 12 " --> pdb=" O SER D 106 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N MET D 119 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL D 9 " --> pdb=" O MET D 119 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N VAL D 121 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE D 11 " --> pdb=" O VAL D 121 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 78 through 80 removed outlier: 6.373A pdb=" N LYS D 78 " --> pdb=" O ILE D 97 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 130 through 131 removed outlier: 6.388A pdb=" N ILE D 130 " --> pdb=" O TYR D 217 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N ILE D 219 " --> pdb=" O ILE D 130 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N CYS D 187 " --> pdb=" O ILE D 166 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 381 through 383 removed outlier: 6.055A pdb=" N GLN E 364 " --> pdb=" O ILE E 395 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE E 379 " --> pdb=" O ALA E 374 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N LEU E 380 " --> pdb=" O LEU E 442 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL E 437 " --> pdb=" O PHE E 433 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE E 433 " --> pdb=" O VAL E 437 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL E 426 " --> pdb=" O VAL E 420 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 85 through 90 removed outlier: 6.775A pdb=" N ASN E 117 " --> pdb=" O PRO E 85 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N LEU E 188 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEU E 118 " --> pdb=" O PHE E 186 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N PHE E 186 " --> pdb=" O LEU E 118 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY E 150 " --> pdb=" O ASN E 147 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 85 through 90 removed outlier: 6.775A pdb=" N ASN E 117 " --> pdb=" O PRO E 85 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 234 through 235 Processing sheet with id=AC2, first strand: chain 'E' and resid 244 through 247 removed outlier: 8.190A pdb=" N TYR E 355 " --> pdb=" O MET E 300 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE E 302 " --> pdb=" O TYR E 355 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N PHE E 357 " --> pdb=" O ILE E 302 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N THR E 304 " --> pdb=" O PHE E 357 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 411 through 413 Processing sheet with id=AC4, first strand: chain 'F' and resid 227 through 229 Processing sheet with id=AC5, first strand: chain 'G' and resid 262 through 263 removed outlier: 4.041A pdb=" N ILE G 263 " --> pdb=" O MET H 106 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET H 106 " --> pdb=" O ILE G 263 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLU H 107 " --> pdb=" O CYS H 134 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N VAL H 136 " --> pdb=" O GLU H 107 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL H 109 " --> pdb=" O VAL H 136 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 8 through 12 Processing sheet with id=AC7, first strand: chain 'I' and resid 107 through 109 Processing sheet with id=AC8, first strand: chain 'J' and resid 69 through 73 removed outlier: 6.317A pdb=" N HIS J 22 " --> pdb=" O TYR J 45 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N ILE J 47 " --> pdb=" O HIS J 22 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU J 24 " --> pdb=" O ILE J 47 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N GLN J 49 " --> pdb=" O LEU J 24 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N LEU J 26 " --> pdb=" O GLN J 49 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N MET J 97 " --> pdb=" O LEU J 116 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 199 through 201 removed outlier: 3.746A pdb=" N ILE J 199 " --> pdb=" O LEU J 173 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TRP J 176 " --> pdb=" O PHE J 139 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL J 136 " --> pdb=" O THR J 272 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N VAL J 274 " --> pdb=" O VAL J 136 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N VAL J 138 " --> pdb=" O VAL J 274 " (cutoff:3.500A) 1285 hydrogen bonds defined for protein. 3633 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.13 Time building geometry restraints manager: 3.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9712 1.34 - 1.47: 7270 1.47 - 1.59: 13375 1.59 - 1.71: 0 1.71 - 1.83: 310 Bond restraints: 30667 Sorted by residual: bond pdb=" CG HIS B 570 " pdb=" ND1 HIS B 570 " ideal model delta sigma weight residual 1.378 1.350 0.028 1.10e-02 8.26e+03 6.29e+00 bond pdb=" CB VAL X 172 " pdb=" CG2 VAL X 172 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 3.95e+00 bond pdb=" CD GLN B 571 " pdb=" NE2 GLN B 571 " ideal model delta sigma weight residual 1.328 1.367 -0.039 2.10e-02 2.27e+03 3.49e+00 bond pdb=" CB HIS B 570 " pdb=" CG HIS B 570 " ideal model delta sigma weight residual 1.497 1.473 0.024 1.40e-02 5.10e+03 3.03e+00 bond pdb=" N ARG F 175 " pdb=" CA ARG F 175 " ideal model delta sigma weight residual 1.463 1.442 0.021 1.22e-02 6.72e+03 2.95e+00 ... (remaining 30662 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 40982 2.12 - 4.24: 461 4.24 - 6.36: 51 6.36 - 8.48: 7 8.48 - 10.60: 3 Bond angle restraints: 41504 Sorted by residual: angle pdb=" CA ARG Z 178 " pdb=" C ARG Z 178 " pdb=" N PHE Z 179 " ideal model delta sigma weight residual 116.37 123.80 -7.43 1.28e+00 6.10e-01 3.37e+01 angle pdb=" O ARG Z 178 " pdb=" C ARG Z 178 " pdb=" N PHE Z 179 " ideal model delta sigma weight residual 123.13 115.88 7.25 1.26e+00 6.30e-01 3.31e+01 angle pdb=" N THR Z 183 " pdb=" CA THR Z 183 " pdb=" C THR Z 183 " ideal model delta sigma weight residual 110.43 117.30 -6.87 1.31e+00 5.83e-01 2.75e+01 angle pdb=" N ASP X 175 " pdb=" CA ASP X 175 " pdb=" C ASP X 175 " ideal model delta sigma weight residual 113.18 107.18 6.00 1.33e+00 5.65e-01 2.03e+01 angle pdb=" C ARG E 172 " pdb=" CA ARG E 172 " pdb=" CB ARG E 172 " ideal model delta sigma weight residual 116.63 111.97 4.66 1.16e+00 7.43e-01 1.61e+01 ... (remaining 41499 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 17420 17.84 - 35.68: 979 35.68 - 53.53: 150 53.53 - 71.37: 40 71.37 - 89.21: 22 Dihedral angle restraints: 18611 sinusoidal: 7670 harmonic: 10941 Sorted by residual: dihedral pdb=" CB CYS A 512 " pdb=" SG CYS A 512 " pdb=" SG CYS A 514 " pdb=" CB CYS A 514 " ideal model delta sinusoidal sigma weight residual -86.00 -155.09 69.09 1 1.00e+01 1.00e-02 6.17e+01 dihedral pdb=" CB CYS B 512 " pdb=" SG CYS B 512 " pdb=" SG CYS B 514 " pdb=" CB CYS B 514 " ideal model delta sinusoidal sigma weight residual -86.00 -151.26 65.26 1 1.00e+01 1.00e-02 5.58e+01 dihedral pdb=" CB CYS X 169 " pdb=" SG CYS X 169 " pdb=" SG CYS D 187 " pdb=" CB CYS D 187 " ideal model delta sinusoidal sigma weight residual -86.00 -139.83 53.83 1 1.00e+01 1.00e-02 3.93e+01 ... (remaining 18608 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 4329 0.084 - 0.169: 305 0.169 - 0.253: 2 0.253 - 0.337: 0 0.337 - 0.421: 1 Chirality restraints: 4637 Sorted by residual: chirality pdb=" CA PHE Z 180 " pdb=" N PHE Z 180 " pdb=" C PHE Z 180 " pdb=" CB PHE Z 180 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.44e+00 chirality pdb=" CA ASP Z 181 " pdb=" N ASP Z 181 " pdb=" C ASP Z 181 " pdb=" CB ASP Z 181 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA TYR D 134 " pdb=" N TYR D 134 " pdb=" C TYR D 134 " pdb=" CB TYR D 134 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.61e-01 ... (remaining 4634 not shown) Planarity restraints: 5337 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET D 342 " -0.052 5.00e-02 4.00e+02 7.81e-02 9.75e+00 pdb=" N PRO D 343 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO D 343 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO D 343 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 175 " 0.234 9.50e-02 1.11e+02 1.05e-01 7.59e+00 pdb=" NE ARG F 175 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG F 175 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG F 175 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG F 175 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN X 164 " -0.045 5.00e-02 4.00e+02 6.79e-02 7.38e+00 pdb=" N PRO X 165 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO X 165 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO X 165 " -0.038 5.00e-02 4.00e+02 ... (remaining 5334 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 317 2.57 - 3.15: 26298 3.15 - 3.73: 45727 3.73 - 4.32: 61241 4.32 - 4.90: 100084 Nonbonded interactions: 233667 Sorted by model distance: nonbonded pdb=" O PHE Z 180 " pdb=" OD1 ASP Z 181 " model vdw 1.984 3.040 nonbonded pdb=" OG1 THR E 295 " pdb=" OG SER E 298 " model vdw 2.197 3.040 nonbonded pdb=" O MET I 57 " pdb=" OG1 THR I 60 " model vdw 2.203 3.040 nonbonded pdb=" O ARG G 215 " pdb=" OG SER G 219 " model vdw 2.208 3.040 nonbonded pdb=" O VAL W 83 " pdb=" ND2 ASN W 251 " model vdw 2.209 3.120 ... (remaining 233662 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' selection = chain 'B' } ncs_group { reference = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } 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: 15.890 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: 0.390 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 24.930 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6195 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 : 0.004 0.066 30679 Z= 0.176 Angle : 0.583 10.598 41528 Z= 0.320 Chirality : 0.041 0.421 4637 Planarity : 0.004 0.105 5337 Dihedral : 11.829 89.211 11455 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.86 % Favored : 92.05 % Rotamer: Outliers : 0.56 % Allowed : 3.17 % Favored : 96.27 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.14), residues: 3612 helix: 1.47 (0.13), residues: 1535 sheet: -0.95 (0.29), residues: 334 loop : -1.41 (0.15), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG F 175 TYR 0.024 0.001 TYR F 172 PHE 0.017 0.001 PHE E 143 TRP 0.009 0.001 TRP J 300 HIS 0.025 0.001 HIS B 570 Details of bonding type rmsd covalent geometry : bond 0.00370 (30667) covalent geometry : angle 0.58265 (41504) SS BOND : bond 0.00286 ( 12) SS BOND : angle 1.38347 ( 24) hydrogen bonds : bond 0.15615 ( 1281) hydrogen bonds : angle 6.19080 ( 3633) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1099 residues out of total 3405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 1080 time to evaluate : 1.103 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 20 PHE cc_start: 0.8679 (m-80) cc_final: 0.8436 (m-10) REVERT: W 229 CYS cc_start: 0.5097 (m) cc_final: 0.3965 (m) REVERT: W 233 ILE cc_start: 0.8989 (tp) cc_final: 0.8724 (mm) REVERT: X 41 TYR cc_start: 0.9069 (m-80) cc_final: 0.8703 (m-80) REVERT: X 42 HIS cc_start: 0.8568 (m90) cc_final: 0.8093 (m90) REVERT: X 58 LYS cc_start: 0.8425 (mmtm) cc_final: 0.7526 (mmmm) REVERT: X 75 LYS cc_start: 0.8874 (ptpt) cc_final: 0.8671 (pttt) REVERT: X 228 ASN cc_start: 0.7737 (p0) cc_final: 0.6777 (p0) REVERT: X 282 ASP cc_start: 0.7549 (m-30) cc_final: 0.7348 (m-30) REVERT: Y 42 HIS cc_start: 0.7759 (m170) cc_final: 0.7336 (t70) REVERT: Y 48 ILE cc_start: 0.8876 (mt) cc_final: 0.8356 (mt) REVERT: Y 50 ASN cc_start: 0.9422 (t0) cc_final: 0.9131 (t0) REVERT: Y 110 MET cc_start: 0.8452 (pmm) cc_final: 0.7687 (pmm) REVERT: Y 111 MET cc_start: 0.8589 (mtt) cc_final: 0.8148 (ptt) REVERT: Y 116 LEU cc_start: 0.8819 (tp) cc_final: 0.8474 (pp) REVERT: Y 153 TYR cc_start: 0.8782 (t80) cc_final: 0.8379 (t80) REVERT: Y 157 LYS cc_start: 0.8591 (mmmm) cc_final: 0.8332 (mmmm) REVERT: Z 110 MET cc_start: 0.7931 (pmm) cc_final: 0.7640 (pmm) REVERT: Z 291 TYR cc_start: 0.7831 (t80) cc_final: 0.7113 (t80) REVERT: A 494 LYS cc_start: 0.8640 (mttt) cc_final: 0.8431 (tppt) REVERT: A 534 LEU cc_start: 0.8761 (mt) cc_final: 0.8385 (mt) REVERT: A 543 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8174 (mp0) REVERT: A 584 GLN cc_start: 0.8756 (mt0) cc_final: 0.8539 (mt0) REVERT: A 608 PHE cc_start: 0.8148 (m-80) cc_final: 0.7815 (m-80) REVERT: A 648 MET cc_start: 0.9124 (mmt) cc_final: 0.8923 (mmm) REVERT: A 649 ARG cc_start: 0.8865 (mmt180) cc_final: 0.7658 (mmm160) REVERT: B 518 LEU cc_start: 0.9014 (tp) cc_final: 0.8509 (tp) REVERT: B 581 ASN cc_start: 0.8949 (m-40) cc_final: 0.8725 (t0) REVERT: B 609 MET cc_start: 0.9412 (mtm) cc_final: 0.8975 (mtp) REVERT: B 615 LYS cc_start: 0.9467 (mttt) cc_final: 0.9250 (mmmm) REVERT: B 618 PHE cc_start: 0.9459 (t80) cc_final: 0.9156 (t80) REVERT: B 620 CYS cc_start: 0.8902 (m) cc_final: 0.8138 (m) REVERT: B 627 LYS cc_start: 0.9048 (tttt) cc_final: 0.8813 (tptt) REVERT: B 642 ILE cc_start: 0.9554 (mm) cc_final: 0.9333 (mt) REVERT: B 646 LEU cc_start: 0.9729 (mt) cc_final: 0.9525 (mt) REVERT: C 470 ARG cc_start: 0.8797 (mmt90) cc_final: 0.8392 (mmp-170) REVERT: C 574 ASN cc_start: 0.8963 (t0) cc_final: 0.8694 (m-40) REVERT: C 575 TYR cc_start: 0.8937 (t80) cc_final: 0.7445 (t80) REVERT: C 584 GLN cc_start: 0.9228 (mt0) cc_final: 0.8704 (mt0) REVERT: C 592 TYR cc_start: 0.8957 (t80) cc_final: 0.8717 (t80) REVERT: C 609 MET cc_start: 0.8830 (mtt) cc_final: 0.8571 (mtp) REVERT: C 622 MET cc_start: 0.8993 (ttm) cc_final: 0.8658 (tpt) REVERT: C 665 PHE cc_start: 0.5205 (t80) cc_final: 0.4981 (m-10) REVERT: D 8 GLN cc_start: 0.8542 (mm-40) cc_final: 0.8178 (mp10) REVERT: D 46 ASP cc_start: 0.8587 (m-30) cc_final: 0.8194 (m-30) REVERT: D 209 GLN cc_start: 0.9026 (mt0) cc_final: 0.8809 (mt0) REVERT: E 63 LEU cc_start: 0.9353 (tp) cc_final: 0.9116 (mt) REVERT: E 195 MET cc_start: 0.9289 (mmm) cc_final: 0.8803 (tpp) REVERT: E 223 MET cc_start: 0.7824 (mtp) cc_final: 0.6869 (mpp) REVERT: E 322 ILE cc_start: 0.9523 (mt) cc_final: 0.9266 (mm) REVERT: E 378 ARG cc_start: 0.9067 (mtm180) cc_final: 0.8814 (mtm-85) REVERT: E 424 GLU cc_start: 0.8893 (mm-30) cc_final: 0.8455 (mm-30) REVERT: F 128 HIS cc_start: 0.8382 (m-70) cc_final: 0.7963 (m170) REVERT: F 129 HIS cc_start: 0.8496 (t70) cc_final: 0.7979 (t-170) REVERT: F 175 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7766 (tpt-90) REVERT: F 177 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.8107 (tm-30) REVERT: F 178 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.8257 (mmm) REVERT: F 182 GLN cc_start: 0.9279 (mt0) cc_final: 0.9065 (pt0) REVERT: F 188 ASP cc_start: 0.9047 (m-30) cc_final: 0.8768 (t70) REVERT: F 194 LEU cc_start: 0.8999 (mt) cc_final: 0.8514 (tp) REVERT: F 209 MET cc_start: 0.9100 (ttp) cc_final: 0.8829 (mmp) REVERT: F 226 LYS cc_start: 0.8925 (pttt) cc_final: 0.7879 (ptmt) REVERT: F 228 VAL cc_start: 0.9267 (t) cc_final: 0.8512 (t) REVERT: F 229 LEU cc_start: 0.9002 (mp) cc_final: 0.8610 (tp) REVERT: F 316 PHE cc_start: 0.5627 (p90) cc_final: 0.5370 (p90) REVERT: G 116 MET cc_start: 0.8952 (mmm) cc_final: 0.8663 (mmm) REVERT: G 129 HIS cc_start: 0.9181 (t-90) cc_final: 0.8259 (t-90) REVERT: G 149 MET cc_start: 0.9353 (mmm) cc_final: 0.9137 (mmp) REVERT: G 174 CYS cc_start: 0.3230 (OUTLIER) cc_final: 0.2290 (t) REVERT: G 182 GLN cc_start: 0.8902 (mt0) cc_final: 0.8653 (mt0) REVERT: G 209 MET cc_start: 0.9023 (mtp) cc_final: 0.8790 (mmm) REVERT: G 246 LEU cc_start: 0.8869 (tp) cc_final: 0.8529 (tt) REVERT: G 263 ILE cc_start: 0.7911 (mt) cc_final: 0.7662 (pt) REVERT: G 273 ASP cc_start: 0.8443 (m-30) cc_final: 0.7629 (p0) REVERT: G 290 LEU cc_start: 0.9107 (tp) cc_final: 0.8782 (tt) REVERT: G 294 TYR cc_start: 0.9060 (m-80) cc_final: 0.8611 (m-80) REVERT: G 316 PHE cc_start: 0.8675 (t80) cc_final: 0.7670 (t80) REVERT: H 40 GLU cc_start: 0.9025 (mm-30) cc_final: 0.8766 (mm-30) REVERT: H 70 ILE cc_start: 0.9410 (mt) cc_final: 0.9191 (mm) REVERT: H 76 ASP cc_start: 0.8716 (t0) cc_final: 0.8072 (t0) REVERT: H 134 CYS cc_start: 0.8859 (t) cc_final: 0.8340 (t) REVERT: H 137 ASP cc_start: 0.8761 (t0) cc_final: 0.8470 (t0) REVERT: H 238 LEU cc_start: 0.9374 (mt) cc_final: 0.8969 (mt) REVERT: I 49 LEU cc_start: 0.6969 (mt) cc_final: 0.6506 (tp) REVERT: I 71 PHE cc_start: 0.5848 (m-80) cc_final: 0.5456 (m-10) REVERT: I 99 VAL cc_start: 0.7308 (t) cc_final: 0.6881 (t) REVERT: I 136 VAL cc_start: 0.7571 (t) cc_final: 0.6961 (t) REVERT: J 134 PRO cc_start: 0.5419 (Cg_endo) cc_final: 0.4930 (Cg_exo) REVERT: J 136 VAL cc_start: 0.3409 (t) cc_final: 0.3159 (t) REVERT: J 181 ARG cc_start: 0.5499 (mtm-85) cc_final: 0.5272 (tpt170) REVERT: J 280 ASN cc_start: 0.4209 (m-40) cc_final: 0.3838 (m110) outliers start: 19 outliers final: 7 residues processed: 1096 average time/residue: 0.2075 time to fit residues: 349.0726 Evaluate side-chains 596 residues out of total 3405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 585 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.1980 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.2980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 146 GLN ** W 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 42 HIS ** Y 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 198 ASN ** Y 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 42 HIS ** Z 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 ASN ** A 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 GLN B 574 ASN B 661 GLN B 678 GLN B 685 ASN ** C 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 637 GLN D 209 GLN E 117 ASN E 464 GLN F 296 ASN G 231 GLN G 313 ASN ** G 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 258 ASN I 208 GLN J 22 HIS ** J 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 118 HIS J 241 HIS ** J 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 298 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.102667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.075801 restraints weight = 117660.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.077536 restraints weight = 66584.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.079144 restraints weight = 43419.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.079144 restraints weight = 36955.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.079308 restraints weight = 32311.889| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 30679 Z= 0.187 Angle : 0.664 11.215 41528 Z= 0.352 Chirality : 0.045 0.254 4637 Planarity : 0.005 0.078 5337 Dihedral : 4.695 40.750 4013 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.23 % Favored : 92.72 % Rotamer: Outliers : 0.21 % Allowed : 3.47 % Favored : 96.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.14), residues: 3612 helix: 1.13 (0.13), residues: 1564 sheet: -0.89 (0.29), residues: 321 loop : -1.38 (0.15), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 82 TYR 0.028 0.002 TYR E 62 PHE 0.034 0.002 PHE H 125 TRP 0.017 0.002 TRP Z 46 HIS 0.015 0.002 HIS A 570 Details of bonding type rmsd covalent geometry : bond 0.00407 (30667) covalent geometry : angle 0.66238 (41504) SS BOND : bond 0.00381 ( 12) SS BOND : angle 1.78272 ( 24) hydrogen bonds : bond 0.05129 ( 1281) hydrogen bonds : angle 5.26428 ( 3633) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 763 residues out of total 3405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 756 time to evaluate : 0.844 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 115 GLN cc_start: 0.9154 (mt0) cc_final: 0.8938 (mt0) REVERT: W 206 ASN cc_start: 0.8683 (m110) cc_final: 0.8436 (m-40) REVERT: X 41 TYR cc_start: 0.9289 (m-80) cc_final: 0.8783 (m-80) REVERT: X 42 HIS cc_start: 0.8860 (m90) cc_final: 0.8149 (m170) REVERT: X 58 LYS cc_start: 0.8652 (mmtm) cc_final: 0.8037 (mmmm) REVERT: X 59 MET cc_start: 0.8618 (mmp) cc_final: 0.8310 (mmt) REVERT: X 75 LYS cc_start: 0.9112 (ptpt) cc_final: 0.8688 (pttt) REVERT: X 163 THR cc_start: 0.9496 (p) cc_final: 0.9287 (t) REVERT: X 288 TYR cc_start: 0.7128 (m-80) cc_final: 0.6595 (m-10) REVERT: Y 48 ILE cc_start: 0.9065 (mt) cc_final: 0.8752 (mt) REVERT: Y 50 ASN cc_start: 0.9270 (t0) cc_final: 0.8996 (t0) REVERT: Y 59 MET cc_start: 0.9014 (mpp) cc_final: 0.8461 (mpp) REVERT: Y 116 LEU cc_start: 0.8802 (tp) cc_final: 0.8464 (pp) REVERT: Y 153 TYR cc_start: 0.8834 (t80) cc_final: 0.8394 (t80) REVERT: Y 157 LYS cc_start: 0.8626 (mmmm) cc_final: 0.8351 (mmmm) REVERT: Z 22 SER cc_start: 0.8109 (t) cc_final: 0.7724 (m) REVERT: Z 229 CYS cc_start: 0.6207 (m) cc_final: 0.5931 (m) REVERT: Z 291 TYR cc_start: 0.8056 (t80) cc_final: 0.7787 (t80) REVERT: A 519 GLU cc_start: 0.8324 (tm-30) cc_final: 0.7988 (tt0) REVERT: A 544 MET cc_start: 0.6542 (ttp) cc_final: 0.6102 (ttt) REVERT: A 584 GLN cc_start: 0.8811 (mt0) cc_final: 0.8511 (mt0) REVERT: A 608 PHE cc_start: 0.7858 (m-80) cc_final: 0.7391 (m-80) REVERT: A 649 ARG cc_start: 0.8842 (mmt180) cc_final: 0.8574 (mmm160) REVERT: B 518 LEU cc_start: 0.8921 (tp) cc_final: 0.8283 (tp) REVERT: B 519 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8289 (mt-10) REVERT: B 592 TYR cc_start: 0.8347 (t80) cc_final: 0.8038 (t80) REVERT: B 594 ARG cc_start: 0.8815 (ttm110) cc_final: 0.8290 (mtm180) REVERT: B 595 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8411 (pm20) REVERT: B 609 MET cc_start: 0.9430 (mtm) cc_final: 0.9014 (mtp) REVERT: C 470 ARG cc_start: 0.8917 (mmt90) cc_final: 0.8669 (mmp-170) REVERT: C 592 TYR cc_start: 0.9065 (t80) cc_final: 0.8802 (t80) REVERT: C 609 MET cc_start: 0.8808 (mtt) cc_final: 0.8596 (mtp) REVERT: C 665 PHE cc_start: 0.5347 (t80) cc_final: 0.4970 (m-10) REVERT: D 8 GLN cc_start: 0.8592 (mm-40) cc_final: 0.8127 (mp10) REVERT: D 39 VAL cc_start: 0.9493 (t) cc_final: 0.9256 (p) REVERT: D 206 CYS cc_start: 0.9258 (m) cc_final: 0.9008 (m) REVERT: D 342 MET cc_start: 0.6579 (pmm) cc_final: 0.6133 (pmm) REVERT: D 352 ASP cc_start: 0.8980 (p0) cc_final: 0.8596 (p0) REVERT: E 67 GLN cc_start: 0.9150 (mm-40) cc_final: 0.8833 (mm-40) REVERT: E 127 MET cc_start: 0.8839 (mmt) cc_final: 0.8614 (mmt) REVERT: E 195 MET cc_start: 0.9346 (mmm) cc_final: 0.8926 (mmt) REVERT: E 223 MET cc_start: 0.7455 (mtp) cc_final: 0.7033 (mpp) REVERT: E 257 GLU cc_start: 0.7970 (tp30) cc_final: 0.6891 (tp30) REVERT: E 424 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8543 (mm-30) REVERT: E 468 LEU cc_start: 0.9450 (tp) cc_final: 0.9196 (tp) REVERT: F 129 HIS cc_start: 0.8205 (t70) cc_final: 0.7367 (t70) REVERT: F 170 ASP cc_start: 0.8791 (m-30) cc_final: 0.8456 (t0) REVERT: F 181 VAL cc_start: 0.9483 (t) cc_final: 0.9190 (p) REVERT: F 188 ASP cc_start: 0.9089 (m-30) cc_final: 0.8855 (t70) REVERT: F 195 GLU cc_start: 0.8896 (tm-30) cc_final: 0.8540 (tm-30) REVERT: F 209 MET cc_start: 0.9251 (ttp) cc_final: 0.8945 (tmm) REVERT: F 222 MET cc_start: 0.8748 (tmm) cc_final: 0.8304 (tmm) REVERT: F 229 LEU cc_start: 0.9128 (mp) cc_final: 0.8626 (tt) REVERT: F 246 LEU cc_start: 0.8764 (mm) cc_final: 0.8497 (tt) REVERT: F 299 ASN cc_start: 0.8934 (m-40) cc_final: 0.8631 (m-40) REVERT: F 301 MET cc_start: 0.8409 (tmm) cc_final: 0.8007 (tmm) REVERT: G 116 MET cc_start: 0.9057 (mmm) cc_final: 0.8554 (mmm) REVERT: G 129 HIS cc_start: 0.9184 (t-90) cc_final: 0.8049 (t-90) REVERT: G 131 SER cc_start: 0.8516 (p) cc_final: 0.7737 (p) REVERT: G 144 ASP cc_start: 0.9187 (m-30) cc_final: 0.8934 (m-30) REVERT: G 149 MET cc_start: 0.9284 (mmm) cc_final: 0.9057 (mmp) REVERT: G 184 ASP cc_start: 0.9084 (m-30) cc_final: 0.8851 (m-30) REVERT: G 188 ASP cc_start: 0.9340 (m-30) cc_final: 0.9065 (t0) REVERT: G 246 LEU cc_start: 0.8980 (tp) cc_final: 0.8706 (tp) REVERT: G 252 GLU cc_start: 0.9178 (mt-10) cc_final: 0.8973 (mt-10) REVERT: G 273 ASP cc_start: 0.8354 (m-30) cc_final: 0.7586 (p0) REVERT: G 315 LYS cc_start: 0.9148 (mmpt) cc_final: 0.8848 (mmmt) REVERT: H 22 ILE cc_start: 0.8133 (tp) cc_final: 0.7647 (tp) REVERT: H 40 GLU cc_start: 0.9267 (mm-30) cc_final: 0.8849 (mm-30) REVERT: H 76 ASP cc_start: 0.9089 (t0) cc_final: 0.8577 (t0) REVERT: H 105 LYS cc_start: 0.8942 (ptmt) cc_final: 0.8693 (ptmm) REVERT: H 134 CYS cc_start: 0.8766 (t) cc_final: 0.8538 (t) REVERT: H 144 MET cc_start: 0.8740 (mtp) cc_final: 0.8446 (mtp) REVERT: H 208 GLN cc_start: 0.9468 (mt0) cc_final: 0.9203 (mt0) REVERT: I 54 TYR cc_start: 0.8733 (t80) cc_final: 0.8017 (t80) REVERT: I 99 VAL cc_start: 0.5749 (t) cc_final: 0.5536 (t) REVERT: I 140 SER cc_start: 0.9213 (t) cc_final: 0.8826 (t) REVERT: I 205 GLU cc_start: 0.9243 (mm-30) cc_final: 0.8729 (tp30) REVERT: I 223 TYR cc_start: 0.8485 (t80) cc_final: 0.8258 (t80) REVERT: J 85 ILE cc_start: 0.9083 (mt) cc_final: 0.8876 (mt) REVERT: J 93 VAL cc_start: 0.8406 (t) cc_final: 0.7618 (p) REVERT: J 97 MET cc_start: 0.8578 (pmm) cc_final: 0.8173 (pmm) REVERT: J 106 MET cc_start: 0.6257 (ppp) cc_final: 0.6011 (ppp) REVERT: J 114 PHE cc_start: 0.8518 (t80) cc_final: 0.8244 (t80) REVERT: J 116 LEU cc_start: 0.9233 (tp) cc_final: 0.8869 (tp) REVERT: J 130 THR cc_start: 0.6952 (p) cc_final: 0.6530 (p) REVERT: J 241 HIS cc_start: 0.6592 (t-90) cc_final: 0.6233 (t70) REVERT: J 300 TRP cc_start: 0.8932 (t-100) cc_final: 0.8542 (t-100) REVERT: J 304 HIS cc_start: 0.8772 (t70) cc_final: 0.8229 (t70) outliers start: 7 outliers final: 2 residues processed: 762 average time/residue: 0.1935 time to fit residues: 234.1792 Evaluate side-chains 524 residues out of total 3405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 521 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 62 optimal weight: 0.4980 chunk 304 optimal weight: 0.6980 chunk 129 optimal weight: 3.9990 chunk 258 optimal weight: 2.9990 chunk 110 optimal weight: 0.0070 chunk 354 optimal weight: 6.9990 chunk 97 optimal weight: 0.6980 chunk 351 optimal weight: 9.9990 chunk 6 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 102 optimal weight: 0.7980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 112 GLN ** X 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 42 HIS ** Y 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 42 HIS A 513 ASN ** A 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 574 ASN E 14 HIS F 128 HIS ** F 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 236 GLN ** G 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 22 HIS ** J 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 298 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.103055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.076956 restraints weight = 119461.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.077896 restraints weight = 75438.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.078448 restraints weight = 54806.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.078932 restraints weight = 46203.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.079051 restraints weight = 40167.237| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30679 Z= 0.145 Angle : 0.617 9.407 41528 Z= 0.328 Chirality : 0.044 0.229 4637 Planarity : 0.005 0.089 5337 Dihedral : 4.677 44.240 4013 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.00 % Favored : 92.97 % Rotamer: Outliers : 0.12 % Allowed : 3.29 % Favored : 96.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.14), residues: 3612 helix: 1.12 (0.13), residues: 1551 sheet: -0.65 (0.30), residues: 321 loop : -1.32 (0.15), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG W 14 TYR 0.036 0.002 TYR C 511 PHE 0.031 0.002 PHE Y 26 TRP 0.023 0.002 TRP Z 46 HIS 0.016 0.001 HIS A 570 Details of bonding type rmsd covalent geometry : bond 0.00317 (30667) covalent geometry : angle 0.61659 (41504) SS BOND : bond 0.00635 ( 12) SS BOND : angle 1.39132 ( 24) hydrogen bonds : bond 0.04658 ( 1281) hydrogen bonds : angle 5.01131 ( 3633) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 3405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 710 time to evaluate : 1.164 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: W 115 GLN cc_start: 0.9209 (mt0) cc_final: 0.8775 (mt0) REVERT: W 132 CYS cc_start: 0.8787 (m) cc_final: 0.8207 (t) REVERT: X 41 TYR cc_start: 0.9206 (m-80) cc_final: 0.8725 (m-80) REVERT: X 42 HIS cc_start: 0.8925 (m90) cc_final: 0.8625 (m90) REVERT: X 58 LYS cc_start: 0.8669 (mmtm) cc_final: 0.8376 (mmtm) REVERT: X 175 ASP cc_start: 0.6439 (p0) cc_final: 0.6223 (p0) REVERT: X 222 GLU cc_start: 0.8487 (tp30) cc_final: 0.8239 (tp30) REVERT: X 288 TYR cc_start: 0.7206 (m-80) cc_final: 0.6458 (m-80) REVERT: X 304 ILE cc_start: 0.8936 (mm) cc_final: 0.8383 (mm) REVERT: Y 42 HIS cc_start: 0.8507 (m90) cc_final: 0.7659 (t-90) REVERT: Y 48 ILE cc_start: 0.9120 (mt) cc_final: 0.8439 (mt) REVERT: Y 50 ASN cc_start: 0.9187 (t0) cc_final: 0.8921 (t0) REVERT: Y 59 MET cc_start: 0.9078 (mpp) cc_final: 0.8752 (mpp) REVERT: Y 116 LEU cc_start: 0.8755 (tp) cc_final: 0.8390 (pp) REVERT: Z 22 SER cc_start: 0.8196 (t) cc_final: 0.7732 (m) REVERT: Z 291 TYR cc_start: 0.8000 (t80) cc_final: 0.7746 (t80) REVERT: A 493 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8441 (pt0) REVERT: A 519 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7900 (tt0) REVERT: A 544 MET cc_start: 0.6409 (ttp) cc_final: 0.5785 (ttt) REVERT: A 584 GLN cc_start: 0.8827 (mt0) cc_final: 0.8504 (mt0) REVERT: A 608 PHE cc_start: 0.8078 (m-80) cc_final: 0.7673 (m-80) REVERT: A 609 MET cc_start: 0.8567 (mtm) cc_final: 0.8309 (mtm) REVERT: A 649 ARG cc_start: 0.8803 (mmt180) cc_final: 0.8474 (mmm160) REVERT: B 519 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8169 (mt-10) REVERT: B 609 MET cc_start: 0.9400 (mtm) cc_final: 0.8947 (mtp) REVERT: C 532 LYS cc_start: 0.9294 (mttt) cc_final: 0.8996 (mmtt) REVERT: C 584 GLN cc_start: 0.9137 (mt0) cc_final: 0.8622 (mt0) REVERT: C 592 TYR cc_start: 0.8876 (t80) cc_final: 0.8363 (t80) REVERT: C 609 MET cc_start: 0.8801 (mtt) cc_final: 0.8561 (mtp) REVERT: C 622 MET cc_start: 0.8466 (tpt) cc_final: 0.8215 (tpt) REVERT: C 665 PHE cc_start: 0.5291 (t80) cc_final: 0.4988 (m-10) REVERT: D 8 GLN cc_start: 0.8532 (mm-40) cc_final: 0.8008 (mp10) REVERT: D 39 VAL cc_start: 0.9507 (t) cc_final: 0.9277 (p) REVERT: D 175 PHE cc_start: 0.7855 (p90) cc_final: 0.7381 (p90) REVERT: D 206 CYS cc_start: 0.9213 (m) cc_final: 0.8949 (m) REVERT: D 325 CYS cc_start: 0.7513 (m) cc_final: 0.7248 (m) REVERT: D 352 ASP cc_start: 0.8903 (p0) cc_final: 0.8428 (p0) REVERT: E 40 ILE cc_start: 0.9412 (mm) cc_final: 0.9196 (mt) REVERT: E 66 MET cc_start: 0.8817 (pmm) cc_final: 0.8609 (pmm) REVERT: E 67 GLN cc_start: 0.9113 (mm-40) cc_final: 0.8386 (mt0) REVERT: E 69 LYS cc_start: 0.8341 (mppt) cc_final: 0.7836 (mppt) REVERT: E 195 MET cc_start: 0.9397 (mmm) cc_final: 0.9087 (mmt) REVERT: E 223 MET cc_start: 0.7360 (mtp) cc_final: 0.7011 (mpp) REVERT: E 257 GLU cc_start: 0.8134 (tp30) cc_final: 0.6940 (tp30) REVERT: E 321 GLU cc_start: 0.8118 (pm20) cc_final: 0.7621 (pm20) REVERT: E 468 LEU cc_start: 0.9518 (tp) cc_final: 0.9308 (tp) REVERT: F 129 HIS cc_start: 0.8203 (t70) cc_final: 0.7485 (t-170) REVERT: F 149 MET cc_start: 0.9202 (mmm) cc_final: 0.8983 (mmm) REVERT: F 152 LEU cc_start: 0.9136 (tp) cc_final: 0.8934 (tp) REVERT: F 170 ASP cc_start: 0.8826 (m-30) cc_final: 0.8516 (t0) REVERT: F 181 VAL cc_start: 0.9451 (t) cc_final: 0.8793 (p) REVERT: F 184 ASP cc_start: 0.8976 (m-30) cc_final: 0.8420 (m-30) REVERT: F 188 ASP cc_start: 0.9058 (m-30) cc_final: 0.8845 (t70) REVERT: F 195 GLU cc_start: 0.8934 (tm-30) cc_final: 0.8621 (tm-30) REVERT: F 209 MET cc_start: 0.9249 (ttp) cc_final: 0.8785 (tmm) REVERT: F 229 LEU cc_start: 0.8876 (mp) cc_final: 0.8557 (tt) REVERT: F 246 LEU cc_start: 0.8803 (mm) cc_final: 0.8556 (tt) REVERT: F 252 GLU cc_start: 0.9048 (tt0) cc_final: 0.8624 (mm-30) REVERT: F 290 LEU cc_start: 0.9162 (mt) cc_final: 0.8890 (mp) REVERT: F 293 MET cc_start: 0.9298 (mpp) cc_final: 0.8820 (mpp) REVERT: F 299 ASN cc_start: 0.8903 (m-40) cc_final: 0.7890 (t0) REVERT: F 301 MET cc_start: 0.8451 (tmm) cc_final: 0.8149 (tmm) REVERT: F 320 ASP cc_start: 0.9390 (m-30) cc_final: 0.8947 (t70) REVERT: G 116 MET cc_start: 0.8959 (mmm) cc_final: 0.8451 (mmm) REVERT: G 129 HIS cc_start: 0.9170 (t-90) cc_final: 0.7965 (t-90) REVERT: G 144 ASP cc_start: 0.9189 (m-30) cc_final: 0.8948 (m-30) REVERT: G 163 LYS cc_start: 0.9096 (tppt) cc_final: 0.7542 (tppt) REVERT: G 184 ASP cc_start: 0.8967 (m-30) cc_final: 0.8720 (m-30) REVERT: G 188 ASP cc_start: 0.9307 (m-30) cc_final: 0.9007 (t0) REVERT: G 252 GLU cc_start: 0.9116 (mt-10) cc_final: 0.8743 (mt-10) REVERT: G 273 ASP cc_start: 0.8366 (m-30) cc_final: 0.7567 (p0) REVERT: G 294 TYR cc_start: 0.8996 (m-80) cc_final: 0.8506 (m-80) REVERT: G 315 LYS cc_start: 0.9154 (mmpt) cc_final: 0.8840 (mmmt) REVERT: H 22 ILE cc_start: 0.8269 (tp) cc_final: 0.7722 (tp) REVERT: H 40 GLU cc_start: 0.9250 (mm-30) cc_final: 0.8884 (mm-30) REVERT: H 70 ILE cc_start: 0.9130 (mt) cc_final: 0.8907 (mt) REVERT: H 134 CYS cc_start: 0.8788 (t) cc_final: 0.8453 (t) REVERT: H 208 GLN cc_start: 0.9410 (mt0) cc_final: 0.9156 (mt0) REVERT: H 238 LEU cc_start: 0.9424 (mt) cc_final: 0.9189 (mt) REVERT: H 249 ARG cc_start: 0.8498 (ptt-90) cc_final: 0.7702 (mpp-170) REVERT: I 51 LEU cc_start: 0.9507 (tp) cc_final: 0.9114 (pp) REVERT: I 52 SER cc_start: 0.9335 (m) cc_final: 0.8911 (m) REVERT: I 54 TYR cc_start: 0.8501 (t80) cc_final: 0.8040 (t80) REVERT: I 137 ASP cc_start: 0.9020 (t0) cc_final: 0.8812 (t0) REVERT: I 140 SER cc_start: 0.9216 (t) cc_final: 0.8767 (t) REVERT: I 141 ILE cc_start: 0.9325 (mm) cc_final: 0.9094 (pt) REVERT: I 144 MET cc_start: 0.8559 (tpp) cc_final: 0.8269 (mmt) REVERT: I 205 GLU cc_start: 0.9245 (mm-30) cc_final: 0.8710 (tp30) REVERT: I 212 LEU cc_start: 0.9385 (mp) cc_final: 0.9177 (mp) REVERT: J 106 MET cc_start: 0.6077 (ppp) cc_final: 0.5859 (ppp) REVERT: J 116 LEU cc_start: 0.9296 (tp) cc_final: 0.8831 (tp) REVERT: J 265 VAL cc_start: 0.9133 (t) cc_final: 0.8725 (t) REVERT: J 300 TRP cc_start: 0.8894 (t-100) cc_final: 0.8534 (t-100) outliers start: 4 outliers final: 2 residues processed: 714 average time/residue: 0.1889 time to fit residues: 216.7083 Evaluate side-chains 511 residues out of total 3405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 509 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 164 optimal weight: 2.9990 chunk 67 optimal weight: 7.9990 chunk 65 optimal weight: 0.7980 chunk 155 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 190 optimal weight: 0.1980 chunk 35 optimal weight: 0.7980 chunk 34 optimal weight: 0.0170 chunk 22 optimal weight: 0.9990 chunk 241 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 73 GLN ** Y 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 678 GLN ** C 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 571 GLN D 263 GLN E 464 GLN F 128 HIS ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 313 ASN ** G 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 22 HIS ** J 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 247 ASN ** J 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 298 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.103121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.076772 restraints weight = 117955.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.078318 restraints weight = 66169.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.078786 restraints weight = 43337.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.079198 restraints weight = 40736.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.079339 restraints weight = 35866.708| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.4322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30679 Z= 0.148 Angle : 0.618 9.522 41528 Z= 0.327 Chirality : 0.044 0.332 4637 Planarity : 0.005 0.086 5337 Dihedral : 4.725 45.382 4013 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.95 % Favored : 93.00 % Rotamer: Outliers : 0.03 % Allowed : 2.47 % Favored : 97.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.14), residues: 3612 helix: 1.04 (0.13), residues: 1547 sheet: -0.53 (0.30), residues: 311 loop : -1.34 (0.15), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 210 TYR 0.025 0.002 TYR G 321 PHE 0.025 0.002 PHE C 548 TRP 0.021 0.002 TRP J 113 HIS 0.014 0.001 HIS A 570 Details of bonding type rmsd covalent geometry : bond 0.00325 (30667) covalent geometry : angle 0.61716 (41504) SS BOND : bond 0.00201 ( 12) SS BOND : angle 1.40718 ( 24) hydrogen bonds : bond 0.04492 ( 1281) hydrogen bonds : angle 4.88426 ( 3633) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 3405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 680 time to evaluate : 1.191 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 78 ILE cc_start: 0.8722 (tp) cc_final: 0.8218 (tp) REVERT: W 115 GLN cc_start: 0.9189 (mt0) cc_final: 0.8701 (mt0) REVERT: W 132 CYS cc_start: 0.8992 (m) cc_final: 0.8332 (t) REVERT: W 204 LEU cc_start: 0.9447 (mt) cc_final: 0.9062 (tt) REVERT: X 41 TYR cc_start: 0.9214 (m-80) cc_final: 0.8666 (m-10) REVERT: X 42 HIS cc_start: 0.8968 (m90) cc_final: 0.8663 (m90) REVERT: X 58 LYS cc_start: 0.8631 (mmtm) cc_final: 0.8301 (mmtm) REVERT: X 222 GLU cc_start: 0.8506 (tp30) cc_final: 0.8205 (tp30) REVERT: X 286 SER cc_start: 0.8297 (t) cc_final: 0.8044 (p) REVERT: X 288 TYR cc_start: 0.6909 (m-80) cc_final: 0.6004 (m-80) REVERT: Y 42 HIS cc_start: 0.8513 (m90) cc_final: 0.7677 (t-90) REVERT: Y 48 ILE cc_start: 0.9119 (mt) cc_final: 0.8327 (mm) REVERT: Y 50 ASN cc_start: 0.9214 (t0) cc_final: 0.8976 (t0) REVERT: Z 22 SER cc_start: 0.8128 (t) cc_final: 0.7684 (m) REVERT: Z 75 LYS cc_start: 0.7221 (ptpt) cc_final: 0.7000 (ptmt) REVERT: A 493 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8356 (tt0) REVERT: A 519 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7788 (tt0) REVERT: A 544 MET cc_start: 0.6318 (ttp) cc_final: 0.5802 (ttt) REVERT: A 608 PHE cc_start: 0.8165 (m-80) cc_final: 0.7750 (m-80) REVERT: A 609 MET cc_start: 0.8522 (mtm) cc_final: 0.8282 (mtm) REVERT: A 641 ARG cc_start: 0.8215 (ttt90) cc_final: 0.7728 (mtm110) REVERT: A 649 ARG cc_start: 0.8813 (mmt180) cc_final: 0.8490 (mmm160) REVERT: B 519 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8118 (mt-10) REVERT: B 609 MET cc_start: 0.9393 (mtm) cc_final: 0.8948 (mtp) REVERT: B 611 MET cc_start: 0.8987 (mmm) cc_final: 0.8582 (mmm) REVERT: B 615 LYS cc_start: 0.9291 (mttt) cc_final: 0.8996 (tttt) REVERT: C 584 GLN cc_start: 0.9184 (mt0) cc_final: 0.8713 (mt0) REVERT: C 592 TYR cc_start: 0.8867 (t80) cc_final: 0.8495 (t80) REVERT: C 609 MET cc_start: 0.8786 (mtt) cc_final: 0.8558 (mtp) REVERT: C 622 MET cc_start: 0.8485 (tpt) cc_final: 0.8196 (tpt) REVERT: C 665 PHE cc_start: 0.5324 (t80) cc_final: 0.5066 (m-10) REVERT: D 8 GLN cc_start: 0.8568 (mm-40) cc_final: 0.8114 (mp10) REVERT: D 39 VAL cc_start: 0.9476 (t) cc_final: 0.9233 (p) REVERT: D 175 PHE cc_start: 0.7856 (p90) cc_final: 0.7347 (p90) REVERT: D 206 CYS cc_start: 0.9236 (m) cc_final: 0.9010 (m) REVERT: D 352 ASP cc_start: 0.8940 (p0) cc_final: 0.8448 (p0) REVERT: E 40 ILE cc_start: 0.9443 (mm) cc_final: 0.9236 (mt) REVERT: E 67 GLN cc_start: 0.9095 (mm-40) cc_final: 0.8787 (mt0) REVERT: E 223 MET cc_start: 0.7438 (mtp) cc_final: 0.6950 (mpp) REVERT: E 257 GLU cc_start: 0.8032 (tp30) cc_final: 0.6629 (tp30) REVERT: E 318 MET cc_start: 0.4178 (mpp) cc_final: 0.3860 (mmt) REVERT: E 321 GLU cc_start: 0.8151 (pm20) cc_final: 0.7659 (pm20) REVERT: F 129 HIS cc_start: 0.8168 (t70) cc_final: 0.7232 (t70) REVERT: F 152 LEU cc_start: 0.9179 (tp) cc_final: 0.8915 (tp) REVERT: F 170 ASP cc_start: 0.8849 (m-30) cc_final: 0.8495 (t0) REVERT: F 188 ASP cc_start: 0.9062 (m-30) cc_final: 0.8832 (t70) REVERT: F 195 GLU cc_start: 0.8950 (tm-30) cc_final: 0.8707 (tm-30) REVERT: F 209 MET cc_start: 0.9173 (ttp) cc_final: 0.8922 (tmm) REVERT: F 229 LEU cc_start: 0.8984 (mp) cc_final: 0.8511 (tt) REVERT: F 246 LEU cc_start: 0.8871 (mm) cc_final: 0.8644 (tt) REVERT: F 252 GLU cc_start: 0.9056 (tt0) cc_final: 0.8615 (mm-30) REVERT: F 290 LEU cc_start: 0.9041 (mt) cc_final: 0.8804 (mp) REVERT: F 299 ASN cc_start: 0.8576 (m-40) cc_final: 0.8026 (t0) REVERT: F 301 MET cc_start: 0.8565 (tmm) cc_final: 0.8179 (tmm) REVERT: G 116 MET cc_start: 0.8943 (mmm) cc_final: 0.8565 (mmt) REVERT: G 129 HIS cc_start: 0.9144 (t-90) cc_final: 0.8167 (t-90) REVERT: G 144 ASP cc_start: 0.9122 (m-30) cc_final: 0.8905 (m-30) REVERT: G 181 VAL cc_start: 0.9531 (t) cc_final: 0.9232 (p) REVERT: G 184 ASP cc_start: 0.9000 (m-30) cc_final: 0.8777 (m-30) REVERT: G 188 ASP cc_start: 0.9289 (m-30) cc_final: 0.9009 (t0) REVERT: G 208 ILE cc_start: 0.9332 (tp) cc_final: 0.8959 (pt) REVERT: G 252 GLU cc_start: 0.9047 (mt-10) cc_final: 0.8843 (mt-10) REVERT: G 273 ASP cc_start: 0.8341 (m-30) cc_final: 0.7538 (p0) REVERT: G 293 MET cc_start: 0.9052 (mtm) cc_final: 0.8445 (mpp) REVERT: G 294 TYR cc_start: 0.9022 (m-80) cc_final: 0.8612 (m-80) REVERT: G 315 LYS cc_start: 0.9224 (mmpt) cc_final: 0.8887 (mmmt) REVERT: H 40 GLU cc_start: 0.9237 (mm-30) cc_final: 0.8878 (mm-30) REVERT: H 70 ILE cc_start: 0.9157 (mt) cc_final: 0.8905 (mm) REVERT: H 134 CYS cc_start: 0.8753 (t) cc_final: 0.8504 (t) REVERT: H 208 GLN cc_start: 0.9474 (mt0) cc_final: 0.9208 (mt0) REVERT: H 213 LEU cc_start: 0.9423 (mt) cc_final: 0.9170 (mt) REVERT: H 223 TYR cc_start: 0.8828 (t80) cc_final: 0.8562 (t80) REVERT: H 238 LEU cc_start: 0.9505 (mt) cc_final: 0.8998 (mt) REVERT: I 51 LEU cc_start: 0.9486 (tp) cc_final: 0.9071 (pp) REVERT: I 52 SER cc_start: 0.9316 (m) cc_final: 0.8876 (m) REVERT: I 137 ASP cc_start: 0.8932 (t0) cc_final: 0.8598 (t0) REVERT: I 140 SER cc_start: 0.9315 (t) cc_final: 0.8815 (p) REVERT: I 205 GLU cc_start: 0.9226 (mm-30) cc_final: 0.8681 (tp30) REVERT: J 10 ILE cc_start: 0.8879 (mm) cc_final: 0.8605 (mt) REVERT: J 97 MET cc_start: 0.8523 (pmm) cc_final: 0.8087 (pmm) REVERT: J 114 PHE cc_start: 0.8216 (t80) cc_final: 0.7984 (t80) REVERT: J 116 LEU cc_start: 0.9280 (tp) cc_final: 0.8977 (tp) REVERT: J 118 HIS cc_start: 0.5863 (p-80) cc_final: 0.5610 (p-80) REVERT: J 241 HIS cc_start: 0.6019 (t-90) cc_final: 0.5635 (t70) REVERT: J 300 TRP cc_start: 0.8826 (t-100) cc_final: 0.8458 (t-100) REVERT: J 304 HIS cc_start: 0.8673 (t70) cc_final: 0.8292 (t70) outliers start: 1 outliers final: 0 residues processed: 681 average time/residue: 0.1905 time to fit residues: 208.6461 Evaluate side-chains 501 residues out of total 3405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 501 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 350 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 243 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 280 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 233 optimal weight: 0.9990 chunk 151 optimal weight: 0.9990 chunk 320 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 589 ASN D 263 GLN ** F 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 22 HIS ** J 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 264 ASN ** 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 = 0.3839 r_free = 0.3839 target = 0.101158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.074070 restraints weight = 121729.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.076784 restraints weight = 70921.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.077412 restraints weight = 42298.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.077852 restraints weight = 35753.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.077902 restraints weight = 33387.448| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.4601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 30679 Z= 0.201 Angle : 0.655 10.278 41528 Z= 0.347 Chirality : 0.044 0.295 4637 Planarity : 0.005 0.089 5337 Dihedral : 4.902 49.965 4013 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.53 % Favored : 92.41 % Rotamer: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.14), residues: 3612 helix: 0.84 (0.13), residues: 1547 sheet: -0.49 (0.30), residues: 312 loop : -1.33 (0.15), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 210 TYR 0.030 0.002 TYR F 303 PHE 0.017 0.002 PHE C 548 TRP 0.012 0.002 TRP J 113 HIS 0.012 0.001 HIS W 52 Details of bonding type rmsd covalent geometry : bond 0.00439 (30667) covalent geometry : angle 0.65447 (41504) SS BOND : bond 0.00365 ( 12) SS BOND : angle 1.39264 ( 24) hydrogen bonds : bond 0.04505 ( 1281) hydrogen bonds : angle 4.96519 ( 3633) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 3405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 641 time to evaluate : 1.169 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: symmetry clash revert: symmetry clash REVERT: W 62 MET cc_start: 0.8342 (pmm) cc_final: 0.7953 (pmm) REVERT: W 71 ASP cc_start: 0.6210 (t0) cc_final: 0.5998 (m-30) REVERT: W 115 GLN cc_start: 0.9248 (mt0) cc_final: 0.8913 (mp10) REVERT: W 132 CYS cc_start: 0.8975 (m) cc_final: 0.8327 (t) REVERT: X 41 TYR cc_start: 0.9242 (m-80) cc_final: 0.8672 (m-10) REVERT: X 42 HIS cc_start: 0.9002 (m90) cc_final: 0.8511 (m90) REVERT: X 58 LYS cc_start: 0.8681 (mmtm) cc_final: 0.8434 (mmtm) REVERT: X 179 PHE cc_start: 0.8595 (m-80) cc_final: 0.8386 (m-80) REVERT: X 222 GLU cc_start: 0.8437 (tp30) cc_final: 0.8227 (tp30) REVERT: X 286 SER cc_start: 0.8360 (t) cc_final: 0.8124 (p) REVERT: X 288 TYR cc_start: 0.6939 (m-80) cc_final: 0.5742 (m-10) REVERT: Y 48 ILE cc_start: 0.8900 (mt) cc_final: 0.8175 (mm) REVERT: Y 55 LYS cc_start: 0.8959 (mtmm) cc_final: 0.8555 (ptpt) REVERT: Y 59 MET cc_start: 0.8460 (mpp) cc_final: 0.8082 (mpp) REVERT: Y 111 MET cc_start: 0.8102 (tmm) cc_final: 0.7723 (tmm) REVERT: Y 153 TYR cc_start: 0.8854 (t80) cc_final: 0.8590 (t80) REVERT: Y 207 LEU cc_start: 0.9293 (pp) cc_final: 0.9056 (pp) REVERT: Z 22 SER cc_start: 0.7880 (t) cc_final: 0.7495 (m) REVERT: Z 110 MET cc_start: 0.7925 (pmm) cc_final: 0.7434 (pmm) REVERT: A 493 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8368 (tt0) REVERT: A 544 MET cc_start: 0.6448 (ttp) cc_final: 0.6170 (ttt) REVERT: A 584 GLN cc_start: 0.8834 (mt0) cc_final: 0.8507 (mt0) REVERT: A 608 PHE cc_start: 0.8119 (m-80) cc_final: 0.7665 (m-80) REVERT: A 609 MET cc_start: 0.8430 (mtm) cc_final: 0.8223 (mtm) REVERT: A 641 ARG cc_start: 0.8221 (ttt90) cc_final: 0.7826 (mtm-85) REVERT: A 649 ARG cc_start: 0.8816 (mmt180) cc_final: 0.8434 (mmm160) REVERT: B 519 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8025 (mt-10) REVERT: B 549 TYR cc_start: 0.8841 (t80) cc_final: 0.8546 (t80) REVERT: B 609 MET cc_start: 0.9394 (mtm) cc_final: 0.9005 (mtp) REVERT: B 622 MET cc_start: 0.8777 (mmm) cc_final: 0.8213 (mmm) REVERT: C 532 LYS cc_start: 0.9308 (mttt) cc_final: 0.8976 (mmtt) REVERT: C 545 ASN cc_start: 0.9475 (t0) cc_final: 0.8824 (t0) REVERT: C 584 GLN cc_start: 0.9088 (mt0) cc_final: 0.8600 (mt0) REVERT: C 622 MET cc_start: 0.8473 (tpt) cc_final: 0.8213 (tpt) REVERT: D 8 GLN cc_start: 0.8610 (mm-40) cc_final: 0.8172 (mp10) REVERT: D 39 VAL cc_start: 0.9499 (t) cc_final: 0.9248 (p) REVERT: D 206 CYS cc_start: 0.9186 (m) cc_final: 0.8967 (m) REVERT: D 352 ASP cc_start: 0.9041 (p0) cc_final: 0.8630 (p0) REVERT: E 40 ILE cc_start: 0.9449 (mm) cc_final: 0.9231 (mt) REVERT: E 69 LYS cc_start: 0.8334 (mppt) cc_final: 0.8089 (mppt) REVERT: E 195 MET cc_start: 0.9209 (mmt) cc_final: 0.8930 (mmm) REVERT: E 223 MET cc_start: 0.7398 (mtp) cc_final: 0.6827 (mpp) REVERT: E 257 GLU cc_start: 0.8086 (tp30) cc_final: 0.6583 (tp30) REVERT: E 279 ASP cc_start: 0.8349 (m-30) cc_final: 0.7941 (m-30) REVERT: E 318 MET cc_start: 0.4364 (mpp) cc_final: 0.3970 (mmt) REVERT: E 321 GLU cc_start: 0.8246 (pm20) cc_final: 0.7716 (pm20) REVERT: E 378 ARG cc_start: 0.8829 (mtm-85) cc_final: 0.8429 (mtt90) REVERT: F 129 HIS cc_start: 0.8177 (t70) cc_final: 0.6558 (t-170) REVERT: F 170 ASP cc_start: 0.8819 (m-30) cc_final: 0.8597 (t0) REVERT: F 184 ASP cc_start: 0.9008 (m-30) cc_final: 0.8551 (m-30) REVERT: F 188 ASP cc_start: 0.9064 (m-30) cc_final: 0.8847 (t70) REVERT: F 195 GLU cc_start: 0.8959 (tm-30) cc_final: 0.8697 (tm-30) REVERT: F 209 MET cc_start: 0.9161 (ttp) cc_final: 0.8883 (tmm) REVERT: F 246 LEU cc_start: 0.9027 (mm) cc_final: 0.8728 (tt) REVERT: F 252 GLU cc_start: 0.8978 (tt0) cc_final: 0.8596 (mm-30) REVERT: F 290 LEU cc_start: 0.9015 (mt) cc_final: 0.8798 (mp) REVERT: F 299 ASN cc_start: 0.8696 (m-40) cc_final: 0.8182 (t0) REVERT: F 301 MET cc_start: 0.8629 (tmm) cc_final: 0.8294 (tmm) REVERT: F 320 ASP cc_start: 0.9401 (m-30) cc_final: 0.9099 (t70) REVERT: F 328 MET cc_start: 0.6235 (ttm) cc_final: 0.5875 (tpp) REVERT: G 116 MET cc_start: 0.8938 (mmm) cc_final: 0.8368 (mmm) REVERT: G 129 HIS cc_start: 0.9050 (t-90) cc_final: 0.8069 (t-90) REVERT: G 147 MET cc_start: 0.8814 (mtm) cc_final: 0.8561 (mtt) REVERT: G 184 ASP cc_start: 0.8963 (m-30) cc_final: 0.8626 (m-30) REVERT: G 188 ASP cc_start: 0.9260 (m-30) cc_final: 0.9002 (t0) REVERT: G 252 GLU cc_start: 0.9108 (mt-10) cc_final: 0.8681 (mt-10) REVERT: G 253 LYS cc_start: 0.9317 (mppt) cc_final: 0.9030 (mmtm) REVERT: G 273 ASP cc_start: 0.8445 (m-30) cc_final: 0.7594 (p0) REVERT: G 294 TYR cc_start: 0.8891 (m-80) cc_final: 0.8568 (m-80) REVERT: H 70 ILE cc_start: 0.9210 (mt) cc_final: 0.8953 (mm) REVERT: H 134 CYS cc_start: 0.8651 (t) cc_final: 0.8336 (t) REVERT: H 208 GLN cc_start: 0.9468 (mt0) cc_final: 0.9257 (mt0) REVERT: I 51 LEU cc_start: 0.9506 (tp) cc_final: 0.9189 (pp) REVERT: I 52 SER cc_start: 0.9335 (m) cc_final: 0.8883 (m) REVERT: I 134 CYS cc_start: 0.6921 (t) cc_final: 0.6659 (t) REVERT: I 140 SER cc_start: 0.9334 (t) cc_final: 0.9035 (t) REVERT: I 144 MET cc_start: 0.8582 (tpp) cc_final: 0.8353 (mmt) REVERT: I 205 GLU cc_start: 0.9196 (mm-30) cc_final: 0.8638 (tp30) REVERT: J 97 MET cc_start: 0.8282 (pmm) cc_final: 0.7746 (pmm) REVERT: J 114 PHE cc_start: 0.8687 (t80) cc_final: 0.8296 (t80) REVERT: J 116 LEU cc_start: 0.9236 (tp) cc_final: 0.8680 (pp) REVERT: J 300 TRP cc_start: 0.8973 (t-100) cc_final: 0.8555 (t-100) outliers start: 0 outliers final: 0 residues processed: 641 average time/residue: 0.1918 time to fit residues: 198.7234 Evaluate side-chains 469 residues out of total 3405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 469 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 272 optimal weight: 0.6980 chunk 110 optimal weight: 4.9990 chunk 180 optimal weight: 2.9990 chunk 270 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 290 optimal weight: 2.9990 chunk 211 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 227 optimal weight: 0.4980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 42 HIS Y 50 ASN ** Y 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 ASN ** J 264 ASN ** 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 = 0.3830 r_free = 0.3830 target = 0.100743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.074503 restraints weight = 121429.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.076651 restraints weight = 67439.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.076910 restraints weight = 43738.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.077180 restraints weight = 40099.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.077278 restraints weight = 36454.365| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.4861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 30679 Z= 0.205 Angle : 0.658 10.322 41528 Z= 0.349 Chirality : 0.045 0.256 4637 Planarity : 0.005 0.085 5337 Dihedral : 5.046 59.391 4013 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.75 % Favored : 92.19 % Rotamer: Outliers : 0.03 % Allowed : 2.58 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.14), residues: 3612 helix: 0.71 (0.13), residues: 1547 sheet: -0.55 (0.30), residues: 310 loop : -1.36 (0.15), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 210 TYR 0.028 0.002 TYR E 62 PHE 0.042 0.002 PHE I 90 TRP 0.013 0.002 TRP D 235 HIS 0.013 0.002 HIS B 570 Details of bonding type rmsd covalent geometry : bond 0.00450 (30667) covalent geometry : angle 0.65651 (41504) SS BOND : bond 0.00377 ( 12) SS BOND : angle 1.65170 ( 24) hydrogen bonds : bond 0.04505 ( 1281) hydrogen bonds : angle 5.02008 ( 3633) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 3405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 619 time to evaluate : 1.063 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: W 62 MET cc_start: 0.8337 (pmm) cc_final: 0.7812 (pmm) REVERT: W 71 ASP cc_start: 0.6662 (t0) cc_final: 0.6352 (m-30) REVERT: W 115 GLN cc_start: 0.9255 (mt0) cc_final: 0.8917 (mp10) REVERT: W 132 CYS cc_start: 0.8779 (m) cc_final: 0.8180 (t) REVERT: X 41 TYR cc_start: 0.9252 (m-80) cc_final: 0.8718 (m-10) REVERT: X 58 LYS cc_start: 0.8772 (mmtm) cc_final: 0.8406 (mmtp) REVERT: X 137 TYR cc_start: 0.8301 (m-10) cc_final: 0.6257 (t80) REVERT: X 175 ASP cc_start: 0.6592 (p0) cc_final: 0.6307 (p0) REVERT: X 286 SER cc_start: 0.8372 (t) cc_final: 0.8085 (p) REVERT: X 288 TYR cc_start: 0.6993 (m-80) cc_final: 0.5864 (m-80) REVERT: X 304 ILE cc_start: 0.9189 (mm) cc_final: 0.8524 (mm) REVERT: Y 48 ILE cc_start: 0.8970 (mt) cc_final: 0.8309 (mm) REVERT: Y 55 LYS cc_start: 0.8933 (mtmm) cc_final: 0.8405 (ptpp) REVERT: Y 111 MET cc_start: 0.8155 (tmm) cc_final: 0.7721 (tmm) REVERT: Y 236 GLU cc_start: 0.8239 (tp30) cc_final: 0.7689 (tp30) REVERT: Z 22 SER cc_start: 0.7868 (t) cc_final: 0.7474 (m) REVERT: A 544 MET cc_start: 0.6103 (ttt) cc_final: 0.5445 (ttt) REVERT: A 584 GLN cc_start: 0.8812 (mt0) cc_final: 0.8497 (mt0) REVERT: A 608 PHE cc_start: 0.8137 (m-80) cc_final: 0.7731 (m-80) REVERT: A 609 MET cc_start: 0.8442 (mtm) cc_final: 0.8208 (mtm) REVERT: A 641 ARG cc_start: 0.8268 (ttt90) cc_final: 0.7973 (mtp85) REVERT: A 649 ARG cc_start: 0.8849 (mmt180) cc_final: 0.8470 (mmm160) REVERT: B 519 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8090 (mt-10) REVERT: B 609 MET cc_start: 0.9334 (mtm) cc_final: 0.9011 (mtp) REVERT: B 611 MET cc_start: 0.8766 (mmm) cc_final: 0.8346 (mmm) REVERT: B 622 MET cc_start: 0.8760 (mmm) cc_final: 0.8512 (mmm) REVERT: C 518 LEU cc_start: 0.8700 (mt) cc_final: 0.8295 (tp) REVERT: C 532 LYS cc_start: 0.9317 (mttt) cc_final: 0.8987 (mmtm) REVERT: C 584 GLN cc_start: 0.9092 (mt0) cc_final: 0.8633 (mt0) REVERT: C 622 MET cc_start: 0.8631 (tpt) cc_final: 0.8347 (tpt) REVERT: D 8 GLN cc_start: 0.8571 (mm-40) cc_final: 0.8174 (mp10) REVERT: D 39 VAL cc_start: 0.9506 (t) cc_final: 0.9249 (p) REVERT: D 206 CYS cc_start: 0.9212 (m) cc_final: 0.8982 (m) REVERT: D 352 ASP cc_start: 0.9094 (p0) cc_final: 0.8676 (p0) REVERT: E 40 ILE cc_start: 0.9459 (mm) cc_final: 0.9242 (mt) REVERT: E 66 MET cc_start: 0.8904 (pmm) cc_final: 0.8672 (pmm) REVERT: E 67 GLN cc_start: 0.9218 (mm-40) cc_final: 0.8981 (mt0) REVERT: E 171 VAL cc_start: 0.7785 (m) cc_final: 0.7506 (m) REVERT: E 223 MET cc_start: 0.7400 (mtp) cc_final: 0.6883 (mpp) REVERT: E 257 GLU cc_start: 0.8133 (tp30) cc_final: 0.6619 (tp30) REVERT: E 421 ASP cc_start: 0.8596 (t70) cc_final: 0.7738 (p0) REVERT: F 129 HIS cc_start: 0.8270 (t70) cc_final: 0.7112 (t-170) REVERT: F 170 ASP cc_start: 0.8940 (m-30) cc_final: 0.8655 (t0) REVERT: F 188 ASP cc_start: 0.9097 (m-30) cc_final: 0.8872 (t70) REVERT: F 194 LEU cc_start: 0.9445 (mt) cc_final: 0.9098 (tp) REVERT: F 209 MET cc_start: 0.9208 (ttp) cc_final: 0.8823 (tmm) REVERT: F 229 LEU cc_start: 0.8726 (mm) cc_final: 0.8002 (tp) REVERT: F 246 LEU cc_start: 0.9068 (mm) cc_final: 0.8711 (tt) REVERT: F 252 GLU cc_start: 0.8928 (tt0) cc_final: 0.8417 (mm-30) REVERT: F 256 MET cc_start: 0.7262 (tpt) cc_final: 0.6659 (ppp) REVERT: F 290 LEU cc_start: 0.9060 (mt) cc_final: 0.8839 (mp) REVERT: F 299 ASN cc_start: 0.8718 (m-40) cc_final: 0.8125 (t0) REVERT: F 301 MET cc_start: 0.8585 (tmm) cc_final: 0.8193 (tmm) REVERT: F 328 MET cc_start: 0.5886 (ttm) cc_final: 0.5300 (tpp) REVERT: G 116 MET cc_start: 0.8931 (mmm) cc_final: 0.8579 (mmt) REVERT: G 144 ASP cc_start: 0.9140 (m-30) cc_final: 0.8920 (m-30) REVERT: G 147 MET cc_start: 0.8778 (mtm) cc_final: 0.8528 (mtt) REVERT: G 162 PHE cc_start: 0.9276 (t80) cc_final: 0.8983 (t80) REVERT: G 181 VAL cc_start: 0.9540 (t) cc_final: 0.9231 (p) REVERT: G 184 ASP cc_start: 0.9012 (m-30) cc_final: 0.8712 (m-30) REVERT: G 252 GLU cc_start: 0.9093 (mt-10) cc_final: 0.8702 (mt-10) REVERT: G 253 LYS cc_start: 0.9278 (mppt) cc_final: 0.9017 (mmtm) REVERT: G 273 ASP cc_start: 0.8446 (m-30) cc_final: 0.7598 (p0) REVERT: G 293 MET cc_start: 0.9013 (mtm) cc_final: 0.8503 (mpp) REVERT: G 294 TYR cc_start: 0.8901 (m-80) cc_final: 0.8617 (m-80) REVERT: G 315 LYS cc_start: 0.9287 (mmpt) cc_final: 0.9060 (mmmt) REVERT: H 43 GLU cc_start: 0.8972 (mp0) cc_final: 0.8742 (mp0) REVERT: H 134 CYS cc_start: 0.8760 (t) cc_final: 0.8428 (t) REVERT: H 208 GLN cc_start: 0.9443 (mt0) cc_final: 0.9014 (mm-40) REVERT: H 249 ARG cc_start: 0.7397 (mpp-170) cc_final: 0.6089 (tpt170) REVERT: I 51 LEU cc_start: 0.9472 (tp) cc_final: 0.9141 (pp) REVERT: I 80 ILE cc_start: 0.8541 (pt) cc_final: 0.8327 (pt) REVERT: I 140 SER cc_start: 0.9362 (t) cc_final: 0.9054 (t) REVERT: I 147 ARG cc_start: 0.6666 (ttt-90) cc_final: 0.6444 (ttp80) REVERT: I 205 GLU cc_start: 0.9196 (mm-30) cc_final: 0.8640 (tp30) REVERT: J 97 MET cc_start: 0.8447 (pmm) cc_final: 0.7891 (pmm) REVERT: J 116 LEU cc_start: 0.9228 (tp) cc_final: 0.8744 (pp) REVERT: J 118 HIS cc_start: 0.5830 (p-80) cc_final: 0.5579 (p-80) REVERT: J 166 LEU cc_start: 0.9139 (mt) cc_final: 0.8871 (mt) REVERT: J 241 HIS cc_start: 0.6113 (t-90) cc_final: 0.5675 (t70) REVERT: J 300 TRP cc_start: 0.8958 (t-100) cc_final: 0.8528 (t-100) REVERT: J 304 HIS cc_start: 0.8937 (t70) cc_final: 0.8533 (t70) outliers start: 1 outliers final: 1 residues processed: 620 average time/residue: 0.1901 time to fit residues: 191.3515 Evaluate side-chains 460 residues out of total 3405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 459 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 234 optimal weight: 0.1980 chunk 343 optimal weight: 5.9990 chunk 134 optimal weight: 0.1980 chunk 192 optimal weight: 0.8980 chunk 357 optimal weight: 0.6980 chunk 176 optimal weight: 1.9990 chunk 232 optimal weight: 0.2980 chunk 142 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 346 optimal weight: 0.7980 chunk 159 optimal weight: 0.9980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 42 HIS ** Y 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 ASN ** B 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 ASN ** J 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 264 ASN ** 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 = 0.3870 r_free = 0.3870 target = 0.102777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.076127 restraints weight = 119117.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.078092 restraints weight = 73442.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.079066 restraints weight = 47996.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.079729 restraints weight = 38087.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.079821 restraints weight = 34409.957| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.5142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30679 Z= 0.130 Angle : 0.626 9.385 41528 Z= 0.331 Chirality : 0.044 0.222 4637 Planarity : 0.004 0.092 5337 Dihedral : 4.895 59.140 4013 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.87 % Favored : 93.11 % Rotamer: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.14), residues: 3612 helix: 0.84 (0.13), residues: 1536 sheet: -0.55 (0.30), residues: 327 loop : -1.33 (0.15), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 124 TYR 0.024 0.002 TYR G 224 PHE 0.031 0.001 PHE I 90 TRP 0.012 0.002 TRP E 462 HIS 0.013 0.001 HIS I 222 Details of bonding type rmsd covalent geometry : bond 0.00282 (30667) covalent geometry : angle 0.62425 (41504) SS BOND : bond 0.00736 ( 12) SS BOND : angle 1.78322 ( 24) hydrogen bonds : bond 0.04262 ( 1281) hydrogen bonds : angle 4.83592 ( 3633) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 3405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 640 time to evaluate : 1.182 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: symmetry clash REVERT: W 62 MET cc_start: 0.8312 (pmm) cc_final: 0.7661 (pmm) REVERT: W 71 ASP cc_start: 0.6364 (t0) cc_final: 0.6081 (m-30) REVERT: W 114 GLU cc_start: 0.9097 (mp0) cc_final: 0.8759 (mp0) REVERT: W 132 CYS cc_start: 0.8961 (m) cc_final: 0.8318 (t) REVERT: X 41 TYR cc_start: 0.9255 (m-80) cc_final: 0.8697 (m-10) REVERT: X 42 HIS cc_start: 0.9010 (m90) cc_final: 0.8446 (m90) REVERT: X 43 ASP cc_start: 0.8742 (p0) cc_final: 0.8529 (p0) REVERT: X 58 LYS cc_start: 0.8728 (mmtm) cc_final: 0.8161 (mmtp) REVERT: X 91 LYS cc_start: 0.8886 (ptpp) cc_final: 0.8641 (pttm) REVERT: X 137 TYR cc_start: 0.8283 (m-10) cc_final: 0.6085 (t80) REVERT: X 219 ILE cc_start: 0.9018 (mm) cc_final: 0.8653 (mm) REVERT: X 286 SER cc_start: 0.8317 (t) cc_final: 0.8099 (p) REVERT: X 288 TYR cc_start: 0.6646 (m-80) cc_final: 0.5614 (m-80) REVERT: Y 48 ILE cc_start: 0.8967 (mt) cc_final: 0.8569 (mm) REVERT: Y 59 MET cc_start: 0.8338 (mpp) cc_final: 0.8000 (mpp) REVERT: Y 62 MET cc_start: 0.8049 (ptt) cc_final: 0.7782 (mpp) REVERT: Y 111 MET cc_start: 0.7995 (tmm) cc_final: 0.7391 (tmm) REVERT: Y 116 LEU cc_start: 0.8776 (tp) cc_final: 0.8460 (mt) REVERT: Y 236 GLU cc_start: 0.8217 (tp30) cc_final: 0.7645 (tp30) REVERT: Z 22 SER cc_start: 0.7807 (t) cc_final: 0.7440 (m) REVERT: Z 110 MET cc_start: 0.8113 (pmm) cc_final: 0.7637 (pmm) REVERT: A 493 GLU cc_start: 0.8999 (mt-10) cc_final: 0.8397 (tt0) REVERT: A 544 MET cc_start: 0.6233 (ttt) cc_final: 0.5619 (ttt) REVERT: A 584 GLN cc_start: 0.8853 (mt0) cc_final: 0.8477 (mp10) REVERT: A 608 PHE cc_start: 0.8076 (m-80) cc_final: 0.7649 (m-80) REVERT: A 609 MET cc_start: 0.8344 (mtm) cc_final: 0.8122 (mtm) REVERT: A 641 ARG cc_start: 0.8270 (ttt90) cc_final: 0.8017 (mtp85) REVERT: A 679 ARG cc_start: 0.9254 (tpt170) cc_final: 0.8778 (ptp-170) REVERT: B 519 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8087 (mt-10) REVERT: B 609 MET cc_start: 0.9361 (mtm) cc_final: 0.8950 (mtp) REVERT: B 611 MET cc_start: 0.8780 (mmm) cc_final: 0.8347 (mmm) REVERT: B 618 PHE cc_start: 0.9294 (t80) cc_final: 0.9079 (t80) REVERT: B 622 MET cc_start: 0.8966 (mmm) cc_final: 0.8415 (mmm) REVERT: B 682 MET cc_start: 0.8645 (mpp) cc_final: 0.8415 (ptp) REVERT: C 518 LEU cc_start: 0.8705 (mt) cc_final: 0.8051 (tp) REVERT: C 532 LYS cc_start: 0.9333 (mttt) cc_final: 0.9027 (mmtt) REVERT: C 545 ASN cc_start: 0.9228 (t0) cc_final: 0.8860 (t0) REVERT: C 584 GLN cc_start: 0.9097 (mt0) cc_final: 0.8599 (mt0) REVERT: C 622 MET cc_start: 0.8572 (tpt) cc_final: 0.8366 (tpt) REVERT: D 8 GLN cc_start: 0.8564 (mm-40) cc_final: 0.8098 (mp10) REVERT: D 39 VAL cc_start: 0.9459 (t) cc_final: 0.9230 (p) REVERT: D 352 ASP cc_start: 0.8988 (p0) cc_final: 0.8581 (p0) REVERT: E 40 ILE cc_start: 0.9407 (mm) cc_final: 0.9166 (mt) REVERT: E 67 GLN cc_start: 0.9146 (mm-40) cc_final: 0.8855 (mt0) REVERT: E 223 MET cc_start: 0.7253 (mtp) cc_final: 0.6796 (mpp) REVERT: E 257 GLU cc_start: 0.8068 (tp30) cc_final: 0.6490 (tp30) REVERT: E 279 ASP cc_start: 0.8312 (m-30) cc_final: 0.8061 (m-30) REVERT: E 378 ARG cc_start: 0.8808 (mtm-85) cc_final: 0.8499 (mtt90) REVERT: F 129 HIS cc_start: 0.8277 (t70) cc_final: 0.7587 (t70) REVERT: F 170 ASP cc_start: 0.8848 (m-30) cc_final: 0.8596 (t0) REVERT: F 209 MET cc_start: 0.9162 (ttp) cc_final: 0.8800 (tmm) REVERT: F 229 LEU cc_start: 0.8661 (mm) cc_final: 0.8172 (tp) REVERT: F 246 LEU cc_start: 0.9002 (mm) cc_final: 0.8731 (tt) REVERT: F 252 GLU cc_start: 0.8896 (tt0) cc_final: 0.8400 (mm-30) REVERT: F 256 MET cc_start: 0.7163 (tpt) cc_final: 0.6597 (ppp) REVERT: F 290 LEU cc_start: 0.8982 (mt) cc_final: 0.8753 (mp) REVERT: F 299 ASN cc_start: 0.8517 (m-40) cc_final: 0.7938 (t0) REVERT: F 301 MET cc_start: 0.8661 (tmm) cc_final: 0.8264 (tmm) REVERT: F 319 GLU cc_start: 0.5654 (mt-10) cc_final: 0.4201 (tp30) REVERT: F 320 ASP cc_start: 0.9288 (m-30) cc_final: 0.9053 (t70) REVERT: F 328 MET cc_start: 0.6031 (ttm) cc_final: 0.5710 (tpp) REVERT: G 116 MET cc_start: 0.8867 (mmm) cc_final: 0.8571 (mmt) REVERT: G 147 MET cc_start: 0.8784 (mtm) cc_final: 0.8548 (mtt) REVERT: G 152 LEU cc_start: 0.8445 (tp) cc_final: 0.8204 (tp) REVERT: G 181 VAL cc_start: 0.9590 (t) cc_final: 0.9324 (p) REVERT: G 208 ILE cc_start: 0.9013 (tp) cc_final: 0.8530 (pt) REVERT: G 252 GLU cc_start: 0.9038 (mt-10) cc_final: 0.8737 (mt-10) REVERT: G 273 ASP cc_start: 0.8383 (m-30) cc_final: 0.7515 (p0) REVERT: G 276 GLU cc_start: 0.8482 (tp30) cc_final: 0.8160 (tp30) REVERT: G 293 MET cc_start: 0.8995 (mtm) cc_final: 0.8458 (mpp) REVERT: G 294 TYR cc_start: 0.8972 (m-80) cc_final: 0.8686 (m-80) REVERT: G 315 LYS cc_start: 0.9254 (mmpt) cc_final: 0.9033 (mmmt) REVERT: H 26 TYR cc_start: 0.7938 (m-80) cc_final: 0.6612 (m-10) REVERT: H 70 ILE cc_start: 0.9471 (mm) cc_final: 0.9014 (mm) REVERT: H 208 GLN cc_start: 0.9398 (mt0) cc_final: 0.9175 (mt0) REVERT: H 247 LYS cc_start: 0.8270 (ptmm) cc_final: 0.7986 (ptmm) REVERT: H 249 ARG cc_start: 0.7210 (mpp-170) cc_final: 0.6139 (tpt170) REVERT: I 51 LEU cc_start: 0.9470 (tp) cc_final: 0.9122 (pp) REVERT: I 137 ASP cc_start: 0.9218 (t0) cc_final: 0.8983 (t0) REVERT: I 140 SER cc_start: 0.9353 (t) cc_final: 0.9022 (t) REVERT: I 147 ARG cc_start: 0.6776 (ttt-90) cc_final: 0.6512 (ttp80) REVERT: I 205 GLU cc_start: 0.9126 (mm-30) cc_final: 0.8598 (tp30) REVERT: J 116 LEU cc_start: 0.9218 (tp) cc_final: 0.8726 (tp) REVERT: J 118 HIS cc_start: 0.5822 (p-80) cc_final: 0.5580 (p-80) REVERT: J 121 VAL cc_start: 0.8193 (p) cc_final: 0.7829 (m) REVERT: J 241 HIS cc_start: 0.6210 (t-90) cc_final: 0.5504 (t-170) REVERT: J 265 VAL cc_start: 0.8562 (t) cc_final: 0.7688 (t) REVERT: J 300 TRP cc_start: 0.8914 (t-100) cc_final: 0.8476 (t-100) REVERT: J 304 HIS cc_start: 0.8874 (t70) cc_final: 0.8406 (t70) outliers start: 0 outliers final: 0 residues processed: 640 average time/residue: 0.1893 time to fit residues: 196.0064 Evaluate side-chains 480 residues out of total 3405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 480 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 241 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 204 optimal weight: 0.6980 chunk 55 optimal weight: 0.0970 chunk 174 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 42 HIS ** Y 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 73 GLN ** Z 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 ASN ** F 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 232 ASN ** G 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 ASN J 22 HIS ** J 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.102064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.075223 restraints weight = 121696.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.077425 restraints weight = 68512.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.078337 restraints weight = 42468.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.078486 restraints weight = 37706.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.078577 restraints weight = 35220.411| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.5309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30679 Z= 0.157 Angle : 0.634 9.896 41528 Z= 0.335 Chirality : 0.044 0.206 4637 Planarity : 0.004 0.094 5337 Dihedral : 4.904 59.600 4013 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.23 % Favored : 92.72 % Rotamer: Outliers : 0.03 % Allowed : 1.06 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.14), residues: 3612 helix: 0.83 (0.13), residues: 1532 sheet: -0.46 (0.30), residues: 318 loop : -1.35 (0.15), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 124 TYR 0.024 0.002 TYR G 224 PHE 0.028 0.002 PHE I 90 TRP 0.012 0.002 TRP E 462 HIS 0.013 0.001 HIS I 222 Details of bonding type rmsd covalent geometry : bond 0.00346 (30667) covalent geometry : angle 0.63244 (41504) SS BOND : bond 0.00230 ( 12) SS BOND : angle 1.69592 ( 24) hydrogen bonds : bond 0.04334 ( 1281) hydrogen bonds : angle 4.92020 ( 3633) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 3405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 608 time to evaluate : 1.249 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: W 62 MET cc_start: 0.8316 (pmm) cc_final: 0.7814 (pmm) REVERT: W 115 GLN cc_start: 0.9109 (mt0) cc_final: 0.8831 (mp10) REVERT: W 132 CYS cc_start: 0.8999 (m) cc_final: 0.8256 (t) REVERT: X 41 TYR cc_start: 0.9309 (m-80) cc_final: 0.8769 (m-10) REVERT: X 91 LYS cc_start: 0.8885 (ptpp) cc_final: 0.8674 (pttm) REVERT: X 137 TYR cc_start: 0.8205 (m-10) cc_final: 0.6211 (t80) REVERT: X 175 ASP cc_start: 0.6779 (p0) cc_final: 0.6541 (p0) REVERT: X 219 ILE cc_start: 0.8980 (mm) cc_final: 0.8750 (mm) REVERT: X 220 ASP cc_start: 0.8856 (t70) cc_final: 0.8630 (t70) REVERT: X 288 TYR cc_start: 0.6573 (m-80) cc_final: 0.5469 (m-80) REVERT: X 304 ILE cc_start: 0.9210 (mm) cc_final: 0.8529 (mm) REVERT: Y 48 ILE cc_start: 0.8983 (mt) cc_final: 0.8573 (mm) REVERT: Y 153 TYR cc_start: 0.8821 (t80) cc_final: 0.8537 (t80) REVERT: Y 236 GLU cc_start: 0.8244 (tp30) cc_final: 0.7672 (tp30) REVERT: Z 22 SER cc_start: 0.7761 (t) cc_final: 0.7395 (m) REVERT: Z 110 MET cc_start: 0.8022 (pmm) cc_final: 0.7571 (pmm) REVERT: A 493 GLU cc_start: 0.8977 (mt-10) cc_final: 0.8204 (tt0) REVERT: A 544 MET cc_start: 0.6138 (ttt) cc_final: 0.5243 (ttt) REVERT: A 608 PHE cc_start: 0.8129 (m-80) cc_final: 0.7702 (m-80) REVERT: A 609 MET cc_start: 0.8533 (mtm) cc_final: 0.8239 (mtm) REVERT: A 641 ARG cc_start: 0.8291 (ttt90) cc_final: 0.7985 (mtp85) REVERT: A 649 ARG cc_start: 0.8847 (mmt180) cc_final: 0.8472 (mmm160) REVERT: B 519 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8086 (mt-10) REVERT: B 558 TYR cc_start: 0.7348 (p90) cc_final: 0.6814 (p90) REVERT: B 609 MET cc_start: 0.9388 (mtm) cc_final: 0.8974 (mtp) REVERT: B 611 MET cc_start: 0.8749 (mmm) cc_final: 0.8398 (mmm) REVERT: B 622 MET cc_start: 0.8977 (mmm) cc_final: 0.8479 (mmm) REVERT: B 648 MET cc_start: 0.8898 (tpp) cc_final: 0.8659 (tpp) REVERT: C 532 LYS cc_start: 0.9366 (mttt) cc_final: 0.9050 (mmtt) REVERT: C 545 ASN cc_start: 0.9242 (t0) cc_final: 0.8891 (t0) REVERT: C 584 GLN cc_start: 0.9080 (mt0) cc_final: 0.8595 (mt0) REVERT: D 8 GLN cc_start: 0.8585 (mm-40) cc_final: 0.8195 (mp10) REVERT: D 39 VAL cc_start: 0.9476 (t) cc_final: 0.9230 (p) REVERT: D 325 CYS cc_start: 0.7794 (m) cc_final: 0.7580 (p) REVERT: D 352 ASP cc_start: 0.8979 (p0) cc_final: 0.8508 (p0) REVERT: E 40 ILE cc_start: 0.9410 (mm) cc_final: 0.9186 (mt) REVERT: E 66 MET cc_start: 0.8726 (pmm) cc_final: 0.8513 (pmm) REVERT: E 223 MET cc_start: 0.7303 (mtp) cc_final: 0.6793 (mpp) REVERT: E 257 GLU cc_start: 0.8175 (tp30) cc_final: 0.6688 (tp30) REVERT: E 279 ASP cc_start: 0.8408 (m-30) cc_final: 0.8123 (m-30) REVERT: E 378 ARG cc_start: 0.8839 (mtm-85) cc_final: 0.8600 (mtt90) REVERT: E 421 ASP cc_start: 0.7308 (t70) cc_final: 0.6594 (t0) REVERT: E 424 GLU cc_start: 0.9005 (pm20) cc_final: 0.8303 (pm20) REVERT: F 129 HIS cc_start: 0.8335 (t70) cc_final: 0.7610 (t70) REVERT: F 209 MET cc_start: 0.9147 (ttp) cc_final: 0.8793 (tmm) REVERT: F 229 LEU cc_start: 0.8654 (mm) cc_final: 0.8036 (tp) REVERT: F 246 LEU cc_start: 0.9012 (mm) cc_final: 0.8688 (tt) REVERT: F 252 GLU cc_start: 0.8857 (tt0) cc_final: 0.8407 (mm-30) REVERT: F 256 MET cc_start: 0.7225 (tpt) cc_final: 0.6628 (ppp) REVERT: F 299 ASN cc_start: 0.8528 (m-40) cc_final: 0.8019 (t0) REVERT: F 301 MET cc_start: 0.8671 (tmm) cc_final: 0.8261 (tmm) REVERT: F 319 GLU cc_start: 0.5742 (mt-10) cc_final: 0.4669 (tp30) REVERT: F 328 MET cc_start: 0.5777 (ttm) cc_final: 0.5403 (tpp) REVERT: G 144 ASP cc_start: 0.9140 (m-30) cc_final: 0.8919 (m-30) REVERT: G 147 MET cc_start: 0.8817 (mtm) cc_final: 0.8535 (mtt) REVERT: G 208 ILE cc_start: 0.9089 (tp) cc_final: 0.8556 (pt) REVERT: G 273 ASP cc_start: 0.8399 (m-30) cc_final: 0.7470 (p0) REVERT: G 283 LYS cc_start: 0.9415 (mmmm) cc_final: 0.9197 (mmmm) REVERT: G 294 TYR cc_start: 0.9030 (m-80) cc_final: 0.8728 (m-80) REVERT: G 315 LYS cc_start: 0.9192 (mmpt) cc_final: 0.8975 (mmmt) REVERT: H 43 GLU cc_start: 0.9018 (mp0) cc_final: 0.8731 (mp0) REVERT: H 70 ILE cc_start: 0.9266 (mm) cc_final: 0.8986 (mm) REVERT: I 51 LEU cc_start: 0.9409 (tp) cc_final: 0.9046 (pp) REVERT: I 137 ASP cc_start: 0.9229 (t0) cc_final: 0.8963 (t0) REVERT: I 140 SER cc_start: 0.9369 (t) cc_final: 0.9045 (t) REVERT: I 205 GLU cc_start: 0.9097 (mm-30) cc_final: 0.8477 (tp30) REVERT: J 86 LYS cc_start: 0.9028 (mmtm) cc_final: 0.8431 (pttm) REVERT: J 116 LEU cc_start: 0.9284 (tp) cc_final: 0.8921 (tp) REVERT: J 118 HIS cc_start: 0.5860 (p-80) cc_final: 0.5622 (p-80) REVERT: J 241 HIS cc_start: 0.6068 (t-90) cc_final: 0.5395 (t-170) REVERT: J 300 TRP cc_start: 0.8902 (t-100) cc_final: 0.8498 (t-100) REVERT: J 304 HIS cc_start: 0.8864 (t70) cc_final: 0.8545 (t70) outliers start: 1 outliers final: 0 residues processed: 609 average time/residue: 0.1876 time to fit residues: 185.5156 Evaluate side-chains 460 residues out of total 3405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 460 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 215 optimal weight: 0.9980 chunk 93 optimal weight: 7.9990 chunk 161 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 149 optimal weight: 3.9990 chunk 323 optimal weight: 0.9980 chunk 348 optimal weight: 10.0000 chunk 110 optimal weight: 1.9990 chunk 296 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 chunk 126 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 42 HIS ** X 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 228 ASN Y 42 HIS ** Y 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 73 GLN ** Z 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 ASN E 42 ASN F 128 HIS ** F 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 182 GLN ** F 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 232 ASN G 323 ASN H 35 ASN H 93 ASN ** J 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 118 HIS ** J 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.101401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.074984 restraints weight = 120999.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.077100 restraints weight = 69602.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.077081 restraints weight = 50942.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.077708 restraints weight = 40911.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.077892 restraints weight = 35649.036| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.5443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 30679 Z= 0.174 Angle : 0.644 9.626 41528 Z= 0.343 Chirality : 0.044 0.221 4637 Planarity : 0.005 0.090 5337 Dihedral : 4.963 52.106 4013 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.67 % Favored : 92.28 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.14), residues: 3612 helix: 0.76 (0.13), residues: 1529 sheet: -0.51 (0.30), residues: 313 loop : -1.40 (0.15), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 215 TYR 0.027 0.002 TYR E 62 PHE 0.031 0.002 PHE I 90 TRP 0.012 0.002 TRP E 462 HIS 0.013 0.001 HIS I 222 Details of bonding type rmsd covalent geometry : bond 0.00382 (30667) covalent geometry : angle 0.64319 (41504) SS BOND : bond 0.00268 ( 12) SS BOND : angle 1.61068 ( 24) hydrogen bonds : bond 0.04370 ( 1281) hydrogen bonds : angle 4.95463 ( 3633) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 3405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 600 time to evaluate : 1.263 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: W 62 MET cc_start: 0.8288 (pmm) cc_final: 0.7797 (pmm) REVERT: W 132 CYS cc_start: 0.8950 (m) cc_final: 0.8215 (t) REVERT: X 41 TYR cc_start: 0.9374 (m-80) cc_final: 0.8859 (m-80) REVERT: X 91 LYS cc_start: 0.8903 (ptpp) cc_final: 0.8678 (pttm) REVERT: X 137 TYR cc_start: 0.8239 (m-10) cc_final: 0.6162 (t80) REVERT: X 220 ASP cc_start: 0.8966 (t70) cc_final: 0.8720 (t70) REVERT: X 288 TYR cc_start: 0.6488 (m-80) cc_final: 0.5505 (m-80) REVERT: Y 48 ILE cc_start: 0.8990 (mt) cc_final: 0.8551 (mm) REVERT: Y 62 MET cc_start: 0.8030 (ptt) cc_final: 0.7821 (mpp) REVERT: Y 236 GLU cc_start: 0.8259 (tp30) cc_final: 0.7665 (tp30) REVERT: Z 22 SER cc_start: 0.7715 (t) cc_final: 0.7358 (m) REVERT: Z 110 MET cc_start: 0.7967 (pmm) cc_final: 0.7484 (pmm) REVERT: A 544 MET cc_start: 0.6080 (ttt) cc_final: 0.5189 (ttt) REVERT: A 608 PHE cc_start: 0.8064 (m-80) cc_final: 0.7647 (m-80) REVERT: A 641 ARG cc_start: 0.8277 (ttt90) cc_final: 0.7972 (mtp85) REVERT: A 649 ARG cc_start: 0.8829 (mmt180) cc_final: 0.8465 (mmm160) REVERT: A 679 ARG cc_start: 0.9264 (tpt170) cc_final: 0.8793 (ptp-170) REVERT: B 505 MET cc_start: -0.2634 (mtt) cc_final: -0.2836 (mtt) REVERT: B 519 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8044 (mt-10) REVERT: B 609 MET cc_start: 0.9312 (mtm) cc_final: 0.8994 (mtp) REVERT: B 615 LYS cc_start: 0.9463 (tptp) cc_final: 0.9262 (tttt) REVERT: B 622 MET cc_start: 0.8836 (mmm) cc_final: 0.7920 (mmm) REVERT: B 648 MET cc_start: 0.8914 (tpp) cc_final: 0.8662 (tpp) REVERT: B 682 MET cc_start: 0.8714 (mpp) cc_final: 0.8431 (ptp) REVERT: C 518 LEU cc_start: 0.8742 (tp) cc_final: 0.8242 (tp) REVERT: C 532 LYS cc_start: 0.9370 (mttt) cc_final: 0.9073 (mmtt) REVERT: C 545 ASN cc_start: 0.9192 (t0) cc_final: 0.8914 (t0) REVERT: C 575 TYR cc_start: 0.8459 (t80) cc_final: 0.7678 (t80) REVERT: C 584 GLN cc_start: 0.9089 (mt0) cc_final: 0.8591 (mt0) REVERT: D 8 GLN cc_start: 0.8603 (mm-40) cc_final: 0.8399 (mm-40) REVERT: D 39 VAL cc_start: 0.9486 (t) cc_final: 0.9230 (p) REVERT: D 352 ASP cc_start: 0.9114 (p0) cc_final: 0.8678 (p0) REVERT: E 40 ILE cc_start: 0.9412 (mm) cc_final: 0.9194 (mt) REVERT: E 66 MET cc_start: 0.8837 (pmm) cc_final: 0.8612 (pmm) REVERT: E 223 MET cc_start: 0.7333 (mtp) cc_final: 0.6855 (mpp) REVERT: E 257 GLU cc_start: 0.8286 (tp30) cc_final: 0.6728 (tp30) REVERT: E 279 ASP cc_start: 0.8476 (m-30) cc_final: 0.8149 (m-30) REVERT: E 378 ARG cc_start: 0.8840 (mtm-85) cc_final: 0.8590 (mtt90) REVERT: E 425 LYS cc_start: 0.9122 (ttpt) cc_final: 0.8889 (ttpt) REVERT: F 129 HIS cc_start: 0.8329 (t70) cc_final: 0.7568 (t70) REVERT: F 184 ASP cc_start: 0.9288 (m-30) cc_final: 0.8938 (m-30) REVERT: F 194 LEU cc_start: 0.9020 (tp) cc_final: 0.8734 (tp) REVERT: F 209 MET cc_start: 0.9142 (ttp) cc_final: 0.8803 (tmm) REVERT: F 229 LEU cc_start: 0.8691 (mm) cc_final: 0.8076 (tp) REVERT: F 252 GLU cc_start: 0.8887 (tt0) cc_final: 0.8482 (mm-30) REVERT: F 256 MET cc_start: 0.7166 (tpt) cc_final: 0.6611 (ppp) REVERT: F 299 ASN cc_start: 0.8767 (m-40) cc_final: 0.8138 (t0) REVERT: F 301 MET cc_start: 0.8652 (tmm) cc_final: 0.8205 (tmm) REVERT: F 317 ASN cc_start: 0.7510 (m110) cc_final: 0.6809 (m110) REVERT: F 319 GLU cc_start: 0.6043 (mt-10) cc_final: 0.4195 (mm-30) REVERT: F 320 ASP cc_start: 0.9329 (m-30) cc_final: 0.9030 (t70) REVERT: F 321 TYR cc_start: 0.8720 (m-10) cc_final: 0.8279 (m-10) REVERT: F 328 MET cc_start: 0.6151 (ttm) cc_final: 0.5696 (tpt) REVERT: G 116 MET cc_start: 0.8812 (mmt) cc_final: 0.8381 (mmt) REVERT: G 147 MET cc_start: 0.8800 (mtm) cc_final: 0.8525 (mtt) REVERT: G 162 PHE cc_start: 0.8948 (t80) cc_final: 0.8531 (t80) REVERT: G 208 ILE cc_start: 0.9072 (tp) cc_final: 0.8539 (pt) REVERT: G 244 GLU cc_start: 0.9426 (mp0) cc_final: 0.9193 (pm20) REVERT: G 273 ASP cc_start: 0.8394 (m-30) cc_final: 0.7316 (p0) REVERT: G 276 GLU cc_start: 0.8650 (tp30) cc_final: 0.8379 (tp30) REVERT: G 283 LYS cc_start: 0.9410 (mmmm) cc_final: 0.9194 (mmmm) REVERT: G 293 MET cc_start: 0.9106 (mtm) cc_final: 0.8812 (mpp) REVERT: G 294 TYR cc_start: 0.9049 (m-80) cc_final: 0.8834 (m-80) REVERT: H 43 GLU cc_start: 0.8960 (mp0) cc_final: 0.8734 (mp0) REVERT: H 70 ILE cc_start: 0.9369 (mm) cc_final: 0.8855 (mm) REVERT: H 76 ASP cc_start: 0.8958 (t0) cc_final: 0.8753 (t0) REVERT: H 106 MET cc_start: 0.7970 (mtp) cc_final: 0.6092 (mtp) REVERT: H 125 PHE cc_start: 0.6010 (t80) cc_final: 0.5483 (t80) REVERT: H 134 CYS cc_start: 0.8999 (t) cc_final: 0.8548 (m) REVERT: I 51 LEU cc_start: 0.9353 (tp) cc_final: 0.9072 (pp) REVERT: I 57 MET cc_start: 0.7457 (tpp) cc_final: 0.7187 (mtp) REVERT: I 69 GLU cc_start: 0.9204 (tp30) cc_final: 0.8927 (pp20) REVERT: I 102 PHE cc_start: 0.4318 (t80) cc_final: 0.3984 (t80) REVERT: I 137 ASP cc_start: 0.9190 (t0) cc_final: 0.8934 (t0) REVERT: I 140 SER cc_start: 0.9382 (t) cc_final: 0.9158 (t) REVERT: I 144 MET cc_start: 0.9001 (tpp) cc_final: 0.8675 (tpp) REVERT: I 205 GLU cc_start: 0.9094 (mm-30) cc_final: 0.8486 (tp30) REVERT: I 223 TYR cc_start: 0.8678 (t80) cc_final: 0.8458 (t80) REVERT: J 116 LEU cc_start: 0.9221 (tp) cc_final: 0.8924 (tp) REVERT: J 300 TRP cc_start: 0.8922 (t-100) cc_final: 0.8526 (t-100) outliers start: 0 outliers final: 0 residues processed: 600 average time/residue: 0.1865 time to fit residues: 181.8085 Evaluate side-chains 447 residues out of total 3405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 447 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 287 optimal weight: 0.5980 chunk 320 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 238 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 205 optimal weight: 0.5980 chunk 132 optimal weight: 0.0010 chunk 56 optimal weight: 0.7980 chunk 248 optimal weight: 3.9990 chunk 184 optimal weight: 0.9990 chunk 157 optimal weight: 0.8980 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 42 HIS ** X 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 42 HIS ** Y 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 73 GLN ** Z 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 ASN A 584 GLN ** F 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 323 ASN G 330 ASN H 35 ASN J 96 HIS J 118 HIS ** J 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.102424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.075035 restraints weight = 119639.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.078447 restraints weight = 69853.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.079000 restraints weight = 43104.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.079680 restraints weight = 31688.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.079962 restraints weight = 29039.521| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.5581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30679 Z= 0.139 Angle : 0.641 9.592 41528 Z= 0.338 Chirality : 0.044 0.265 4637 Planarity : 0.004 0.081 5337 Dihedral : 4.925 63.459 4013 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.39 % Favored : 92.58 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.14), residues: 3612 helix: 0.76 (0.13), residues: 1530 sheet: -0.53 (0.30), residues: 308 loop : -1.39 (0.15), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 249 TYR 0.025 0.002 TYR G 224 PHE 0.029 0.001 PHE B 583 TRP 0.012 0.002 TRP E 462 HIS 0.014 0.001 HIS I 222 Details of bonding type rmsd covalent geometry : bond 0.00304 (30667) covalent geometry : angle 0.64000 (41504) SS BOND : bond 0.00233 ( 12) SS BOND : angle 1.50552 ( 24) hydrogen bonds : bond 0.04287 ( 1281) hydrogen bonds : angle 4.90629 ( 3633) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 3405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 596 time to evaluate : 1.430 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: W 62 MET cc_start: 0.8453 (pmm) cc_final: 0.8023 (pmm) REVERT: W 115 GLN cc_start: 0.9146 (mt0) cc_final: 0.8678 (mp10) REVERT: W 132 CYS cc_start: 0.8865 (m) cc_final: 0.8130 (t) REVERT: X 41 TYR cc_start: 0.9381 (m-80) cc_final: 0.8817 (m-80) REVERT: X 91 LYS cc_start: 0.8893 (ptpp) cc_final: 0.8642 (pttm) REVERT: X 137 TYR cc_start: 0.8198 (m-10) cc_final: 0.6074 (t80) REVERT: X 220 ASP cc_start: 0.8902 (t70) cc_final: 0.8680 (t70) REVERT: X 288 TYR cc_start: 0.6362 (m-80) cc_final: 0.5407 (m-80) REVERT: X 304 ILE cc_start: 0.9133 (mm) cc_final: 0.8570 (mm) REVERT: Y 48 ILE cc_start: 0.8972 (mt) cc_final: 0.8531 (mm) REVERT: Y 62 MET cc_start: 0.8010 (ptt) cc_final: 0.7806 (mpp) REVERT: Y 153 TYR cc_start: 0.8834 (t80) cc_final: 0.8586 (t80) REVERT: Z 22 SER cc_start: 0.7848 (t) cc_final: 0.7526 (m) REVERT: Z 110 MET cc_start: 0.8022 (pmm) cc_final: 0.7503 (pmm) REVERT: A 544 MET cc_start: 0.5930 (ttt) cc_final: 0.5057 (ttt) REVERT: A 608 PHE cc_start: 0.8086 (m-80) cc_final: 0.7645 (m-80) REVERT: A 609 MET cc_start: 0.8421 (mtm) cc_final: 0.8049 (mtm) REVERT: A 641 ARG cc_start: 0.8262 (ttt90) cc_final: 0.7975 (mtp85) REVERT: A 649 ARG cc_start: 0.8834 (mmt180) cc_final: 0.8493 (mmm160) REVERT: B 519 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8059 (mt-10) REVERT: B 548 PHE cc_start: 0.8505 (t80) cc_final: 0.8223 (t80) REVERT: B 609 MET cc_start: 0.9323 (mtm) cc_final: 0.8942 (mtp) REVERT: B 611 MET cc_start: 0.8711 (mmm) cc_final: 0.8468 (mmm) REVERT: B 618 PHE cc_start: 0.9142 (t80) cc_final: 0.8438 (t80) REVERT: B 622 MET cc_start: 0.9235 (mmm) cc_final: 0.8902 (mmm) REVERT: B 648 MET cc_start: 0.8874 (tpp) cc_final: 0.8611 (tpp) REVERT: B 682 MET cc_start: 0.8649 (mpp) cc_final: 0.8376 (ptp) REVERT: C 518 LEU cc_start: 0.8647 (tp) cc_final: 0.8124 (tp) REVERT: C 532 LYS cc_start: 0.9349 (mttt) cc_final: 0.8980 (mmtt) REVERT: C 545 ASN cc_start: 0.9114 (t0) cc_final: 0.8804 (t0) REVERT: C 575 TYR cc_start: 0.8449 (t80) cc_final: 0.7651 (t80) REVERT: C 584 GLN cc_start: 0.9079 (mt0) cc_final: 0.8566 (mt0) REVERT: D 8 GLN cc_start: 0.8574 (mm-40) cc_final: 0.8208 (mp10) REVERT: D 39 VAL cc_start: 0.9484 (t) cc_final: 0.9248 (p) REVERT: D 175 PHE cc_start: 0.7929 (p90) cc_final: 0.7316 (p90) REVERT: D 352 ASP cc_start: 0.9039 (p0) cc_final: 0.8646 (p0) REVERT: E 40 ILE cc_start: 0.9374 (mm) cc_final: 0.9163 (mt) REVERT: E 66 MET cc_start: 0.8790 (pmm) cc_final: 0.8573 (pmm) REVERT: E 223 MET cc_start: 0.7260 (mtp) cc_final: 0.6836 (mpp) REVERT: E 257 GLU cc_start: 0.8189 (tp30) cc_final: 0.6563 (tp30) REVERT: E 279 ASP cc_start: 0.8421 (m-30) cc_final: 0.8136 (m-30) REVERT: E 378 ARG cc_start: 0.8777 (mtm-85) cc_final: 0.8576 (mtt90) REVERT: F 129 HIS cc_start: 0.8202 (t70) cc_final: 0.7442 (t70) REVERT: F 209 MET cc_start: 0.9047 (ttp) cc_final: 0.8731 (tmm) REVERT: F 229 LEU cc_start: 0.8600 (mm) cc_final: 0.8186 (tp) REVERT: F 252 GLU cc_start: 0.8823 (tt0) cc_final: 0.8452 (mm-30) REVERT: F 256 MET cc_start: 0.7145 (tpt) cc_final: 0.6625 (ppp) REVERT: F 299 ASN cc_start: 0.8613 (m-40) cc_final: 0.8171 (t0) REVERT: F 301 MET cc_start: 0.8608 (tmm) cc_final: 0.8263 (tmm) REVERT: F 319 GLU cc_start: 0.6001 (mt-10) cc_final: 0.4542 (tp30) REVERT: F 328 MET cc_start: 0.6174 (ttm) cc_final: 0.5767 (tpp) REVERT: G 116 MET cc_start: 0.8809 (mmt) cc_final: 0.8553 (mmt) REVERT: G 144 ASP cc_start: 0.9079 (m-30) cc_final: 0.8855 (m-30) REVERT: G 147 MET cc_start: 0.8773 (mtm) cc_final: 0.8473 (mtt) REVERT: G 162 PHE cc_start: 0.8931 (t80) cc_final: 0.8461 (t80) REVERT: G 208 ILE cc_start: 0.9002 (tp) cc_final: 0.8588 (pt) REVERT: G 273 ASP cc_start: 0.8368 (m-30) cc_final: 0.7427 (p0) REVERT: G 276 GLU cc_start: 0.8541 (tp30) cc_final: 0.8307 (tp30) REVERT: G 283 LYS cc_start: 0.9412 (mmmm) cc_final: 0.9180 (mmmm) REVERT: G 293 MET cc_start: 0.9164 (mtm) cc_final: 0.8846 (mpp) REVERT: G 294 TYR cc_start: 0.9093 (m-80) cc_final: 0.8801 (m-80) REVERT: H 43 GLU cc_start: 0.8934 (mp0) cc_final: 0.8680 (mp0) REVERT: H 70 ILE cc_start: 0.9240 (mm) cc_final: 0.8954 (mm) REVERT: H 76 ASP cc_start: 0.8896 (t0) cc_final: 0.8656 (t0) REVERT: H 106 MET cc_start: 0.7650 (mtp) cc_final: 0.6656 (mtp) REVERT: H 125 PHE cc_start: 0.5975 (t80) cc_final: 0.5467 (t80) REVERT: I 137 ASP cc_start: 0.9250 (t0) cc_final: 0.9029 (t0) REVERT: I 138 ARG cc_start: 0.8614 (tpp80) cc_final: 0.8298 (ttm-80) REVERT: I 140 SER cc_start: 0.9365 (t) cc_final: 0.9116 (t) REVERT: I 144 MET cc_start: 0.8928 (tpp) cc_final: 0.8728 (tpt) REVERT: I 205 GLU cc_start: 0.9050 (mm-30) cc_final: 0.8451 (tp30) REVERT: J 116 LEU cc_start: 0.9189 (tp) cc_final: 0.8807 (tp) REVERT: J 300 TRP cc_start: 0.9001 (t-100) cc_final: 0.8518 (t-100) outliers start: 0 outliers final: 0 residues processed: 596 average time/residue: 0.1837 time to fit residues: 178.2853 Evaluate side-chains 449 residues out of total 3405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 449 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 3 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 224 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 324 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 287 optimal weight: 0.5980 chunk 293 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 184 optimal weight: 0.5980 chunk 143 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 42 HIS ** X 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 42 HIS ** Y 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 73 GLN ** Z 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 ASN B 643 HIS E 122 ASN F 128 HIS ** F 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 323 ASN H 35 ASN J 22 HIS J 62 ASN ** J 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 118 HIS ** J 264 ASN ** 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 = 0.3849 r_free = 0.3849 target = 0.101837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.075510 restraints weight = 121154.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.077525 restraints weight = 70100.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.077804 restraints weight = 44462.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.078196 restraints weight = 43287.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.078356 restraints weight = 38264.001| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.5700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30679 Z= 0.153 Angle : 0.642 10.037 41528 Z= 0.339 Chirality : 0.044 0.211 4637 Planarity : 0.004 0.085 5337 Dihedral : 4.946 63.262 4013 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.67 % Favored : 92.30 % Rotamer: Outliers : 0.03 % Allowed : 0.41 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.14), residues: 3612 helix: 0.74 (0.13), residues: 1527 sheet: -0.58 (0.30), residues: 308 loop : -1.42 (0.15), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG E 124 TYR 0.034 0.002 TYR F 303 PHE 0.020 0.002 PHE B 583 TRP 0.012 0.002 TRP E 462 HIS 0.018 0.001 HIS I 222 Details of bonding type rmsd covalent geometry : bond 0.00339 (30667) covalent geometry : angle 0.64157 (41504) SS BOND : bond 0.00243 ( 12) SS BOND : angle 1.48476 ( 24) hydrogen bonds : bond 0.04264 ( 1281) hydrogen bonds : angle 4.91717 ( 3633) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6018.99 seconds wall clock time: 104 minutes 49.23 seconds (6289.23 seconds total)