Starting phenix.real_space_refine on Tue Jul 7 04:11:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cq3_45807/07_2026/9cq3_45807.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cq3_45807/07_2026/9cq3_45807.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cq3_45807/07_2026/9cq3_45807.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cq3_45807/07_2026/9cq3_45807.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cq3_45807/07_2026/9cq3_45807.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cq3_45807/07_2026/9cq3_45807.map" } resolution = 2.8 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= 0.010 sd= 1.448 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: 6 Type Number sf(0) Gaussians P 153 5.49 5 Mg 2 5.21 5 S 219 5.16 5 C 27497 2.51 5 N 7547 2.21 5 O 8554 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 73 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 43972 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 4188 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 516, 4177 Classifications: {'peptide': 516} Link IDs: {'PTRANS': 28, 'TRANS': 487} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 516, 4177 Classifications: {'peptide': 516} Link IDs: {'PTRANS': 28, 'TRANS': 487} Chain breaks: 1 bond proxies already assigned to first conformer: 4249 Chain: "B" Number of atoms: 4211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4211 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 26, 'TRANS': 499} Chain breaks: 1 Chain: "C" Number of atoms: 1831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1831 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 11, 'TRANS': 219} Chain: "D" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1633 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 3, 'TRANS': 198} Chain: "E" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1628 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 3, 'TRANS': 197} Chain: "F" Number of atoms: 5503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 679, 5503 Classifications: {'peptide': 679} Link IDs: {'PTRANS': 25, 'TRANS': 653} Chain breaks: 3 Chain: "G" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1219 Classifications: {'peptide': 164} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 147} Chain breaks: 1 Chain: "H" Number of atoms: 1114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1114 Classifications: {'peptide': 149} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 132} Chain breaks: 3 Chain: "I" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 771 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain: "J" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 857 Classifications: {'DNA': 42} Link IDs: {'rna3p': 41} Chain: "K" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 702 Classifications: {'DNA': 34} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 33} Chain: "L" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 763 Classifications: {'DNA': 37} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 36} Chain: "M" Number of atoms: 3375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3375 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 25, 'TRANS': 400} Chain breaks: 3 Chain: "a" Number of atoms: 4081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 4081 Classifications: {'peptide': 505} Link IDs: {'PTRANS': 28, 'TRANS': 476} Chain: "b" Number of atoms: 4204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4204 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 25, 'TRANS': 499} Chain breaks: 1 Chain: "c" Number of atoms: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1813 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 11, 'TRANS': 216} Chain: "d" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1623 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 3, 'TRANS': 196} Chain: "e" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1623 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 3, 'TRANS': 196} Chain: "f" Number of atoms: 2069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2069 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 10, 'TRANS': 244} Chain: "m" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 732 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 8, 'TRANS': 87} Chain: "M" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 2, 'DZ4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG A 444 " occ=0.35 ... (20 atoms not shown) pdb=" NH2BARG A 444 " occ=0.65 Time building chain proxies: 8.06, per 1000 atoms: 0.18 Number of scatterers: 43972 At special positions: 0 Unit cell: (205.751, 244.069, 187.425, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 219 16.00 P 153 15.00 Mg 2 11.99 O 8554 8.00 N 7547 7.00 C 27497 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.15 Conformation dependent library (CDL) restraints added in 2.3 seconds 10096 Ramachandran restraints generated. 5048 Oldfield, 0 Emsley, 5048 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9712 Finding SS restraints... Secondary structure from input PDB file: 171 helices and 44 sheets defined 45.1% alpha, 17.9% beta 74 base pairs and 128 stacking pairs defined. Time for finding SS restraints: 5.07 Creating SS restraints... Processing helix chain 'A' and resid 3 through 8 removed outlier: 3.667A pdb=" N TYR A 7 " --> pdb=" O GLY A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 50 removed outlier: 3.633A pdb=" N GLU A 50 " --> pdb=" O ALA A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 78 removed outlier: 3.645A pdb=" N ILE A 76 " --> pdb=" O ILE A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 121 Processing helix chain 'A' and resid 124 through 135 Processing helix chain 'A' and resid 142 through 157 removed outlier: 3.551A pdb=" N VAL A 146 " --> pdb=" O SER A 142 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL A 157 " --> pdb=" O LEU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 197 Processing helix chain 'A' and resid 216 through 220 removed outlier: 3.926A pdb=" N ASP A 219 " --> pdb=" O PHE A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 244 removed outlier: 3.788A pdb=" N ASP A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 338 removed outlier: 4.073A pdb=" N LYS A 338 " --> pdb=" O THR A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 356 No H-bonds generated for 'chain 'A' and resid 354 through 356' Processing helix chain 'A' and resid 377 through 393 removed outlier: 3.672A pdb=" N LEU A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 469 Processing helix chain 'A' and resid 480 through 496 Processing helix chain 'A' and resid 510 through 518 removed outlier: 3.531A pdb=" N MET A 514 " --> pdb=" O LYS A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 530 Processing helix chain 'B' and resid 18 through 22 Processing helix chain 'B' and resid 29 through 48 Processing helix chain 'B' and resid 87 through 96 removed outlier: 3.611A pdb=" N LEU B 91 " --> pdb=" O ASP B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 122 removed outlier: 4.135A pdb=" N ALA B 110 " --> pdb=" O ASP B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 158 Processing helix chain 'B' and resid 198 through 217 Processing helix chain 'B' and resid 218 through 222 Processing helix chain 'B' and resid 227 through 231 Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 324 through 332 Processing helix chain 'B' and resid 349 through 351 No H-bonds generated for 'chain 'B' and resid 349 through 351' Processing helix chain 'B' and resid 352 through 356 Processing helix chain 'B' and resid 370 through 388 Processing helix chain 'B' and resid 426 through 430 removed outlier: 3.512A pdb=" N LEU B 430 " --> pdb=" O MET B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 461 Processing helix chain 'B' and resid 478 through 482 Processing helix chain 'B' and resid 484 through 500 removed outlier: 4.043A pdb=" N GLN B 488 " --> pdb=" O ASN B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 517 removed outlier: 3.567A pdb=" N TRP B 513 " --> pdb=" O GLN B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 537 removed outlier: 3.735A pdb=" N THR B 523 " --> pdb=" O PRO B 519 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ILE B 528 " --> pdb=" O THR B 524 " (cutoff:3.500A) Proline residue: B 529 - end of helix Processing helix chain 'C' and resid 0 through 11 Processing helix chain 'C' and resid 51 through 62 Processing helix chain 'C' and resid 68 through 86 Proline residue: C 82 - end of helix Processing helix chain 'C' and resid 127 through 170 removed outlier: 5.127A pdb=" N ARG C 137 " --> pdb=" O GLN C 133 " (cutoff:3.500A) Proline residue: C 138 - end of helix Processing helix chain 'C' and resid 185 through 197 removed outlier: 3.611A pdb=" N ILE C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 202 Processing helix chain 'C' and resid 207 through 214 Processing helix chain 'C' and resid 214 through 229 Processing helix chain 'D' and resid 48 through 60 Processing helix chain 'D' and resid 62 through 75 Processing helix chain 'D' and resid 118 through 202 removed outlier: 3.614A pdb=" N VAL D 122 " --> pdb=" O ASN D 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 60 Processing helix chain 'E' and resid 62 through 75 Processing helix chain 'E' and resid 118 through 201 removed outlier: 4.040A pdb=" N VAL E 122 " --> pdb=" O ASN E 118 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLU E 170 " --> pdb=" O VAL E 166 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ALA E 171 " --> pdb=" O SER E 167 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU E 173 " --> pdb=" O LYS E 169 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA E 201 " --> pdb=" O LYS E 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 13 Processing helix chain 'F' and resid 15 through 29 removed outlier: 3.802A pdb=" N LEU F 19 " --> pdb=" O PRO F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 54 Processing helix chain 'F' and resid 64 through 72 removed outlier: 4.009A pdb=" N LEU F 70 " --> pdb=" O PRO F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 76 Processing helix chain 'F' and resid 85 through 98 Processing helix chain 'F' and resid 103 through 111 Processing helix chain 'F' and resid 124 through 134 Processing helix chain 'F' and resid 144 through 162 Processing helix chain 'F' and resid 163 through 177 removed outlier: 3.754A pdb=" N ILE F 167 " --> pdb=" O ARG F 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 192 Processing helix chain 'F' and resid 199 through 208 Processing helix chain 'F' and resid 211 through 219 Processing helix chain 'F' and resid 221 through 228 Processing helix chain 'F' and resid 234 through 240 removed outlier: 3.853A pdb=" N ILE F 238 " --> pdb=" O GLY F 234 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE F 240 " --> pdb=" O SER F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 262 removed outlier: 5.361A pdb=" N GLU F 260 " --> pdb=" O GLU F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 303 removed outlier: 3.811A pdb=" N PHE F 302 " --> pdb=" O TYR F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 316 removed outlier: 3.509A pdb=" N ILE F 315 " --> pdb=" O LEU F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 381 through 390 removed outlier: 3.818A pdb=" N SER F 390 " --> pdb=" O TYR F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 410 through 424 Processing helix chain 'F' and resid 674 through 684 removed outlier: 4.106A pdb=" N ASN F 680 " --> pdb=" O PRO F 676 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ARG F 681 " --> pdb=" O ASP F 677 " (cutoff:3.500A) Processing helix chain 'F' and resid 706 through 715 Processing helix chain 'F' and resid 722 through 730 removed outlier: 4.348A pdb=" N LEU F 726 " --> pdb=" O LYS F 722 " (cutoff:3.500A) Processing helix chain 'F' and resid 747 through 756 removed outlier: 3.766A pdb=" N ARG F 756 " --> pdb=" O GLU F 752 " (cutoff:3.500A) Processing helix chain 'F' and resid 770 through 781 Processing helix chain 'F' and resid 788 through 803 removed outlier: 3.561A pdb=" N TYR F 803 " --> pdb=" O LEU F 799 " (cutoff:3.500A) Processing helix chain 'F' and resid 836 through 849 removed outlier: 3.972A pdb=" N ILE F 840 " --> pdb=" O THR F 836 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY F 849 " --> pdb=" O LEU F 845 " (cutoff:3.500A) Processing helix chain 'F' and resid 871 through 882 Processing helix chain 'F' and resid 891 through 901 removed outlier: 4.328A pdb=" N ASP F 899 " --> pdb=" O THR F 895 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS F 900 " --> pdb=" O ASP F 896 " (cutoff:3.500A) Processing helix chain 'F' and resid 905 through 909 removed outlier: 3.833A pdb=" N GLN F 908 " --> pdb=" O GLU F 905 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 64 removed outlier: 3.570A pdb=" N PHE G 64 " --> pdb=" O LEU G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 83 Processing helix chain 'G' and resid 113 through 144 Proline residue: G 119 - end of helix removed outlier: 3.873A pdb=" N GLU G 144 " --> pdb=" O ALA G 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 65 Processing helix chain 'H' and resid 72 through 83 Processing helix chain 'H' and resid 113 through 141 Proline residue: H 119 - end of helix Processing helix chain 'M' and resid 35 through 40 removed outlier: 3.826A pdb=" N MET M 39 " --> pdb=" O VAL M 35 " (cutoff:3.500A) Processing helix chain 'M' and resid 40 through 54 Processing helix chain 'M' and resid 75 through 88 Processing helix chain 'M' and resid 102 through 112 Processing helix chain 'M' and resid 153 through 170 removed outlier: 3.537A pdb=" N GLU M 170 " --> pdb=" O ALA M 166 " (cutoff:3.500A) Processing helix chain 'M' and resid 172 through 188 Processing helix chain 'M' and resid 195 through 200 removed outlier: 3.843A pdb=" N GLN M 200 " --> pdb=" O SER M 197 " (cutoff:3.500A) Processing helix chain 'M' and resid 206 through 219 removed outlier: 3.592A pdb=" N HIS M 219 " --> pdb=" O GLU M 215 " (cutoff:3.500A) Processing helix chain 'M' and resid 222 through 231 Processing helix chain 'M' and resid 231 through 242 Processing helix chain 'M' and resid 247 through 258 Processing helix chain 'M' and resid 261 through 268 removed outlier: 4.092A pdb=" N LEU M 265 " --> pdb=" O THR M 261 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG M 266 " --> pdb=" O LEU M 262 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN M 268 " --> pdb=" O ASP M 264 " (cutoff:3.500A) Processing helix chain 'M' and resid 273 through 282 Processing helix chain 'M' and resid 282 through 288 removed outlier: 3.510A pdb=" N THR M 288 " --> pdb=" O GLN M 284 " (cutoff:3.500A) Processing helix chain 'M' and resid 291 through 310 removed outlier: 3.647A pdb=" N GLU M 304 " --> pdb=" O GLN M 300 " (cutoff:3.500A) Processing helix chain 'M' and resid 320 through 324 Processing helix chain 'M' and resid 345 through 358 removed outlier: 3.812A pdb=" N ARG M 349 " --> pdb=" O GLY M 345 " (cutoff:3.500A) Processing helix chain 'M' and resid 426 through 436 Processing helix chain 'M' and resid 437 through 451 Processing helix chain 'M' and resid 475 through 482 removed outlier: 3.982A pdb=" N PHE M 479 " --> pdb=" O GLU M 475 " (cutoff:3.500A) Processing helix chain 'M' and resid 488 through 492 Processing helix chain 'a' and resid 46 through 50 Processing helix chain 'a' and resid 58 through 78 Processing helix chain 'a' and resid 112 through 121 Processing helix chain 'a' and resid 124 through 136 Processing helix chain 'a' and resid 142 through 156 Processing helix chain 'a' and resid 180 through 197 Processing helix chain 'a' and resid 216 through 220 removed outlier: 3.832A pdb=" N ASP a 219 " --> pdb=" O PHE a 216 " (cutoff:3.500A) Processing helix chain 'a' and resid 236 through 244 removed outlier: 4.184A pdb=" N GLU a 240 " --> pdb=" O SER a 236 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP a 241 " --> pdb=" O SER a 237 " (cutoff:3.500A) Processing helix chain 'a' and resid 312 through 316 Processing helix chain 'a' and resid 330 through 338 removed outlier: 3.996A pdb=" N LYS a 338 " --> pdb=" O THR a 334 " (cutoff:3.500A) Processing helix chain 'a' and resid 354 through 356 No H-bonds generated for 'chain 'a' and resid 354 through 356' Processing helix chain 'a' and resid 377 through 393 removed outlier: 3.756A pdb=" N LEU a 381 " --> pdb=" O GLY a 377 " (cutoff:3.500A) Processing helix chain 'a' and resid 422 through 424 No H-bonds generated for 'chain 'a' and resid 422 through 424' Processing helix chain 'a' and resid 455 through 469 Processing helix chain 'a' and resid 480 through 496 Processing helix chain 'a' and resid 510 through 519 Processing helix chain 'a' and resid 520 through 530 Processing helix chain 'b' and resid 17 through 22 removed outlier: 3.810A pdb=" N SER b 21 " --> pdb=" O GLY b 17 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASN b 22 " --> pdb=" O PHE b 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 17 through 22' Processing helix chain 'b' and resid 29 through 48 Processing helix chain 'b' and resid 87 through 96 removed outlier: 3.791A pdb=" N LEU b 91 " --> pdb=" O ASP b 87 " (cutoff:3.500A) Processing helix chain 'b' and resid 106 through 122 Processing helix chain 'b' and resid 146 through 158 Processing helix chain 'b' and resid 198 through 217 Processing helix chain 'b' and resid 219 through 222 Processing helix chain 'b' and resid 227 through 231 Processing helix chain 'b' and resid 306 through 308 No H-bonds generated for 'chain 'b' and resid 306 through 308' Processing helix chain 'b' and resid 324 through 332 Processing helix chain 'b' and resid 349 through 351 No H-bonds generated for 'chain 'b' and resid 349 through 351' Processing helix chain 'b' and resid 352 through 356 Processing helix chain 'b' and resid 370 through 388 Processing helix chain 'b' and resid 447 through 461 Processing helix chain 'b' and resid 484 through 500 removed outlier: 3.971A pdb=" N GLN b 488 " --> pdb=" O ASN b 484 " (cutoff:3.500A) Processing helix chain 'b' and resid 509 through 516 Processing helix chain 'b' and resid 519 through 526 removed outlier: 3.666A pdb=" N THR b 523 " --> pdb=" O PRO b 519 " (cutoff:3.500A) Processing helix chain 'b' and resid 527 through 537 Processing helix chain 'c' and resid 1 through 10 Processing helix chain 'c' and resid 51 through 62 removed outlier: 3.517A pdb=" N GLU c 60 " --> pdb=" O GLN c 56 " (cutoff:3.500A) Processing helix chain 'c' and resid 68 through 86 Proline residue: c 82 - end of helix Processing helix chain 'c' and resid 127 through 170 removed outlier: 5.109A pdb=" N ARG c 137 " --> pdb=" O GLN c 133 " (cutoff:3.500A) Proline residue: c 138 - end of helix Processing helix chain 'c' and resid 176 through 180 removed outlier: 3.535A pdb=" N LYS c 180 " --> pdb=" O ASP c 177 " (cutoff:3.500A) Processing helix chain 'c' and resid 185 through 197 Processing helix chain 'c' and resid 197 through 202 Processing helix chain 'c' and resid 207 through 214 removed outlier: 3.662A pdb=" N LEU c 214 " --> pdb=" O PHE c 210 " (cutoff:3.500A) Processing helix chain 'c' and resid 215 through 227 Processing helix chain 'd' and resid 49 through 58 removed outlier: 3.553A pdb=" N ASP d 58 " --> pdb=" O GLN d 54 " (cutoff:3.500A) Processing helix chain 'd' and resid 62 through 75 Processing helix chain 'd' and resid 119 through 197 removed outlier: 3.685A pdb=" N ILE d 123 " --> pdb=" O PRO d 119 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS d 197 " --> pdb=" O SER d 193 " (cutoff:3.500A) Processing helix chain 'e' and resid 49 through 60 Processing helix chain 'e' and resid 62 through 75 Processing helix chain 'e' and resid 118 through 200 removed outlier: 3.852A pdb=" N VAL e 122 " --> pdb=" O ASN e 118 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER e 167 " --> pdb=" O GLU e 163 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU e 170 " --> pdb=" O VAL e 166 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TYR e 177 " --> pdb=" O GLU e 173 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS e 178 " --> pdb=" O THR e 174 " (cutoff:3.500A) Processing helix chain 'f' and resid 674 through 685 removed outlier: 3.594A pdb=" N LEU f 678 " --> pdb=" O PRO f 674 " (cutoff:3.500A) Processing helix chain 'f' and resid 706 through 715 Processing helix chain 'f' and resid 722 through 733 removed outlier: 4.240A pdb=" N LEU f 726 " --> pdb=" O LYS f 722 " (cutoff:3.500A) Processing helix chain 'f' and resid 747 through 758 removed outlier: 3.550A pdb=" N GLU f 757 " --> pdb=" O HIS f 753 " (cutoff:3.500A) Processing helix chain 'f' and resid 770 through 781 Processing helix chain 'f' and resid 788 through 803 Processing helix chain 'f' and resid 828 through 832 removed outlier: 3.649A pdb=" N THR f 831 " --> pdb=" O ASP f 828 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS f 832 " --> pdb=" O LEU f 829 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 828 through 832' Processing helix chain 'f' and resid 836 through 848 removed outlier: 3.785A pdb=" N ILE f 840 " --> pdb=" O THR f 836 " (cutoff:3.500A) Processing helix chain 'f' and resid 871 through 882 removed outlier: 3.783A pdb=" N ARG f 880 " --> pdb=" O LYS f 876 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N THR f 881 " --> pdb=" O ALA f 877 " (cutoff:3.500A) Processing helix chain 'f' and resid 891 through 901 removed outlier: 3.658A pdb=" N THR f 895 " --> pdb=" O GLU f 891 " (cutoff:3.500A) Processing helix chain 'f' and resid 905 through 909 removed outlier: 3.689A pdb=" N GLN f 908 " --> pdb=" O GLU f 905 " (cutoff:3.500A) Processing helix chain 'm' and resid 36 through 39 removed outlier: 3.509A pdb=" N MET m 39 " --> pdb=" O GLU m 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 36 through 39' Processing helix chain 'm' and resid 41 through 54 Processing helix chain 'm' and resid 75 through 89 removed outlier: 3.805A pdb=" N ALA m 89 " --> pdb=" O ARG m 85 " (cutoff:3.500A) Processing helix chain 'm' and resid 102 through 112 Processing sheet with id=AA1, first strand: chain 'A' and resid 102 through 109 removed outlier: 6.462A pdb=" N VAL A 85 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N GLU A 107 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N LEU A 83 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ARG A 35 " --> pdb=" O HIS A 163 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N ARG A 165 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N SER A 37 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N MET A 167 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE A 39 " --> pdb=" O MET A 167 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N PHE A 169 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU A 41 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 9.115A pdb=" N PHE A 199 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LYS A 164 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ASP A 201 " --> pdb=" O LYS A 164 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ILE A 166 " --> pdb=" O ASP A 201 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N MET A 203 " --> pdb=" O ILE A 166 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU A 168 " --> pdb=" O MET A 203 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 211 through 212 Processing sheet with id=AA3, first strand: chain 'A' and resid 257 through 262 removed outlier: 3.605A pdb=" N SER A 257 " --> pdb=" O ILE A 273 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N VAL A 394 " --> pdb=" O PRO A 415 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ALA A 395 " --> pdb=" O PHE A 350 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N PHE A 350 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LEU A 397 " --> pdb=" O MET A 348 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 286 through 289 Processing sheet with id=AA5, first strand: chain 'A' and resid 297 through 304 Processing sheet with id=AA6, first strand: chain 'A' and resid 326 through 329 Processing sheet with id=AA7, first strand: chain 'A' and resid 375 through 376 Processing sheet with id=AA8, first strand: chain 'A' and resid 419 through 420 removed outlier: 6.840A pdb=" N GLU A 419 " --> pdb=" O VAL A 427 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 77 through 84 removed outlier: 6.449A pdb=" N LEU B 56 " --> pdb=" O HIS B 80 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N HIS B 82 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ILE B 54 " --> pdb=" O HIS B 82 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ARG B 130 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N GLN B 162 " --> pdb=" O ARG B 130 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE B 132 " --> pdb=" O GLN B 162 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N PHE B 164 " --> pdb=" O ILE B 132 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE B 134 " --> pdb=" O PHE B 164 " (cutoff:3.500A) removed outlier: 8.660A pdb=" N TYR B 225 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N PHE B 163 " --> pdb=" O TYR B 225 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 247 through 252 removed outlier: 6.770A pdb=" N VAL B 361 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N LEU B 268 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 9.819A pdb=" N ASN B 359 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N GLN B 360 " --> pdb=" O GLN B 423 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N GLN B 423 " --> pdb=" O GLN B 360 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ALA B 366 " --> pdb=" O GLU B 417 " (cutoff:3.500A) removed outlier: 10.572A pdb=" N GLU B 417 " --> pdb=" O ALA B 366 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N MET B 389 " --> pdb=" O PRO B 410 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL B 390 " --> pdb=" O PHE B 345 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N PHE B 345 " --> pdb=" O VAL B 390 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ILE B 392 " --> pdb=" O LEU B 343 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N PHE B 340 " --> pdb=" O PRO B 248 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ARG B 250 " --> pdb=" O PHE B 340 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N VAL B 342 " --> pdb=" O ARG B 250 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N THR B 252 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N GLY B 344 " --> pdb=" O THR B 252 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 464 through 466 Processing sheet with id=AB3, first strand: chain 'C' and resid 14 through 17 removed outlier: 6.159A pdb=" N GLN C 48 " --> pdb=" O HIS C 122 " (cutoff:3.500A) removed outlier: 8.813A pdb=" N HIS C 122 " --> pdb=" O GLN C 48 " (cutoff:3.500A) removed outlier: 10.869A pdb=" N ASP C 50 " --> pdb=" O ASN C 120 " (cutoff:3.500A) removed outlier: 12.415A pdb=" N ASN C 120 " --> pdb=" O ASP C 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 65 through 66 removed outlier: 6.821A pdb=" N PHE E 97 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N SER E 110 " --> pdb=" O PHE E 95 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N PHE E 95 " --> pdb=" O SER E 110 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL E 83 " --> pdb=" O ASN E 100 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 2 through 9 removed outlier: 3.969A pdb=" N GLU D 2 " --> pdb=" O TRP D 24 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 85 through 89 removed outlier: 3.981A pdb=" N PHE D 97 " --> pdb=" O GLY D 109 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLY D 109 " --> pdb=" O PHE D 97 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 2 through 9 Processing sheet with id=AB8, first strand: chain 'F' and resid 250 through 253 removed outlier: 7.089A pdb=" N LEU F 250 " --> pdb=" O TRP F 447 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N LYS F 449 " --> pdb=" O LEU F 250 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ALA F 252 " --> pdb=" O LYS F 449 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 287 through 292 removed outlier: 13.134A pdb=" N MET F 332 " --> pdb=" O LYS F 345 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N LYS F 345 " --> pdb=" O MET F 332 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ALA F 334 " --> pdb=" O MET F 343 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 287 through 292 removed outlier: 3.889A pdb=" N MET F 371 " --> pdb=" O ILE F 327 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ASP F 329 " --> pdb=" O VAL F 369 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N VAL F 369 " --> pdb=" O ASP F 329 " (cutoff:3.500A) removed outlier: 9.051A pdb=" N GLU F 331 " --> pdb=" O PHE F 367 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N PHE F 367 " --> pdb=" O GLU F 331 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N MET F 333 " --> pdb=" O CYS F 365 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N CYS F 365 " --> pdb=" O MET F 333 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N TYR F 335 " --> pdb=" O CYS F 363 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N CYS F 363 " --> pdb=" O TYR F 335 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 688 through 690 removed outlier: 6.296A pdb=" N PHE F 664 " --> pdb=" O VAL F 690 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N ILE F 701 " --> pdb=" O GLU F 663 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N CYS F 665 " --> pdb=" O ILE F 701 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL F 700 " --> pdb=" O VAL F 721 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL F 720 " --> pdb=" O ILE F 744 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 851 through 853 removed outlier: 6.386A pdb=" N VAL F 818 " --> pdb=" O VAL F 853 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N THR F 817 " --> pdb=" O HIS F 862 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ILE F 864 " --> pdb=" O THR F 817 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N TYR F 819 " --> pdb=" O ILE F 864 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N VAL F 863 " --> pdb=" O LEU F 889 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'G' and resid 8 through 11 removed outlier: 3.566A pdb=" N SER G 110 " --> pdb=" O SER G 49 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 8 through 11 removed outlier: 3.505A pdb=" N SER H 49 " --> pdb=" O SER H 110 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 32 through 33 removed outlier: 7.114A pdb=" N TYR M 33 " --> pdb=" O VAL M 70 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N VAL M 69 " --> pdb=" O LEU M 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'M' and resid 314 through 318 removed outlier: 3.982A pdb=" N ASP M 332 " --> pdb=" O THR M 318 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 455 through 456 Processing sheet with id=AC9, first strand: chain 'a' and resid 102 through 109 removed outlier: 6.502A pdb=" N VAL a 85 " --> pdb=" O LEU a 105 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N GLU a 107 " --> pdb=" O LEU a 83 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N LEU a 83 " --> pdb=" O GLU a 107 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ASP a 36 " --> pdb=" O LEU a 82 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ALA a 84 " --> pdb=" O ASP a 36 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU a 38 " --> pdb=" O ALA a 84 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N VAL a 86 " --> pdb=" O LEU a 38 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N PHE a 40 " --> pdb=" O VAL a 86 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N TYR a 88 " --> pdb=" O PHE a 40 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL a 42 " --> pdb=" O TYR a 88 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ARG a 35 " --> pdb=" O HIS a 163 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ARG a 165 " --> pdb=" O ARG a 35 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N SER a 37 " --> pdb=" O ARG a 165 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N MET a 167 " --> pdb=" O SER a 37 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ILE a 39 " --> pdb=" O MET a 167 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N PHE a 169 " --> pdb=" O ILE a 39 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU a 41 " --> pdb=" O PHE a 169 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N PHE a 199 " --> pdb=" O SER a 162 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LYS a 164 " --> pdb=" O PHE a 199 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N ASP a 201 " --> pdb=" O LYS a 164 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE a 166 " --> pdb=" O ASP a 201 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'a' and resid 257 through 262 removed outlier: 3.663A pdb=" N SER a 257 " --> pdb=" O ILE a 273 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY a 431 " --> pdb=" O GLN a 416 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N VAL a 394 " --> pdb=" O PRO a 415 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ARG a 399 " --> pdb=" O LEU a 347 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N LEU a 347 " --> pdb=" O ARG a 399 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N THR a 401 " --> pdb=" O LEU a 345 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N LEU a 345 " --> pdb=" O THR a 401 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N LEU a 345 " --> pdb=" O ARG a 258 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N LYS a 260 " --> pdb=" O LEU a 345 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LEU a 347 " --> pdb=" O LYS a 260 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LYS a 262 " --> pdb=" O LEU a 347 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N GLY a 349 " --> pdb=" O LYS a 262 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'a' and resid 286 through 289 Processing sheet with id=AD3, first strand: chain 'a' and resid 296 through 303 removed outlier: 3.502A pdb=" N PHE a 303 " --> pdb=" O GLN b 290 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN b 290 " --> pdb=" O PHE a 303 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'a' and resid 325 through 329 Processing sheet with id=AD5, first strand: chain 'a' and resid 375 through 376 removed outlier: 3.592A pdb=" N ILE b 540 " --> pdb=" O ILE a 376 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'a' and resid 419 through 421 removed outlier: 6.512A pdb=" N GLU a 419 " --> pdb=" O VAL a 427 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE a 425 " --> pdb=" O ASP a 421 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'b' and resid 77 through 84 removed outlier: 6.534A pdb=" N LEU b 56 " --> pdb=" O HIS b 80 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N HIS b 82 " --> pdb=" O ILE b 54 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N ILE b 54 " --> pdb=" O HIS b 82 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N MET b 84 " --> pdb=" O ASP b 52 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N ASP b 52 " --> pdb=" O MET b 84 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ALA b 8 " --> pdb=" O GLU b 53 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N ALA b 55 " --> pdb=" O ALA b 8 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL b 10 " --> pdb=" O ALA b 55 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N VAL b 57 " --> pdb=" O VAL b 10 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N LEU b 12 " --> pdb=" O VAL b 57 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N PHE b 59 " --> pdb=" O LEU b 12 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N MET b 14 " --> pdb=" O PHE b 59 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ARG b 130 " --> pdb=" O SER b 160 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N GLN b 162 " --> pdb=" O ARG b 130 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE b 132 " --> pdb=" O GLN b 162 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N PHE b 164 " --> pdb=" O ILE b 132 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE b 134 " --> pdb=" O PHE b 164 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N TYR b 225 " --> pdb=" O LEU b 161 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N PHE b 163 " --> pdb=" O TYR b 225 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'b' and resid 247 through 252 removed outlier: 6.838A pdb=" N VAL b 361 " --> pdb=" O SER b 266 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N LEU b 268 " --> pdb=" O ASN b 359 " (cutoff:3.500A) removed outlier: 9.823A pdb=" N ASN b 359 " --> pdb=" O LEU b 268 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N GLN b 360 " --> pdb=" O GLN b 423 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N GLN b 423 " --> pdb=" O GLN b 360 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ALA b 366 " --> pdb=" O GLU b 417 " (cutoff:3.500A) removed outlier: 10.277A pdb=" N GLU b 417 " --> pdb=" O ALA b 366 " (cutoff:3.500A) removed outlier: 8.819A pdb=" N MET b 389 " --> pdb=" O PRO b 410 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL b 390 " --> pdb=" O PHE b 345 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N PHE b 345 " --> pdb=" O VAL b 390 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE b 392 " --> pdb=" O LEU b 343 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N CYS b 339 " --> pdb=" O ALA b 396 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N PHE b 340 " --> pdb=" O PRO b 248 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ARG b 250 " --> pdb=" O PHE b 340 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N VAL b 342 " --> pdb=" O ARG b 250 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N THR b 252 " --> pdb=" O VAL b 342 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N GLY b 344 " --> pdb=" O THR b 252 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'b' and resid 464 through 467 Processing sheet with id=AE1, first strand: chain 'c' and resid 14 through 17 removed outlier: 6.762A pdb=" N GLN c 48 " --> pdb=" O HIS c 122 " (cutoff:3.500A) removed outlier: 8.791A pdb=" N HIS c 122 " --> pdb=" O GLN c 48 " (cutoff:3.500A) removed outlier: 10.783A pdb=" N ASP c 50 " --> pdb=" O ASN c 120 " (cutoff:3.500A) removed outlier: 12.112A pdb=" N ASN c 120 " --> pdb=" O ASP c 50 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'c' and resid 65 through 66 removed outlier: 6.767A pdb=" N PHE e 97 " --> pdb=" O LEU e 108 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N SER e 110 " --> pdb=" O PHE e 95 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N PHE e 95 " --> pdb=" O SER e 110 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N VAL e 83 " --> pdb=" O ASN e 100 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'd' and resid 2 through 9 Processing sheet with id=AE4, first strand: chain 'd' and resid 84 through 89 removed outlier: 3.768A pdb=" N PHE d 97 " --> pdb=" O GLY d 109 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY d 109 " --> pdb=" O PHE d 97 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LYS d 99 " --> pdb=" O ARG d 107 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ARG d 107 " --> pdb=" O LYS d 99 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'e' and resid 2 through 8 Processing sheet with id=AE6, first strand: chain 'f' and resid 688 through 690 removed outlier: 5.904A pdb=" N PHE f 664 " --> pdb=" O VAL f 690 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ILE f 701 " --> pdb=" O GLU f 663 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N CYS f 665 " --> pdb=" O ILE f 701 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N VAL f 700 " --> pdb=" O VAL f 721 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'f' and resid 818 through 820 removed outlier: 6.359A pdb=" N TYR f 819 " --> pdb=" O ILE f 864 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'm' and resid 32 through 34 removed outlier: 5.655A pdb=" N VAL m 69 " --> pdb=" O LEU m 100 " (cutoff:3.500A) 2074 hydrogen bonds defined for protein. 5907 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 179 hydrogen bonds 358 hydrogen bond angles 0 basepair planarities 74 basepair parallelities 128 stacking parallelities Total time for adding SS restraints: 10.95 Time building geometry restraints manager: 5.62 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: 13855 1.34 - 1.46: 9020 1.46 - 1.58: 21669 1.58 - 1.70: 301 1.70 - 1.82: 341 Bond restraints: 45186 Sorted by residual: bond pdb=" C2' DZ4 M 503 " pdb=" C3' DZ4 M 503 " ideal model delta sigma weight residual 1.526 1.310 0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C1' DZ4 M 503 " pdb=" O4' DZ4 M 503 " ideal model delta sigma weight residual 1.396 1.567 -0.171 2.00e-02 2.50e+03 7.29e+01 bond pdb=" C4' DZ4 M 503 " pdb=" O4' DZ4 M 503 " ideal model delta sigma weight residual 1.431 1.292 0.139 2.00e-02 2.50e+03 4.80e+01 bond pdb=" C6 DZ4 M 503 " pdb=" N6 DZ4 M 503 " ideal model delta sigma weight residual 1.336 1.462 -0.126 2.00e-02 2.50e+03 3.94e+01 bond pdb=" C1' DZ4 M 503 " pdb=" N9 DZ4 M 503 " ideal model delta sigma weight residual 1.466 1.345 0.121 2.00e-02 2.50e+03 3.67e+01 ... (remaining 45181 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.94: 61279 2.94 - 5.89: 365 5.89 - 8.83: 12 8.83 - 11.77: 2 11.77 - 14.72: 2 Bond angle restraints: 61660 Sorted by residual: angle pdb=" PA DZ4 M 503 " pdb=" N3A DZ4 M 503 " pdb=" PB DZ4 M 503 " ideal model delta sigma weight residual 135.12 120.40 14.72 3.00e+00 1.11e-01 2.41e+01 angle pdb=" O1A DZ4 M 503 " pdb=" PA DZ4 M 503 " pdb=" O2A DZ4 M 503 " ideal model delta sigma weight residual 121.65 108.16 13.49 3.00e+00 1.11e-01 2.02e+01 angle pdb=" N3 DT I 49 " pdb=" C4 DT I 49 " pdb=" O4 DT I 49 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 angle pdb=" N3 DT I 52 " pdb=" C4 DT I 52 " pdb=" O4 DT I 52 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 angle pdb=" N3 DT J 67 " pdb=" C4 DT J 67 " pdb=" O4 DT J 67 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.79e+01 ... (remaining 61655 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.67: 24344 25.67 - 51.35: 2453 51.35 - 77.02: 388 77.02 - 102.69: 36 102.69 - 128.37: 2 Dihedral angle restraints: 27223 sinusoidal: 12304 harmonic: 14919 Sorted by residual: dihedral pdb=" C5' DZ4 M 503 " pdb=" O5' DZ4 M 503 " pdb=" PA DZ4 M 503 " pdb=" O1A DZ4 M 503 " ideal model delta sinusoidal sigma weight residual -49.78 -178.15 128.37 1 3.00e+01 1.11e-03 1.73e+01 dihedral pdb=" C5' DZ4 M 503 " pdb=" O5' DZ4 M 503 " pdb=" PA DZ4 M 503 " pdb=" O2A DZ4 M 503 " ideal model delta sinusoidal sigma weight residual -179.58 -59.61 -119.97 1 3.00e+01 1.11e-03 1.60e+01 dihedral pdb=" CG ARG F 383 " pdb=" CD ARG F 383 " pdb=" NE ARG F 383 " pdb=" CZ ARG F 383 " ideal model delta sinusoidal sigma weight residual 90.00 37.33 52.67 2 1.50e+01 4.44e-03 1.35e+01 ... (remaining 27220 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 5013 0.033 - 0.067: 1122 0.067 - 0.100: 326 0.100 - 0.134: 288 0.134 - 0.167: 96 Chirality restraints: 6845 Sorted by residual: chirality pdb=" C1' DZ4 M 503 " pdb=" C2' DZ4 M 503 " pdb=" N9 DZ4 M 503 " pdb=" O4' DZ4 M 503 " both_signs ideal model delta sigma weight residual False 2.41 2.57 -0.17 2.00e-01 2.50e+01 6.98e-01 chirality pdb=" C3' DA I 36 " pdb=" C4' DA I 36 " pdb=" O3' DA I 36 " pdb=" C2' DA I 36 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.72e-01 chirality pdb=" C3' DA L 14 " pdb=" C4' DA L 14 " pdb=" O3' DA L 14 " pdb=" C2' DA L 14 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.52e-01 ... (remaining 6842 not shown) Planarity restraints: 7415 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 383 " -0.232 9.50e-02 1.11e+02 1.04e-01 7.28e+00 pdb=" NE ARG F 383 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG F 383 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG F 383 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG F 383 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 226 " 0.205 9.50e-02 1.11e+02 9.20e-02 5.58e+00 pdb=" NE ARG F 226 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG F 226 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG F 226 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG F 226 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 531 " -0.037 5.00e-02 4.00e+02 5.62e-02 5.06e+00 pdb=" N PRO A 532 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 532 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 532 " -0.031 5.00e-02 4.00e+02 ... (remaining 7412 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 212 2.57 - 3.15: 33986 3.15 - 3.73: 68802 3.73 - 4.32: 91381 4.32 - 4.90: 154201 Nonbonded interactions: 348582 Sorted by model distance: nonbonded pdb="MG MG M 501 " pdb=" O1B DZ4 M 503 " model vdw 1.982 2.170 nonbonded pdb=" OD2 ASP M 330 " pdb="MG MG M 502 " model vdw 1.988 2.170 nonbonded pdb=" OD2 ASP M 418 " pdb="MG MG M 502 " model vdw 2.109 2.170 nonbonded pdb="MG MG M 501 " pdb=" O2A DZ4 M 503 " model vdw 2.115 2.170 nonbonded pdb=" O3' DT I 68 " pdb="MG MG M 502 " model vdw 2.129 2.170 ... (remaining 348577 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 32 through 443 or resid 445 through 536)) selection = (chain 'a' and (resid 32 through 443 or resid 445 through 536)) } ncs_group { reference = (chain 'B' and (resid 6 through 169 or resid 183 through 542)) selection = (chain 'b' and resid 6 through 542) } ncs_group { reference = (chain 'C' and resid 0 through 227) selection = chain 'c' } ncs_group { reference = (chain 'D' and resid 1 through 200) selection = (chain 'E' and resid 1 through 200) selection = chain 'd' selection = chain 'e' } ncs_group { reference = (chain 'G' and (resid 5 through 27 or resid 36 through 66 or resid 71 through 14 \ 2 or resid 398 through 420)) selection = chain 'H' } 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=0.35 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 11.490 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: 0.030 Extract box with map and model: 0.790 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 44.840 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.090 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:7.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 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 : 0.003 0.216 45186 Z= 0.233 Angle : 0.534 14.716 61660 Z= 0.342 Chirality : 0.041 0.167 6845 Planarity : 0.004 0.104 7415 Dihedral : 18.949 128.368 17511 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.13 % Allowed : 21.16 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.83 % 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: 2.46 (0.13), residues: 5048 helix: 3.59 (0.12), residues: 2037 sheet: 0.78 (0.18), residues: 816 loop : 0.07 (0.14), residues: 2195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG F 383 TYR 0.013 0.001 TYR E 177 PHE 0.020 0.001 PHE B 59 TRP 0.033 0.001 TRP m 104 HIS 0.003 0.000 HIS m 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.23 (45186) covalent geometry : angle 0.53400 / 0.34 (61660) hydrogen bonds : bond 0.11776 / 7.53 ( 2239) hydrogen bonds : angle 4.80179 / 3.37 ( 6265) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10096 Ramachandran restraints generated. 5048 Oldfield, 0 Emsley, 5048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10096 Ramachandran restraints generated. 5048 Oldfield, 0 Emsley, 5048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 4521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 569 time to evaluate : 1.900 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: A 201 ASP cc_start: 0.7410 (p0) cc_final: 0.7162 (p0) REVERT: F 68 MET cc_start: 0.8866 (tpp) cc_final: 0.8621 (tpp) REVERT: F 371 MET cc_start: 0.7462 (ttt) cc_final: 0.6789 (tmm) REVERT: H 37 PHE cc_start: 0.6511 (OUTLIER) cc_final: 0.5418 (t80) REVERT: H 409 LYS cc_start: 0.8825 (tppt) cc_final: 0.8605 (tppt) REVERT: a 66 CYS cc_start: 0.8766 (m) cc_final: 0.8506 (m) REVERT: e 59 MET cc_start: 0.7665 (mtp) cc_final: 0.7454 (ttm) outliers start: 6 outliers final: 7 residues processed: 573 average time/residue: 0.8408 time to fit residues: 581.7643 Evaluate side-chains 363 residues out of total 4521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 355 time to evaluate : 1.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain H residue 37 PHE Chi-restraints excluded: chain M residue 470 PHE Chi-restraints excluded: chain a residue 425 ILE Chi-restraints excluded: chain d residue 172 LEU Chi-restraints excluded: chain e residue 175 ASP Chi-restraints excluded: chain f residue 801 TYR Chi-restraints excluded: chain m residue 102 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 394 optimal weight: 5.9990 chunk 430 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 265 optimal weight: 10.0000 chunk 497 optimal weight: 2.9990 chunk 414 optimal weight: 2.9990 chunk 310 optimal weight: 0.8980 chunk 488 optimal weight: 1.9990 chunk 366 optimal weight: 1.9990 chunk 223 optimal weight: 8.9990 chunk 142 optimal weight: 6.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 95 ASN A 121 GLN A 132 GLN A 360 HIS B 76 ASN B 243 HIS C 62 ASN C 134 HIS D 21 GLN F 13 HIS F 27 GLN F 294 ASN F 373 ASN ** F 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 816 HIS M 153 ASN M 396 GLN ** a 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 104 GLN c 6 GLN c 89 HIS c 134 HIS ** d 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.103219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.068673 restraints weight = 162971.845| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 4.32 r_work: 0.3008 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3009 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3009 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 45186 Z= 0.178 Angle : 0.595 11.492 61660 Z= 0.315 Chirality : 0.040 0.208 6845 Planarity : 0.004 0.077 7415 Dihedral : 15.753 132.211 7204 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.07 % Allowed : 22.55 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.83 % 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: 2.05 (0.12), residues: 5048 helix: 3.02 (0.12), residues: 2063 sheet: 0.80 (0.18), residues: 804 loop : -0.05 (0.13), residues: 2181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG f 884 TYR 0.021 0.001 TYR d 129 PHE 0.031 0.001 PHE E 180 TRP 0.023 0.001 TRP m 104 HIS 0.007 0.001 HIS f 745 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.18 (45186) covalent geometry : angle 0.59513 / 0.32 (61660) hydrogen bonds : bond 0.04146 / 2.74 ( 2239) hydrogen bonds : angle 4.23952 / 2.97 ( 6265) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10096 Ramachandran restraints generated. 5048 Oldfield, 0 Emsley, 5048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10096 Ramachandran restraints generated. 5048 Oldfield, 0 Emsley, 5048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 4521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 367 time to evaluate : 1.662 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: A 514 MET cc_start: 0.9295 (mtp) cc_final: 0.9037 (mtp) REVERT: B 184 ARG cc_start: 0.7528 (mtp-110) cc_final: 0.7010 (mtm180) REVERT: B 533 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8704 (mp) REVERT: C 165 GLN cc_start: 0.7915 (tp-100) cc_final: 0.7607 (tp-100) REVERT: D 153 ARG cc_start: 0.8954 (ptp-110) cc_final: 0.8701 (ptp-110) REVERT: E 89 SER cc_start: 0.8804 (OUTLIER) cc_final: 0.8543 (p) REVERT: E 106 PHE cc_start: 0.8072 (OUTLIER) cc_final: 0.6759 (m-80) REVERT: E 144 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8842 (tp) REVERT: E 191 ILE cc_start: 0.9436 (tp) cc_final: 0.9109 (pp) REVERT: F 302 PHE cc_start: 0.8273 (m-80) cc_final: 0.7947 (m-80) REVERT: F 332 MET cc_start: 0.7702 (mpm) cc_final: 0.6918 (mpt) REVERT: F 333 MET cc_start: 0.5764 (pmm) cc_final: 0.4853 (mmm) REVERT: F 371 MET cc_start: 0.7289 (ttt) cc_final: 0.6305 (tmm) REVERT: F 375 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8418 (mppt) REVERT: F 667 MET cc_start: 0.8864 (OUTLIER) cc_final: 0.8399 (mtp) REVERT: H 37 PHE cc_start: 0.7709 (OUTLIER) cc_final: 0.6166 (t80) REVERT: H 401 GLU cc_start: 0.7851 (tp30) cc_final: 0.7304 (tp30) REVERT: H 409 LYS cc_start: 0.9164 (tppt) cc_final: 0.8636 (tppt) REVERT: H 412 LYS cc_start: 0.9214 (tppp) cc_final: 0.9010 (tppp) REVERT: M 39 MET cc_start: 0.8002 (ttm) cc_final: 0.7753 (ttm) REVERT: M 41 ARG cc_start: 0.7447 (ttp80) cc_final: 0.7226 (ttp80) REVERT: M 85 ARG cc_start: 0.9103 (mtm110) cc_final: 0.8867 (ptm-80) REVERT: M 285 ASP cc_start: 0.8868 (OUTLIER) cc_final: 0.8528 (t0) REVERT: a 66 CYS cc_start: 0.9122 (m) cc_final: 0.8839 (m) REVERT: a 135 MET cc_start: 0.8663 (tpp) cc_final: 0.8179 (tpp) REVERT: a 315 ASP cc_start: 0.8997 (t0) cc_final: 0.8611 (m-30) REVERT: a 316 THR cc_start: 0.8658 (OUTLIER) cc_final: 0.8435 (m) REVERT: b 212 MET cc_start: 0.9143 (mmm) cc_final: 0.8932 (mmm) REVERT: b 238 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8347 (ttmt) REVERT: b 347 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8680 (mmmm) REVERT: c 186 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8649 (mp0) REVERT: d 192 ARG cc_start: 0.8924 (mmm160) cc_final: 0.8489 (tpm-80) REVERT: e 54 GLN cc_start: 0.8340 (tm-30) cc_final: 0.8083 (tm-30) REVERT: e 59 MET cc_start: 0.8015 (mtp) cc_final: 0.7794 (ttm) REVERT: f 773 GLN cc_start: 0.9491 (OUTLIER) cc_final: 0.8745 (mp10) REVERT: f 875 PHE cc_start: 0.8467 (m-80) cc_final: 0.7788 (m-80) REVERT: f 882 PHE cc_start: 0.7003 (OUTLIER) cc_final: 0.6652 (t80) REVERT: m 71 MET cc_start: 0.8779 (mpp) cc_final: 0.8477 (mmt) REVERT: m 107 GLU cc_start: 0.9483 (tp30) cc_final: 0.9197 (tm-30) REVERT: m 115 VAL cc_start: 0.8379 (t) cc_final: 0.7139 (p) outliers start: 139 outliers final: 47 residues processed: 477 average time/residue: 0.7185 time to fit residues: 423.8709 Evaluate side-chains 386 residues out of total 4521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 326 time to evaluate : 1.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 106 PHE Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 268 PHE Chi-restraints excluded: chain F residue 375 LYS Chi-restraints excluded: chain F residue 667 MET Chi-restraints excluded: chain F residue 700 VAL Chi-restraints excluded: chain H residue 37 PHE Chi-restraints excluded: chain H residue 402 SER Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 273 THR Chi-restraints excluded: chain M residue 285 ASP Chi-restraints excluded: chain M residue 424 VAL Chi-restraints excluded: chain a residue 37 SER Chi-restraints excluded: chain a residue 302 THR Chi-restraints excluded: chain a residue 316 THR Chi-restraints excluded: chain a residue 346 MET Chi-restraints excluded: chain a residue 425 ILE Chi-restraints excluded: chain b residue 238 LYS Chi-restraints excluded: chain b residue 339 CYS Chi-restraints excluded: chain b residue 347 LYS Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 55 SER Chi-restraints excluded: chain c residue 74 CYS Chi-restraints excluded: chain c residue 89 HIS Chi-restraints excluded: chain c residue 110 SER Chi-restraints excluded: chain c residue 123 CYS Chi-restraints excluded: chain c residue 129 SER Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain c residue 162 LEU Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 67 VAL Chi-restraints excluded: chain d residue 85 THR Chi-restraints excluded: chain d residue 116 VAL Chi-restraints excluded: chain e residue 15 SER Chi-restraints excluded: chain e residue 165 CYS Chi-restraints excluded: chain f residue 769 THR Chi-restraints excluded: chain f residue 773 GLN Chi-restraints excluded: chain f residue 781 ILE Chi-restraints excluded: chain f residue 882 PHE Chi-restraints excluded: chain m residue 34 LEU Chi-restraints excluded: chain m residue 58 VAL Chi-restraints excluded: chain m residue 63 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 498 optimal weight: 9.9990 chunk 82 optimal weight: 0.9980 chunk 220 optimal weight: 5.9990 chunk 388 optimal weight: 6.9990 chunk 392 optimal weight: 4.9990 chunk 454 optimal weight: 0.9990 chunk 213 optimal weight: 0.9990 chunk 255 optimal weight: 0.0670 chunk 314 optimal weight: 5.9990 chunk 373 optimal weight: 8.9990 chunk 58 optimal weight: 5.9990 overall best weight: 1.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 HIS B 492 GLN D 21 GLN ** F 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 6 GLN c 62 ASN c 89 HIS d 18 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.102299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.069306 restraints weight = 188554.427| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 4.38 r_work: 0.2970 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2968 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2968 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 45186 Z= 0.177 Angle : 0.573 11.331 61660 Z= 0.302 Chirality : 0.040 0.290 6845 Planarity : 0.004 0.056 7415 Dihedral : 15.931 141.932 7192 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.98 % Allowed : 22.35 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.83 % 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: 1.82 (0.12), residues: 5048 helix: 2.80 (0.11), residues: 2064 sheet: 0.71 (0.18), residues: 798 loop : -0.14 (0.13), residues: 2186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 141 TYR 0.027 0.001 TYR d 129 PHE 0.052 0.001 PHE F 268 TRP 0.019 0.001 TRP m 104 HIS 0.016 0.001 HIS c 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.18 (45186) covalent geometry : angle 0.57257 / 0.30 (61660) hydrogen bonds : bond 0.03821 / 2.52 ( 2239) hydrogen bonds : angle 4.11744 / 2.87 ( 6265) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10096 Ramachandran restraints generated. 5048 Oldfield, 0 Emsley, 5048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10096 Ramachandran restraints generated. 5048 Oldfield, 0 Emsley, 5048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 4521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 348 time to evaluate : 1.698 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: A 409 TYR cc_start: 0.8889 (OUTLIER) cc_final: 0.8366 (t80) REVERT: A 498 MET cc_start: 0.8939 (mmp) cc_final: 0.8733 (mmp) REVERT: B 184 ARG cc_start: 0.7634 (mtp-110) cc_final: 0.7084 (mtm180) REVERT: B 533 ILE cc_start: 0.9147 (OUTLIER) cc_final: 0.8745 (mp) REVERT: C 108 VAL cc_start: 0.9155 (OUTLIER) cc_final: 0.8945 (m) REVERT: C 165 GLN cc_start: 0.7993 (tp-100) cc_final: 0.7606 (tp-100) REVERT: D 193 SER cc_start: 0.9323 (OUTLIER) cc_final: 0.9057 (p) REVERT: E 144 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8843 (tp) REVERT: E 191 ILE cc_start: 0.9399 (tp) cc_final: 0.9154 (pp) REVERT: E 194 LEU cc_start: 0.9571 (OUTLIER) cc_final: 0.9368 (mm) REVERT: F 80 MET cc_start: 0.8500 (mmt) cc_final: 0.8279 (mmm) REVERT: F 249 MET cc_start: 0.5284 (OUTLIER) cc_final: 0.4383 (pmm) REVERT: F 275 ASP cc_start: 0.7661 (OUTLIER) cc_final: 0.7015 (t0) REVERT: F 302 PHE cc_start: 0.8460 (m-80) cc_final: 0.8176 (m-80) REVERT: F 371 MET cc_start: 0.7283 (ttt) cc_final: 0.6386 (tmm) REVERT: F 667 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.8309 (mtp) REVERT: F 792 MET cc_start: 0.9603 (tpp) cc_final: 0.9361 (tpt) REVERT: F 812 MET cc_start: 0.9050 (ppp) cc_final: 0.8788 (ppp) REVERT: G 20 PHE cc_start: 0.6830 (OUTLIER) cc_final: 0.6500 (t80) REVERT: H 37 PHE cc_start: 0.7797 (OUTLIER) cc_final: 0.6375 (t80) REVERT: H 401 GLU cc_start: 0.8080 (tp30) cc_final: 0.7651 (tp30) REVERT: H 409 LYS cc_start: 0.9227 (tppt) cc_final: 0.8777 (tppt) REVERT: M 39 MET cc_start: 0.7708 (ttm) cc_final: 0.7447 (ttm) REVERT: M 41 ARG cc_start: 0.7367 (ttp80) cc_final: 0.7121 (ttp80) REVERT: M 73 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7851 (tm-30) REVERT: M 285 ASP cc_start: 0.8859 (OUTLIER) cc_final: 0.8554 (t0) REVERT: a 315 ASP cc_start: 0.9119 (t0) cc_final: 0.8708 (t0) REVERT: a 316 THR cc_start: 0.8640 (OUTLIER) cc_final: 0.8386 (m) REVERT: b 212 MET cc_start: 0.9109 (mmm) cc_final: 0.8903 (mmm) REVERT: b 347 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8725 (mmmm) REVERT: b 427 MET cc_start: 0.9347 (ppp) cc_final: 0.9131 (tmm) REVERT: c 186 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.8682 (mp0) REVERT: c 197 LYS cc_start: 0.9127 (mttp) cc_final: 0.8825 (mtpp) REVERT: d 61 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.8101 (tmm) REVERT: d 93 CYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8447 (t) REVERT: d 145 GLN cc_start: 0.9084 (tm-30) cc_final: 0.8664 (tm-30) REVERT: e 54 GLN cc_start: 0.8205 (tm-30) cc_final: 0.7959 (tm-30) REVERT: e 105 SER cc_start: 0.8091 (OUTLIER) cc_final: 0.7731 (p) REVERT: e 138 GLN cc_start: 0.8745 (tm-30) cc_final: 0.8536 (tm-30) REVERT: f 662 VAL cc_start: 0.8242 (OUTLIER) cc_final: 0.8000 (m) REVERT: f 773 GLN cc_start: 0.9453 (OUTLIER) cc_final: 0.8872 (mp10) REVERT: f 875 PHE cc_start: 0.8570 (m-80) cc_final: 0.7908 (m-80) REVERT: m 41 ARG cc_start: 0.9197 (OUTLIER) cc_final: 0.8952 (ttp80) REVERT: m 107 GLU cc_start: 0.9554 (tp30) cc_final: 0.9195 (tm-30) outliers start: 135 outliers final: 55 residues processed: 452 average time/residue: 0.6633 time to fit residues: 371.8536 Evaluate side-chains 398 residues out of total 4521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 322 time to evaluate : 1.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain F residue 249 MET Chi-restraints excluded: chain F residue 275 ASP Chi-restraints excluded: chain F residue 662 VAL Chi-restraints excluded: chain F residue 667 MET Chi-restraints excluded: chain F residue 700 VAL Chi-restraints excluded: chain G residue 20 PHE Chi-restraints excluded: chain H residue 37 PHE Chi-restraints excluded: chain M residue 273 THR Chi-restraints excluded: chain M residue 285 ASP Chi-restraints excluded: chain M residue 424 VAL Chi-restraints excluded: chain M residue 470 PHE Chi-restraints excluded: chain a residue 37 SER Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 316 THR Chi-restraints excluded: chain a residue 373 SER Chi-restraints excluded: chain a residue 420 LEU Chi-restraints excluded: chain a residue 425 ILE Chi-restraints excluded: chain b residue 219 ASP Chi-restraints excluded: chain b residue 278 VAL Chi-restraints excluded: chain b residue 301 ASP Chi-restraints excluded: chain b residue 339 CYS Chi-restraints excluded: chain b residue 347 LYS Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 53 VAL Chi-restraints excluded: chain c residue 74 CYS Chi-restraints excluded: chain c residue 110 SER Chi-restraints excluded: chain c residue 129 SER Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain c residue 162 LEU Chi-restraints excluded: chain c residue 177 ASP Chi-restraints excluded: chain c residue 186 GLU Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 61 MET Chi-restraints excluded: chain d residue 67 VAL Chi-restraints excluded: chain d residue 85 THR Chi-restraints excluded: chain d residue 93 CYS Chi-restraints excluded: chain d residue 116 VAL Chi-restraints excluded: chain d residue 184 LEU Chi-restraints excluded: chain e residue 15 SER Chi-restraints excluded: chain e residue 30 SER Chi-restraints excluded: chain e residue 57 ASP Chi-restraints excluded: chain e residue 105 SER Chi-restraints excluded: chain e residue 116 VAL Chi-restraints excluded: chain e residue 165 CYS Chi-restraints excluded: chain e residue 189 THR Chi-restraints excluded: chain f residue 662 VAL Chi-restraints excluded: chain f residue 699 CYS Chi-restraints excluded: chain f residue 736 VAL Chi-restraints excluded: chain f residue 764 SER Chi-restraints excluded: chain f residue 769 THR Chi-restraints excluded: chain f residue 773 GLN Chi-restraints excluded: chain f residue 781 ILE Chi-restraints excluded: chain m residue 34 LEU Chi-restraints excluded: chain m residue 41 ARG Chi-restraints excluded: chain m residue 43 ARG Chi-restraints excluded: chain m residue 58 VAL Chi-restraints excluded: chain m residue 63 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 448 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 chunk 479 optimal weight: 6.9990 chunk 18 optimal weight: 0.1980 chunk 246 optimal weight: 30.0000 chunk 69 optimal weight: 4.9990 chunk 424 optimal weight: 1.9990 chunk 158 optimal weight: 0.9990 chunk 293 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 99 GLN B 243 HIS C 215 GLN D 141 ASN F 183 GLN ** F 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 459 HIS ** a 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 304 ASN a 416 GLN c 89 HIS ** m 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.102154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.068283 restraints weight = 162533.523| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 4.18 r_work: 0.2983 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2986 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2986 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 45186 Z= 0.147 Angle : 0.549 12.069 61660 Z= 0.287 Chirality : 0.039 0.230 6845 Planarity : 0.004 0.061 7415 Dihedral : 16.029 144.140 7192 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.23 % Allowed : 22.33 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.83 % 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: 1.73 (0.12), residues: 5048 helix: 2.72 (0.11), residues: 2066 sheet: 0.67 (0.18), residues: 791 loop : -0.19 (0.13), residues: 2191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 192 TYR 0.032 0.001 TYR d 129 PHE 0.026 0.001 PHE e 162 TRP 0.023 0.001 TRP M 82 HIS 0.013 0.001 HIS m 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (45186) covalent geometry : angle 0.54940 / 0.29 (61660) hydrogen bonds : bond 0.03577 / 2.35 ( 2239) hydrogen bonds : angle 4.02518 / 2.81 ( 6265) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10096 Ramachandran restraints generated. 5048 Oldfield, 0 Emsley, 5048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10096 Ramachandran restraints generated. 5048 Oldfield, 0 Emsley, 5048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 4521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 344 time to evaluate : 1.901 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: A 409 TYR cc_start: 0.8938 (OUTLIER) cc_final: 0.8289 (t80) REVERT: A 514 MET cc_start: 0.9260 (mtm) cc_final: 0.9010 (mtp) REVERT: B 184 ARG cc_start: 0.7675 (mtp-110) cc_final: 0.7105 (mtm180) REVERT: B 533 ILE cc_start: 0.9100 (OUTLIER) cc_final: 0.8693 (mp) REVERT: C 108 VAL cc_start: 0.9142 (OUTLIER) cc_final: 0.8926 (m) REVERT: C 165 GLN cc_start: 0.8053 (tp-100) cc_final: 0.7624 (tp-100) REVERT: D 192 ARG cc_start: 0.9087 (mmm160) cc_final: 0.8391 (tpm170) REVERT: D 193 SER cc_start: 0.9375 (OUTLIER) cc_final: 0.9101 (p) REVERT: E 191 ILE cc_start: 0.9387 (tp) cc_final: 0.9154 (pp) REVERT: F 80 MET cc_start: 0.8507 (mmp) cc_final: 0.8300 (mmm) REVERT: F 220 ASP cc_start: 0.7551 (OUTLIER) cc_final: 0.7081 (p0) REVERT: F 263 MET cc_start: 0.7356 (pmm) cc_final: 0.5320 (pp-130) REVERT: F 275 ASP cc_start: 0.7552 (OUTLIER) cc_final: 0.6969 (t0) REVERT: F 302 PHE cc_start: 0.8096 (m-80) cc_final: 0.7799 (m-80) REVERT: F 332 MET cc_start: 0.7696 (mmp) cc_final: 0.7412 (mpt) REVERT: F 371 MET cc_start: 0.7672 (ttt) cc_final: 0.6738 (tmm) REVERT: F 667 MET cc_start: 0.8838 (OUTLIER) cc_final: 0.8282 (mtp) REVERT: F 792 MET cc_start: 0.9585 (tpp) cc_final: 0.9347 (tpt) REVERT: F 812 MET cc_start: 0.8962 (ppp) cc_final: 0.8719 (ppp) REVERT: F 820 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8213 (tm) REVERT: G 401 GLU cc_start: 0.8264 (tp30) cc_final: 0.8044 (tp30) REVERT: H 37 PHE cc_start: 0.7583 (OUTLIER) cc_final: 0.5908 (t80) REVERT: H 401 GLU cc_start: 0.8056 (tp30) cc_final: 0.7586 (tp30) REVERT: H 409 LYS cc_start: 0.9170 (tppt) cc_final: 0.8689 (tppt) REVERT: M 39 MET cc_start: 0.8107 (ttm) cc_final: 0.7758 (ttm) REVERT: M 41 ARG cc_start: 0.7507 (ttp80) cc_final: 0.7231 (ttp80) REVERT: M 73 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7894 (tm-30) REVERT: M 285 ASP cc_start: 0.8838 (OUTLIER) cc_final: 0.8522 (t0) REVERT: M 476 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8387 (pm20) REVERT: a 315 ASP cc_start: 0.9114 (t0) cc_final: 0.8688 (t0) REVERT: a 316 THR cc_start: 0.8546 (OUTLIER) cc_final: 0.8296 (m) REVERT: b 84 MET cc_start: 0.8251 (ptp) cc_final: 0.7979 (ptp) REVERT: b 238 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8511 (ttmt) REVERT: b 347 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8690 (mmmm) REVERT: b 427 MET cc_start: 0.9288 (ppp) cc_final: 0.9044 (tmm) REVERT: c 186 GLU cc_start: 0.8960 (OUTLIER) cc_final: 0.8686 (mp0) REVERT: c 212 MET cc_start: 0.9155 (mmt) cc_final: 0.8933 (mmt) REVERT: d 21 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.8470 (tt0) REVERT: d 145 GLN cc_start: 0.9079 (tm-30) cc_final: 0.8611 (tm-30) REVERT: d 192 ARG cc_start: 0.8967 (mmm160) cc_final: 0.8545 (tpm-80) REVERT: e 54 GLN cc_start: 0.8331 (tm-30) cc_final: 0.8084 (tm-30) REVERT: e 58 ASP cc_start: 0.9093 (t0) cc_final: 0.8885 (t0) REVERT: e 105 SER cc_start: 0.8097 (OUTLIER) cc_final: 0.7755 (p) REVERT: e 138 GLN cc_start: 0.8822 (tm-30) cc_final: 0.8586 (tm-30) REVERT: f 773 GLN cc_start: 0.9459 (OUTLIER) cc_final: 0.8923 (mp10) REVERT: f 875 PHE cc_start: 0.8481 (m-80) cc_final: 0.7771 (m-80) REVERT: m 41 ARG cc_start: 0.9231 (OUTLIER) cc_final: 0.9007 (ttp80) REVERT: m 46 PHE cc_start: 0.9403 (t80) cc_final: 0.9191 (t80) REVERT: m 71 MET cc_start: 0.8448 (mmt) cc_final: 0.8199 (mpm) REVERT: m 107 GLU cc_start: 0.9491 (tp30) cc_final: 0.9146 (tm-30) outliers start: 146 outliers final: 59 residues processed: 458 average time/residue: 0.6956 time to fit residues: 398.2006 Evaluate side-chains 396 residues out of total 4521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 318 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 220 ASP Chi-restraints excluded: chain F residue 265 HIS Chi-restraints excluded: chain F residue 275 ASP Chi-restraints excluded: chain F residue 662 VAL Chi-restraints excluded: chain F residue 667 MET Chi-restraints excluded: chain F residue 700 VAL Chi-restraints excluded: chain F residue 820 LEU Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 37 PHE Chi-restraints excluded: chain H residue 402 SER Chi-restraints excluded: chain H residue 411 LYS Chi-restraints excluded: chain M residue 273 THR Chi-restraints excluded: chain M residue 285 ASP Chi-restraints excluded: chain M residue 424 VAL Chi-restraints excluded: chain M residue 470 PHE Chi-restraints excluded: chain M residue 476 GLU Chi-restraints excluded: chain a residue 180 SER Chi-restraints excluded: chain a residue 302 THR Chi-restraints excluded: chain a residue 316 THR Chi-restraints excluded: chain a residue 373 SER Chi-restraints excluded: chain a residue 420 LEU Chi-restraints excluded: chain b residue 238 LYS Chi-restraints excluded: chain b residue 278 VAL Chi-restraints excluded: chain b residue 301 ASP Chi-restraints excluded: chain b residue 339 CYS Chi-restraints excluded: chain b residue 347 LYS Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 53 VAL Chi-restraints excluded: chain c residue 55 SER Chi-restraints excluded: chain c residue 74 CYS Chi-restraints excluded: chain c residue 110 SER Chi-restraints excluded: chain c residue 123 CYS Chi-restraints excluded: chain c residue 129 SER Chi-restraints excluded: chain c residue 162 LEU Chi-restraints excluded: chain c residue 177 ASP Chi-restraints excluded: chain c residue 186 GLU Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 21 GLN Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 67 VAL Chi-restraints excluded: chain d residue 85 THR Chi-restraints excluded: chain d residue 116 VAL Chi-restraints excluded: chain d residue 184 LEU Chi-restraints excluded: chain d residue 191 ILE Chi-restraints excluded: chain e residue 15 SER Chi-restraints excluded: chain e residue 46 THR Chi-restraints excluded: chain e residue 105 SER Chi-restraints excluded: chain e residue 116 VAL Chi-restraints excluded: chain e residue 165 CYS Chi-restraints excluded: chain e residue 189 THR Chi-restraints excluded: chain f residue 688 TYR Chi-restraints excluded: chain f residue 699 CYS Chi-restraints excluded: chain f residue 736 VAL Chi-restraints excluded: chain f residue 769 THR Chi-restraints excluded: chain f residue 773 GLN Chi-restraints excluded: chain f residue 781 ILE Chi-restraints excluded: chain m residue 34 LEU Chi-restraints excluded: chain m residue 41 ARG Chi-restraints excluded: chain m residue 58 VAL Chi-restraints excluded: chain m residue 63 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 500 optimal weight: 7.9990 chunk 355 optimal weight: 0.8980 chunk 376 optimal weight: 1.9990 chunk 198 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 206 optimal weight: 8.9990 chunk 480 optimal weight: 3.9990 chunk 219 optimal weight: 10.0000 chunk 490 optimal weight: 0.8980 chunk 193 optimal weight: 20.0000 chunk 299 optimal weight: 0.0000 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 293 ASN B 243 HIS ** F 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 83 GLN ** a 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 293 ASN c 89 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.102057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.066024 restraints weight = 146179.637| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 4.10 r_work: 0.3005 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3005 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3005 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 45186 Z= 0.142 Angle : 0.552 12.361 61660 Z= 0.286 Chirality : 0.039 0.286 6845 Planarity : 0.004 0.067 7415 Dihedral : 16.082 146.087 7190 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.83 % Allowed : 22.86 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.83 % 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: 1.70 (0.12), residues: 5048 helix: 2.70 (0.12), residues: 2069 sheet: 0.61 (0.18), residues: 798 loop : -0.20 (0.13), residues: 2181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG m 38 TYR 0.034 0.001 TYR d 129 PHE 0.027 0.001 PHE e 162 TRP 0.023 0.001 TRP m 82 HIS 0.012 0.001 HIS m 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (45186) covalent geometry : angle 0.55188 / 0.29 (61660) hydrogen bonds : bond 0.03509 / 2.30 ( 2239) hydrogen bonds : angle 3.98554 / 2.79 ( 6265) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10096 Ramachandran restraints generated. 5048 Oldfield, 0 Emsley, 5048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10096 Ramachandran restraints generated. 5048 Oldfield, 0 Emsley, 5048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 4521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 341 time to evaluate : 1.801 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: A 409 TYR cc_start: 0.8927 (OUTLIER) cc_final: 0.8234 (t80) REVERT: A 498 MET cc_start: 0.8880 (mmp) cc_final: 0.8649 (mmp) REVERT: B 184 ARG cc_start: 0.7669 (mtp-110) cc_final: 0.7055 (mtm180) REVERT: B 428 GLU cc_start: 0.9181 (OUTLIER) cc_final: 0.8924 (pm20) REVERT: B 533 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8944 (mp) REVERT: C 108 VAL cc_start: 0.9143 (OUTLIER) cc_final: 0.8918 (m) REVERT: C 165 GLN cc_start: 0.8061 (tp-100) cc_final: 0.7616 (tp-100) REVERT: D 138 GLN cc_start: 0.9377 (tp40) cc_final: 0.8741 (tm-30) REVERT: D 157 ASP cc_start: 0.9254 (p0) cc_final: 0.8978 (p0) REVERT: D 192 ARG cc_start: 0.9019 (mmm160) cc_final: 0.8292 (tpm170) REVERT: D 193 SER cc_start: 0.9358 (OUTLIER) cc_final: 0.9062 (p) REVERT: F 220 ASP cc_start: 0.7567 (OUTLIER) cc_final: 0.7140 (p0) REVERT: F 241 THR cc_start: 0.8952 (OUTLIER) cc_final: 0.8668 (p) REVERT: F 263 MET cc_start: 0.8807 (pmm) cc_final: 0.7177 (pp-130) REVERT: F 268 PHE cc_start: 0.6965 (p90) cc_final: 0.6736 (p90) REVERT: F 275 ASP cc_start: 0.7444 (OUTLIER) cc_final: 0.6820 (t0) REVERT: F 371 MET cc_start: 0.7249 (ttt) cc_final: 0.6574 (tmm) REVERT: F 792 MET cc_start: 0.9546 (tpp) cc_final: 0.9281 (tpt) REVERT: F 812 MET cc_start: 0.8883 (ppp) cc_final: 0.8665 (ppp) REVERT: F 820 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8182 (tm) REVERT: G 20 PHE cc_start: 0.6537 (OUTLIER) cc_final: 0.6216 (t80) REVERT: H 37 PHE cc_start: 0.8176 (OUTLIER) cc_final: 0.6999 (t80) REVERT: H 401 GLU cc_start: 0.8131 (tp30) cc_final: 0.7655 (tp30) REVERT: H 409 LYS cc_start: 0.9227 (tppt) cc_final: 0.8763 (tppt) REVERT: M 39 MET cc_start: 0.8220 (ttm) cc_final: 0.7844 (ttm) REVERT: M 41 ARG cc_start: 0.7585 (ttp80) cc_final: 0.7125 (ttp80) REVERT: M 73 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7838 (tm-30) REVERT: M 285 ASP cc_start: 0.8861 (OUTLIER) cc_final: 0.8538 (t0) REVERT: a 315 ASP cc_start: 0.9107 (t0) cc_final: 0.8706 (t0) REVERT: a 316 THR cc_start: 0.8563 (OUTLIER) cc_final: 0.8300 (m) REVERT: b 84 MET cc_start: 0.8274 (ptp) cc_final: 0.8024 (ptp) REVERT: b 238 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8571 (ttmt) REVERT: c 89 HIS cc_start: 0.7081 (OUTLIER) cc_final: 0.6749 (p90) REVERT: c 186 GLU cc_start: 0.8951 (OUTLIER) cc_final: 0.8694 (mp0) REVERT: c 212 MET cc_start: 0.9101 (mmt) cc_final: 0.8874 (mmt) REVERT: d 93 CYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8514 (t) REVERT: d 145 GLN cc_start: 0.9103 (tm-30) cc_final: 0.8626 (tm-30) REVERT: d 192 ARG cc_start: 0.8926 (mmm160) cc_final: 0.8409 (tpm-80) REVERT: e 54 GLN cc_start: 0.8310 (tm-30) cc_final: 0.8053 (tm-30) REVERT: e 105 SER cc_start: 0.8071 (OUTLIER) cc_final: 0.7715 (p) REVERT: e 138 GLN cc_start: 0.8814 (tm-30) cc_final: 0.8572 (tm-30) REVERT: e 151 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8509 (tt) REVERT: f 773 GLN cc_start: 0.9435 (OUTLIER) cc_final: 0.8924 (mp10) REVERT: f 875 PHE cc_start: 0.8540 (m-80) cc_final: 0.7819 (m-80) REVERT: m 41 ARG cc_start: 0.9101 (OUTLIER) cc_final: 0.8853 (ttp80) REVERT: m 43 ARG cc_start: 0.9124 (OUTLIER) cc_final: 0.8574 (tpt170) REVERT: m 107 GLU cc_start: 0.9442 (tp30) cc_final: 0.9109 (tm-30) outliers start: 128 outliers final: 68 residues processed: 442 average time/residue: 0.7003 time to fit residues: 389.1294 Evaluate side-chains 408 residues out of total 4521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 318 time to evaluate : 1.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 428 GLU Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 220 ASP Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 275 ASP Chi-restraints excluded: chain F residue 662 VAL Chi-restraints excluded: chain F residue 700 VAL Chi-restraints excluded: chain F residue 754 PHE Chi-restraints excluded: chain F residue 820 LEU Chi-restraints excluded: chain G residue 20 PHE Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 37 PHE Chi-restraints excluded: chain H residue 402 SER Chi-restraints excluded: chain H residue 411 LYS Chi-restraints excluded: chain M residue 273 THR Chi-restraints excluded: chain M residue 285 ASP Chi-restraints excluded: chain M residue 424 VAL Chi-restraints excluded: chain M residue 470 PHE Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 162 SER Chi-restraints excluded: chain a residue 180 SER Chi-restraints excluded: chain a residue 229 LEU Chi-restraints excluded: chain a residue 302 THR Chi-restraints excluded: chain a residue 316 THR Chi-restraints excluded: chain a residue 373 SER Chi-restraints excluded: chain a residue 420 LEU Chi-restraints excluded: chain b residue 238 LYS Chi-restraints excluded: chain b residue 278 VAL Chi-restraints excluded: chain b residue 301 ASP Chi-restraints excluded: chain b residue 339 CYS Chi-restraints excluded: chain b residue 515 MET Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 53 VAL Chi-restraints excluded: chain c residue 55 SER Chi-restraints excluded: chain c residue 74 CYS Chi-restraints excluded: chain c residue 89 HIS Chi-restraints excluded: chain c residue 110 SER Chi-restraints excluded: chain c residue 129 SER Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain c residue 174 LEU Chi-restraints excluded: chain c residue 177 ASP Chi-restraints excluded: chain c residue 186 GLU Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 67 VAL Chi-restraints excluded: chain d residue 85 THR Chi-restraints excluded: chain d residue 93 CYS Chi-restraints excluded: chain d residue 116 VAL Chi-restraints excluded: chain d residue 184 LEU Chi-restraints excluded: chain e residue 6 SER Chi-restraints excluded: chain e residue 15 SER Chi-restraints excluded: chain e residue 30 SER Chi-restraints excluded: chain e residue 46 THR Chi-restraints excluded: chain e residue 105 SER Chi-restraints excluded: chain e residue 116 VAL Chi-restraints excluded: chain e residue 151 LEU Chi-restraints excluded: chain e residue 165 CYS Chi-restraints excluded: chain e residue 189 THR Chi-restraints excluded: chain f residue 688 TYR Chi-restraints excluded: chain f residue 699 CYS Chi-restraints excluded: chain f residue 769 THR Chi-restraints excluded: chain f residue 773 GLN Chi-restraints excluded: chain f residue 781 ILE Chi-restraints excluded: chain m residue 34 LEU Chi-restraints excluded: chain m residue 41 ARG Chi-restraints excluded: chain m residue 43 ARG Chi-restraints excluded: chain m residue 58 VAL Chi-restraints excluded: chain m residue 63 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 23 optimal weight: 3.9990 chunk 156 optimal weight: 0.7980 chunk 174 optimal weight: 0.9980 chunk 176 optimal weight: 0.7980 chunk 211 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 328 optimal weight: 0.0030 chunk 357 optimal weight: 0.8980 chunk 354 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 293 ASN B 243 HIS C 75 HIS C 187 ASN ** F 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.102428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.067636 restraints weight = 169395.289| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 4.49 r_work: 0.2972 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2969 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2969 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 45186 Z= 0.120 Angle : 0.557 12.721 61660 Z= 0.287 Chirality : 0.039 0.351 6845 Planarity : 0.004 0.076 7415 Dihedral : 16.088 147.041 7190 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.90 % Allowed : 23.37 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.83 % 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: 1.73 (0.12), residues: 5048 helix: 2.74 (0.12), residues: 2070 sheet: 0.61 (0.18), residues: 813 loop : -0.21 (0.13), residues: 2165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG m 38 TYR 0.034 0.001 TYR D 129 PHE 0.032 0.001 PHE F 302 TRP 0.028 0.001 TRP m 82 HIS 0.028 0.001 HIS c 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (45186) covalent geometry : angle 0.55741 / 0.29 (61660) hydrogen bonds : bond 0.03368 / 2.21 ( 2239) hydrogen bonds : angle 3.93059 / 2.75 ( 6265) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10096 Ramachandran restraints generated. 5048 Oldfield, 0 Emsley, 5048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10096 Ramachandran restraints generated. 5048 Oldfield, 0 Emsley, 5048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 4521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 342 time to evaluate : 1.902 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: A 409 TYR cc_start: 0.8945 (OUTLIER) cc_final: 0.8203 (t80) REVERT: B 184 ARG cc_start: 0.7613 (mtp-110) cc_final: 0.6989 (mtm180) REVERT: B 533 ILE cc_start: 0.9113 (OUTLIER) cc_final: 0.8709 (mp) REVERT: C 108 VAL cc_start: 0.9171 (OUTLIER) cc_final: 0.8948 (m) REVERT: C 165 GLN cc_start: 0.8078 (tp-100) cc_final: 0.7623 (tp-100) REVERT: D 138 GLN cc_start: 0.9415 (tp40) cc_final: 0.8756 (tm-30) REVERT: D 157 ASP cc_start: 0.9239 (p0) cc_final: 0.8985 (p0) REVERT: D 192 ARG cc_start: 0.9076 (mmm160) cc_final: 0.8297 (tpm170) REVERT: D 193 SER cc_start: 0.9308 (OUTLIER) cc_final: 0.9003 (p) REVERT: E 144 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8637 (tp) REVERT: E 153 ARG cc_start: 0.8950 (mtm110) cc_final: 0.8603 (mtm-85) REVERT: F 51 ASP cc_start: 0.9455 (t70) cc_final: 0.9186 (p0) REVERT: F 220 ASP cc_start: 0.7587 (OUTLIER) cc_final: 0.7200 (p0) REVERT: F 241 THR cc_start: 0.9190 (OUTLIER) cc_final: 0.8888 (p) REVERT: F 263 MET cc_start: 0.7743 (pmm) cc_final: 0.5279 (pp-130) REVERT: F 275 ASP cc_start: 0.7593 (OUTLIER) cc_final: 0.7189 (t0) REVERT: F 333 MET cc_start: 0.5659 (pmm) cc_final: 0.4965 (mtm) REVERT: F 371 MET cc_start: 0.7765 (ttt) cc_final: 0.6807 (tmm) REVERT: F 792 MET cc_start: 0.9571 (tpp) cc_final: 0.9340 (tpt) REVERT: F 812 MET cc_start: 0.8955 (ppp) cc_final: 0.8703 (ppp) REVERT: F 820 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8169 (tm) REVERT: H 37 PHE cc_start: 0.7588 (OUTLIER) cc_final: 0.5880 (t80) REVERT: H 401 GLU cc_start: 0.8077 (tp30) cc_final: 0.7569 (tp30) REVERT: H 409 LYS cc_start: 0.9216 (tppt) cc_final: 0.8747 (tppt) REVERT: M 39 MET cc_start: 0.8107 (ttm) cc_final: 0.7721 (ttm) REVERT: M 73 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7908 (tm-30) REVERT: M 285 ASP cc_start: 0.8835 (OUTLIER) cc_final: 0.8500 (t0) REVERT: a 135 MET cc_start: 0.8860 (tpp) cc_final: 0.8416 (mmt) REVERT: a 315 ASP cc_start: 0.9161 (t0) cc_final: 0.8811 (t0) REVERT: a 316 THR cc_start: 0.8513 (OUTLIER) cc_final: 0.8276 (m) REVERT: b 84 MET cc_start: 0.8187 (ptp) cc_final: 0.7918 (ptp) REVERT: b 238 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8533 (ttmt) REVERT: c 185 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7441 (tm-30) REVERT: c 186 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8702 (pm20) REVERT: c 197 LYS cc_start: 0.9097 (mttp) cc_final: 0.8794 (mtpp) REVERT: c 212 MET cc_start: 0.9179 (mmt) cc_final: 0.8962 (mmt) REVERT: d 21 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.8258 (tt0) REVERT: d 93 CYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8498 (t) REVERT: d 145 GLN cc_start: 0.9112 (tm-30) cc_final: 0.8673 (tm-30) REVERT: e 54 GLN cc_start: 0.8322 (tm-30) cc_final: 0.8064 (tm-30) REVERT: e 105 SER cc_start: 0.8060 (OUTLIER) cc_final: 0.7718 (p) REVERT: e 138 GLN cc_start: 0.8866 (tm-30) cc_final: 0.8603 (tm-30) REVERT: e 151 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8481 (tt) REVERT: f 773 GLN cc_start: 0.9467 (OUTLIER) cc_final: 0.8954 (mp10) REVERT: f 875 PHE cc_start: 0.8560 (m-80) cc_final: 0.7824 (m-80) REVERT: m 41 ARG cc_start: 0.9171 (OUTLIER) cc_final: 0.8920 (ttp80) REVERT: m 43 ARG cc_start: 0.9146 (OUTLIER) cc_final: 0.8901 (tpt170) REVERT: m 107 GLU cc_start: 0.9521 (tp30) cc_final: 0.9188 (tm-30) outliers start: 131 outliers final: 62 residues processed: 440 average time/residue: 0.6060 time to fit residues: 335.3946 Evaluate side-chains 402 residues out of total 4521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 318 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 220 ASP Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 275 ASP Chi-restraints excluded: chain F residue 662 VAL Chi-restraints excluded: chain F residue 754 PHE Chi-restraints excluded: chain F residue 820 LEU Chi-restraints excluded: chain G residue 24 CYS Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 37 PHE Chi-restraints excluded: chain H residue 402 SER Chi-restraints excluded: chain H residue 411 LYS Chi-restraints excluded: chain M residue 273 THR Chi-restraints excluded: chain M residue 285 ASP Chi-restraints excluded: chain M residue 390 CYS Chi-restraints excluded: chain M residue 424 VAL Chi-restraints excluded: chain M residue 468 THR Chi-restraints excluded: chain M residue 470 PHE Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 162 SER Chi-restraints excluded: chain a residue 229 LEU Chi-restraints excluded: chain a residue 302 THR Chi-restraints excluded: chain a residue 316 THR Chi-restraints excluded: chain a residue 373 SER Chi-restraints excluded: chain a residue 420 LEU Chi-restraints excluded: chain a residue 425 ILE Chi-restraints excluded: chain b residue 238 LYS Chi-restraints excluded: chain b residue 278 VAL Chi-restraints excluded: chain b residue 339 CYS Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 53 VAL Chi-restraints excluded: chain c residue 74 CYS Chi-restraints excluded: chain c residue 123 CYS Chi-restraints excluded: chain c residue 129 SER Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain c residue 164 ILE Chi-restraints excluded: chain c residue 174 LEU Chi-restraints excluded: chain c residue 177 ASP Chi-restraints excluded: chain c residue 185 GLU Chi-restraints excluded: chain c residue 186 GLU Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 21 GLN Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 67 VAL Chi-restraints excluded: chain d residue 93 CYS Chi-restraints excluded: chain d residue 116 VAL Chi-restraints excluded: chain e residue 6 SER Chi-restraints excluded: chain e residue 15 SER Chi-restraints excluded: chain e residue 30 SER Chi-restraints excluded: chain e residue 46 THR Chi-restraints excluded: chain e residue 105 SER Chi-restraints excluded: chain e residue 116 VAL Chi-restraints excluded: chain e residue 151 LEU Chi-restraints excluded: chain e residue 165 CYS Chi-restraints excluded: chain e residue 189 THR Chi-restraints excluded: chain f residue 688 TYR Chi-restraints excluded: chain f residue 736 VAL Chi-restraints excluded: chain f residue 769 THR Chi-restraints excluded: chain f residue 773 GLN Chi-restraints excluded: chain m residue 34 LEU Chi-restraints excluded: chain m residue 41 ARG Chi-restraints excluded: chain m residue 43 ARG Chi-restraints excluded: chain m residue 58 VAL Chi-restraints excluded: chain m residue 84 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 489 optimal weight: 2.9990 chunk 410 optimal weight: 0.9980 chunk 211 optimal weight: 4.9990 chunk 158 optimal weight: 0.6980 chunk 240 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 473 optimal weight: 4.9990 chunk 271 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 206 optimal weight: 7.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 293 ASN B 243 HIS ** F 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 132 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.100842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.066088 restraints weight = 154895.672| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 4.26 r_work: 0.2940 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2954 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2954 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 45186 Z= 0.194 Angle : 0.594 15.117 61660 Z= 0.303 Chirality : 0.040 0.411 6845 Planarity : 0.004 0.076 7415 Dihedral : 16.236 149.648 7190 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.07 % Allowed : 23.46 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.83 % 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: 1.63 (0.12), residues: 5048 helix: 2.60 (0.12), residues: 2085 sheet: 0.64 (0.18), residues: 794 loop : -0.25 (0.13), residues: 2169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG m 38 TYR 0.040 0.001 TYR D 129 PHE 0.033 0.001 PHE e 162 TRP 0.033 0.001 TRP m 82 HIS 0.008 0.001 HIS m 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.19 (45186) covalent geometry : angle 0.59378 / 0.30 (61660) hydrogen bonds : bond 0.03680 / 2.41 ( 2239) hydrogen bonds : angle 4.02158 / 2.82 ( 6265) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10096 Ramachandran restraints generated. 5048 Oldfield, 0 Emsley, 5048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10096 Ramachandran restraints generated. 5048 Oldfield, 0 Emsley, 5048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 4521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 322 time to evaluate : 1.927 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: A 409 TYR cc_start: 0.9013 (OUTLIER) cc_final: 0.8278 (t80) REVERT: C 165 GLN cc_start: 0.8062 (tp-100) cc_final: 0.7606 (tp-100) REVERT: D 138 GLN cc_start: 0.9435 (tp40) cc_final: 0.8776 (tm-30) REVERT: D 193 SER cc_start: 0.9301 (OUTLIER) cc_final: 0.9032 (p) REVERT: E 144 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8695 (tp) REVERT: E 153 ARG cc_start: 0.8935 (mtm110) cc_final: 0.8557 (mtm-85) REVERT: E 177 TYR cc_start: 0.8107 (OUTLIER) cc_final: 0.7670 (t80) REVERT: F 80 MET cc_start: 0.8570 (mmt) cc_final: 0.8281 (mmm) REVERT: F 220 ASP cc_start: 0.7733 (OUTLIER) cc_final: 0.7319 (p0) REVERT: F 241 THR cc_start: 0.9195 (OUTLIER) cc_final: 0.8904 (p) REVERT: F 263 MET cc_start: 0.7865 (pmm) cc_final: 0.7498 (pmm) REVERT: F 275 ASP cc_start: 0.7627 (OUTLIER) cc_final: 0.7086 (p0) REVERT: F 333 MET cc_start: 0.5714 (pmm) cc_final: 0.4973 (mtm) REVERT: F 371 MET cc_start: 0.7733 (ttt) cc_final: 0.6760 (tmm) REVERT: F 792 MET cc_start: 0.9588 (tpp) cc_final: 0.9358 (tpt) REVERT: F 812 MET cc_start: 0.8955 (ppp) cc_final: 0.8703 (ppp) REVERT: F 820 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8186 (tm) REVERT: H 37 PHE cc_start: 0.7710 (OUTLIER) cc_final: 0.5998 (t80) REVERT: H 401 GLU cc_start: 0.8129 (tp30) cc_final: 0.7643 (tp30) REVERT: H 409 LYS cc_start: 0.9245 (tppt) cc_final: 0.8799 (tppt) REVERT: M 39 MET cc_start: 0.8064 (ttm) cc_final: 0.7725 (ttm) REVERT: M 41 ARG cc_start: 0.7585 (ttp80) cc_final: 0.7385 (ttp80) REVERT: M 73 GLU cc_start: 0.8083 (tm-30) cc_final: 0.7833 (tm-30) REVERT: M 285 ASP cc_start: 0.8877 (OUTLIER) cc_final: 0.8543 (t0) REVERT: a 315 ASP cc_start: 0.9236 (t0) cc_final: 0.8937 (t0) REVERT: a 316 THR cc_start: 0.8636 (OUTLIER) cc_final: 0.8396 (m) REVERT: b 84 MET cc_start: 0.8266 (ptp) cc_final: 0.7993 (ptp) REVERT: b 347 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8700 (mmmm) REVERT: c 186 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8626 (pm20) REVERT: d 21 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.8286 (tt0) REVERT: d 93 CYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8540 (t) REVERT: d 145 GLN cc_start: 0.9169 (tm-30) cc_final: 0.8726 (tm-30) REVERT: d 192 ARG cc_start: 0.8988 (mmm160) cc_final: 0.8530 (tpm-80) REVERT: e 54 GLN cc_start: 0.8390 (tm-30) cc_final: 0.8117 (tm-30) REVERT: e 105 SER cc_start: 0.8046 (OUTLIER) cc_final: 0.7696 (p) REVERT: e 151 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8457 (tt) REVERT: f 688 TYR cc_start: 0.7992 (OUTLIER) cc_final: 0.7563 (t80) REVERT: f 773 GLN cc_start: 0.9441 (OUTLIER) cc_final: 0.8938 (mp10) REVERT: f 875 PHE cc_start: 0.8603 (m-80) cc_final: 0.7905 (m-80) REVERT: m 107 GLU cc_start: 0.9512 (tp30) cc_final: 0.9170 (tm-30) outliers start: 139 outliers final: 72 residues processed: 432 average time/residue: 0.6269 time to fit residues: 340.2664 Evaluate side-chains 401 residues out of total 4521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 310 time to evaluate : 1.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 177 TYR Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 220 ASP Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 268 PHE Chi-restraints excluded: chain F residue 275 ASP Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 662 VAL Chi-restraints excluded: chain F residue 700 VAL Chi-restraints excluded: chain F residue 754 PHE Chi-restraints excluded: chain F residue 820 LEU Chi-restraints excluded: chain G residue 24 CYS Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 37 PHE Chi-restraints excluded: chain H residue 402 SER Chi-restraints excluded: chain H residue 411 LYS Chi-restraints excluded: chain M residue 273 THR Chi-restraints excluded: chain M residue 285 ASP Chi-restraints excluded: chain M residue 390 CYS Chi-restraints excluded: chain M residue 424 VAL Chi-restraints excluded: chain M residue 468 THR Chi-restraints excluded: chain M residue 470 PHE Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 180 SER Chi-restraints excluded: chain a residue 229 LEU Chi-restraints excluded: chain a residue 316 THR Chi-restraints excluded: chain a residue 346 MET Chi-restraints excluded: chain a residue 373 SER Chi-restraints excluded: chain a residue 380 THR Chi-restraints excluded: chain a residue 420 LEU Chi-restraints excluded: chain b residue 278 VAL Chi-restraints excluded: chain b residue 339 CYS Chi-restraints excluded: chain b residue 347 LYS Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 53 VAL Chi-restraints excluded: chain c residue 55 SER Chi-restraints excluded: chain c residue 74 CYS Chi-restraints excluded: chain c residue 110 SER Chi-restraints excluded: chain c residue 123 CYS Chi-restraints excluded: chain c residue 129 SER Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain c residue 174 LEU Chi-restraints excluded: chain c residue 177 ASP Chi-restraints excluded: chain c residue 186 GLU Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 21 GLN Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 67 VAL Chi-restraints excluded: chain d residue 93 CYS Chi-restraints excluded: chain d residue 116 VAL Chi-restraints excluded: chain d residue 128 CYS Chi-restraints excluded: chain e residue 6 SER Chi-restraints excluded: chain e residue 15 SER Chi-restraints excluded: chain e residue 30 SER Chi-restraints excluded: chain e residue 46 THR Chi-restraints excluded: chain e residue 105 SER Chi-restraints excluded: chain e residue 116 VAL Chi-restraints excluded: chain e residue 151 LEU Chi-restraints excluded: chain e residue 165 CYS Chi-restraints excluded: chain e residue 189 THR Chi-restraints excluded: chain f residue 688 TYR Chi-restraints excluded: chain f residue 699 CYS Chi-restraints excluded: chain f residue 736 VAL Chi-restraints excluded: chain f residue 764 SER Chi-restraints excluded: chain f residue 769 THR Chi-restraints excluded: chain f residue 773 GLN Chi-restraints excluded: chain f residue 781 ILE Chi-restraints excluded: chain m residue 34 LEU Chi-restraints excluded: chain m residue 58 VAL Chi-restraints excluded: chain m residue 78 GLU Chi-restraints excluded: chain m residue 102 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 27 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 480 optimal weight: 3.9990 chunk 276 optimal weight: 7.9990 chunk 33 optimal weight: 0.0000 chunk 79 optimal weight: 2.9990 chunk 275 optimal weight: 10.0000 chunk 305 optimal weight: 3.9990 chunk 502 optimal weight: 30.0000 chunk 343 optimal weight: 0.9980 chunk 94 optimal weight: 0.6980 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 243 HIS ** F 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.100812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.066363 restraints weight = 161482.462| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 4.57 r_work: 0.2914 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2923 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2923 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 45186 Z= 0.180 Angle : 0.603 16.504 61660 Z= 0.305 Chirality : 0.041 0.438 6845 Planarity : 0.004 0.086 7415 Dihedral : 16.301 151.237 7190 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.87 % Allowed : 23.88 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.83 % 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: 1.57 (0.12), residues: 5048 helix: 2.57 (0.12), residues: 2084 sheet: 0.57 (0.18), residues: 804 loop : -0.29 (0.13), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG D 192 TYR 0.048 0.001 TYR D 129 PHE 0.033 0.001 PHE e 162 TRP 0.038 0.001 TRP m 82 HIS 0.006 0.001 HIS m 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (45186) covalent geometry : angle 0.60317 / 0.31 (61660) hydrogen bonds : bond 0.03613 / 2.37 ( 2239) hydrogen bonds : angle 4.02081 / 2.82 ( 6265) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10096 Ramachandran restraints generated. 5048 Oldfield, 0 Emsley, 5048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10096 Ramachandran restraints generated. 5048 Oldfield, 0 Emsley, 5048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 4521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 318 time to evaluate : 1.211 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: A 409 TYR cc_start: 0.9010 (OUTLIER) cc_final: 0.8204 (t80) REVERT: A 462 MET cc_start: 0.9400 (tpt) cc_final: 0.9157 (tpp) REVERT: C 165 GLN cc_start: 0.8041 (tp-100) cc_final: 0.7592 (tp-100) REVERT: C 167 TYR cc_start: 0.7967 (OUTLIER) cc_final: 0.7734 (m-80) REVERT: D 138 GLN cc_start: 0.9455 (tp40) cc_final: 0.8816 (tm-30) REVERT: D 192 ARG cc_start: 0.9070 (mmm160) cc_final: 0.8316 (tpm170) REVERT: D 193 SER cc_start: 0.9287 (OUTLIER) cc_final: 0.8978 (p) REVERT: E 29 GLU cc_start: 0.9399 (OUTLIER) cc_final: 0.9077 (mp0) REVERT: E 59 MET cc_start: 0.8540 (mmm) cc_final: 0.8331 (mmm) REVERT: E 89 SER cc_start: 0.8949 (OUTLIER) cc_final: 0.8694 (p) REVERT: E 144 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8704 (tp) REVERT: E 153 ARG cc_start: 0.8959 (mtm110) cc_final: 0.8577 (mtm-85) REVERT: E 177 TYR cc_start: 0.8134 (OUTLIER) cc_final: 0.7676 (t80) REVERT: F 80 MET cc_start: 0.8585 (mmt) cc_final: 0.8295 (mmm) REVERT: F 220 ASP cc_start: 0.7730 (OUTLIER) cc_final: 0.7364 (p0) REVERT: F 241 THR cc_start: 0.9178 (OUTLIER) cc_final: 0.8889 (p) REVERT: F 263 MET cc_start: 0.8097 (pmm) cc_final: 0.5897 (pp-130) REVERT: F 275 ASP cc_start: 0.7668 (OUTLIER) cc_final: 0.7069 (p0) REVERT: F 333 MET cc_start: 0.5629 (pmm) cc_final: 0.4913 (mtm) REVERT: F 371 MET cc_start: 0.7674 (ttt) cc_final: 0.6736 (tmm) REVERT: F 792 MET cc_start: 0.9587 (tpp) cc_final: 0.9357 (tpt) REVERT: F 812 MET cc_start: 0.8983 (OUTLIER) cc_final: 0.8722 (ppp) REVERT: F 820 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8191 (tm) REVERT: H 37 PHE cc_start: 0.7645 (OUTLIER) cc_final: 0.5945 (t80) REVERT: H 401 GLU cc_start: 0.8112 (tp30) cc_final: 0.7611 (tp30) REVERT: H 409 LYS cc_start: 0.9228 (tppt) cc_final: 0.8761 (tppt) REVERT: M 39 MET cc_start: 0.8007 (ttm) cc_final: 0.7649 (ttm) REVERT: M 41 ARG cc_start: 0.7552 (ttp80) cc_final: 0.7320 (ttp80) REVERT: M 73 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7831 (tm-30) REVERT: M 285 ASP cc_start: 0.8854 (OUTLIER) cc_final: 0.8505 (t0) REVERT: a 315 ASP cc_start: 0.9264 (t0) cc_final: 0.8981 (t0) REVERT: a 316 THR cc_start: 0.8703 (OUTLIER) cc_final: 0.8480 (m) REVERT: b 84 MET cc_start: 0.8227 (ptp) cc_final: 0.7995 (ptp) REVERT: b 238 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8558 (ttmt) REVERT: c 186 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.8599 (pm20) REVERT: c 192 GLN cc_start: 0.8799 (tp40) cc_final: 0.8557 (tp-100) REVERT: c 197 LYS cc_start: 0.9062 (mttp) cc_final: 0.8794 (mtpp) REVERT: d 21 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.8284 (tt0) REVERT: d 93 CYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8513 (t) REVERT: d 145 GLN cc_start: 0.9206 (tm-30) cc_final: 0.8752 (tm-30) REVERT: d 192 ARG cc_start: 0.9040 (mmm160) cc_final: 0.8565 (tpm-80) REVERT: e 54 GLN cc_start: 0.8314 (tm-30) cc_final: 0.8052 (tm-30) REVERT: e 59 MET cc_start: 0.7942 (mmm) cc_final: 0.7722 (mmm) REVERT: e 105 SER cc_start: 0.8036 (OUTLIER) cc_final: 0.7682 (p) REVERT: e 151 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8439 (tt) REVERT: f 688 TYR cc_start: 0.8126 (OUTLIER) cc_final: 0.7670 (t80) REVERT: f 773 GLN cc_start: 0.9455 (OUTLIER) cc_final: 0.8938 (mp10) REVERT: f 875 PHE cc_start: 0.8655 (m-80) cc_final: 0.7970 (m-80) REVERT: m 71 MET cc_start: 0.8753 (mmp) cc_final: 0.8376 (mmp) REVERT: m 107 GLU cc_start: 0.9536 (tp30) cc_final: 0.9193 (tm-30) outliers start: 130 outliers final: 73 residues processed: 428 average time/residue: 0.5491 time to fit residues: 295.3789 Evaluate side-chains 403 residues out of total 4521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 307 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 167 TYR Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 106 PHE Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 177 TYR Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 220 ASP Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 275 ASP Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 662 VAL Chi-restraints excluded: chain F residue 700 VAL Chi-restraints excluded: chain F residue 754 PHE Chi-restraints excluded: chain F residue 812 MET Chi-restraints excluded: chain F residue 820 LEU Chi-restraints excluded: chain G residue 24 CYS Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 37 PHE Chi-restraints excluded: chain H residue 402 SER Chi-restraints excluded: chain H residue 411 LYS Chi-restraints excluded: chain M residue 156 LEU Chi-restraints excluded: chain M residue 273 THR Chi-restraints excluded: chain M residue 285 ASP Chi-restraints excluded: chain M residue 390 CYS Chi-restraints excluded: chain M residue 424 VAL Chi-restraints excluded: chain M residue 468 THR Chi-restraints excluded: chain M residue 470 PHE Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 180 SER Chi-restraints excluded: chain a residue 316 THR Chi-restraints excluded: chain a residue 346 MET Chi-restraints excluded: chain a residue 373 SER Chi-restraints excluded: chain a residue 380 THR Chi-restraints excluded: chain a residue 420 LEU Chi-restraints excluded: chain a residue 475 SER Chi-restraints excluded: chain b residue 238 LYS Chi-restraints excluded: chain b residue 278 VAL Chi-restraints excluded: chain b residue 339 CYS Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 53 VAL Chi-restraints excluded: chain c residue 55 SER Chi-restraints excluded: chain c residue 74 CYS Chi-restraints excluded: chain c residue 110 SER Chi-restraints excluded: chain c residue 123 CYS Chi-restraints excluded: chain c residue 129 SER Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain c residue 174 LEU Chi-restraints excluded: chain c residue 177 ASP Chi-restraints excluded: chain c residue 186 GLU Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 21 GLN Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 67 VAL Chi-restraints excluded: chain d residue 93 CYS Chi-restraints excluded: chain d residue 116 VAL Chi-restraints excluded: chain e residue 6 SER Chi-restraints excluded: chain e residue 15 SER Chi-restraints excluded: chain e residue 30 SER Chi-restraints excluded: chain e residue 46 THR Chi-restraints excluded: chain e residue 105 SER Chi-restraints excluded: chain e residue 116 VAL Chi-restraints excluded: chain e residue 151 LEU Chi-restraints excluded: chain e residue 165 CYS Chi-restraints excluded: chain e residue 189 THR Chi-restraints excluded: chain f residue 688 TYR Chi-restraints excluded: chain f residue 699 CYS Chi-restraints excluded: chain f residue 736 VAL Chi-restraints excluded: chain f residue 769 THR Chi-restraints excluded: chain f residue 773 GLN Chi-restraints excluded: chain f residue 781 ILE Chi-restraints excluded: chain m residue 34 LEU Chi-restraints excluded: chain m residue 54 LYS Chi-restraints excluded: chain m residue 58 VAL Chi-restraints excluded: chain m residue 78 GLU Chi-restraints excluded: chain m residue 84 GLU Chi-restraints excluded: chain m residue 102 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 150 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 261 optimal weight: 10.0000 chunk 178 optimal weight: 3.9990 chunk 469 optimal weight: 0.6980 chunk 448 optimal weight: 6.9990 chunk 105 optimal weight: 0.2980 chunk 498 optimal weight: 20.0000 chunk 346 optimal weight: 7.9990 chunk 199 optimal weight: 10.0000 chunk 477 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 243 HIS ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 673 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.100336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.067619 restraints weight = 180397.369| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 4.43 r_work: 0.2908 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2918 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2918 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 45186 Z= 0.202 Angle : 0.628 15.357 61660 Z= 0.318 Chirality : 0.041 0.443 6845 Planarity : 0.004 0.094 7415 Dihedral : 16.390 153.309 7190 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.68 % Allowed : 23.97 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.83 % 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: 1.49 (0.12), residues: 5048 helix: 2.50 (0.11), residues: 2083 sheet: 0.51 (0.18), residues: 807 loop : -0.33 (0.13), residues: 2158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG m 38 TYR 0.045 0.002 TYR d 129 PHE 0.034 0.001 PHE e 162 TRP 0.044 0.001 TRP m 82 HIS 0.004 0.001 HIS b 511 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.20 (45186) covalent geometry : angle 0.62791 / 0.32 (61660) hydrogen bonds : bond 0.03754 / 2.47 ( 2239) hydrogen bonds : angle 4.10223 / 2.87 ( 6265) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10096 Ramachandran restraints generated. 5048 Oldfield, 0 Emsley, 5048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10096 Ramachandran restraints generated. 5048 Oldfield, 0 Emsley, 5048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 4521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 317 time to evaluate : 2.002 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: A 409 TYR cc_start: 0.9050 (OUTLIER) cc_final: 0.8276 (t80) REVERT: A 462 MET cc_start: 0.9451 (tpt) cc_final: 0.9230 (tpp) REVERT: C 165 GLN cc_start: 0.8099 (tp-100) cc_final: 0.7637 (tp-100) REVERT: C 167 TYR cc_start: 0.8047 (OUTLIER) cc_final: 0.7826 (m-80) REVERT: D 192 ARG cc_start: 0.9004 (mmm160) cc_final: 0.8143 (tpm170) REVERT: D 193 SER cc_start: 0.9236 (OUTLIER) cc_final: 0.8905 (p) REVERT: E 29 GLU cc_start: 0.9379 (OUTLIER) cc_final: 0.9072 (mp0) REVERT: E 89 SER cc_start: 0.8975 (OUTLIER) cc_final: 0.8722 (p) REVERT: E 144 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8750 (tp) REVERT: E 177 TYR cc_start: 0.8225 (OUTLIER) cc_final: 0.7677 (t80) REVERT: F 68 MET cc_start: 0.9584 (tpp) cc_final: 0.9077 (tpp) REVERT: F 80 MET cc_start: 0.8546 (mmt) cc_final: 0.8272 (mmm) REVERT: F 220 ASP cc_start: 0.7746 (OUTLIER) cc_final: 0.7375 (p0) REVERT: F 241 THR cc_start: 0.9134 (OUTLIER) cc_final: 0.8852 (p) REVERT: F 263 MET cc_start: 0.8203 (pmm) cc_final: 0.7792 (pmm) REVERT: F 275 ASP cc_start: 0.7666 (OUTLIER) cc_final: 0.7008 (p0) REVERT: F 279 MET cc_start: 0.7293 (mmp) cc_final: 0.6796 (mmp) REVERT: F 333 MET cc_start: 0.5146 (pmm) cc_final: 0.4812 (mtm) REVERT: F 371 MET cc_start: 0.7531 (ttt) cc_final: 0.6638 (tmm) REVERT: F 792 MET cc_start: 0.9577 (tpp) cc_final: 0.9320 (tpt) REVERT: F 812 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8722 (ppp) REVERT: F 820 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8221 (tm) REVERT: H 37 PHE cc_start: 0.7758 (OUTLIER) cc_final: 0.6177 (t80) REVERT: H 401 GLU cc_start: 0.8072 (tp30) cc_final: 0.7507 (tp30) REVERT: H 409 LYS cc_start: 0.9245 (tppt) cc_final: 0.8773 (tppt) REVERT: M 39 MET cc_start: 0.7977 (ttm) cc_final: 0.7616 (ttm) REVERT: M 73 GLU cc_start: 0.8233 (tm-30) cc_final: 0.7966 (tm-30) REVERT: M 285 ASP cc_start: 0.8862 (OUTLIER) cc_final: 0.8521 (t0) REVERT: a 135 MET cc_start: 0.8889 (tpp) cc_final: 0.8342 (mmt) REVERT: a 315 ASP cc_start: 0.9264 (t0) cc_final: 0.9034 (t0) REVERT: a 316 THR cc_start: 0.8765 (OUTLIER) cc_final: 0.8541 (m) REVERT: c 185 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7441 (tm-30) REVERT: c 186 GLU cc_start: 0.8972 (OUTLIER) cc_final: 0.8688 (pm20) REVERT: c 192 GLN cc_start: 0.8832 (tp40) cc_final: 0.8577 (tp-100) REVERT: c 197 LYS cc_start: 0.9103 (mttp) cc_final: 0.8828 (mtpp) REVERT: c 214 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9027 (pp) REVERT: d 21 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8289 (tt0) REVERT: d 93 CYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8474 (t) REVERT: d 145 GLN cc_start: 0.9188 (tm-30) cc_final: 0.8715 (tm-30) REVERT: d 192 ARG cc_start: 0.8975 (mmm160) cc_final: 0.8500 (tpm170) REVERT: e 54 GLN cc_start: 0.8353 (tm-30) cc_final: 0.8104 (tm-30) REVERT: e 105 SER cc_start: 0.7997 (OUTLIER) cc_final: 0.7637 (p) REVERT: e 151 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8454 (tt) REVERT: f 688 TYR cc_start: 0.8172 (OUTLIER) cc_final: 0.7778 (t80) REVERT: f 773 GLN cc_start: 0.9438 (OUTLIER) cc_final: 0.8925 (mp10) REVERT: f 875 PHE cc_start: 0.8669 (m-80) cc_final: 0.7977 (m-80) REVERT: m 36 GLU cc_start: 0.8745 (mp0) cc_final: 0.8207 (mp0) REVERT: m 59 LEU cc_start: 0.7283 (pt) cc_final: 0.6896 (pp) REVERT: m 71 MET cc_start: 0.8812 (mmp) cc_final: 0.8429 (mmp) REVERT: m 107 GLU cc_start: 0.9528 (tp30) cc_final: 0.9179 (tm-30) outliers start: 121 outliers final: 75 residues processed: 418 average time/residue: 0.5148 time to fit residues: 267.2684 Evaluate side-chains 406 residues out of total 4521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 307 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 167 TYR Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 106 PHE Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 177 TYR Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 220 ASP Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 268 PHE Chi-restraints excluded: chain F residue 275 ASP Chi-restraints excluded: chain F residue 662 VAL Chi-restraints excluded: chain F residue 700 VAL Chi-restraints excluded: chain F residue 754 PHE Chi-restraints excluded: chain F residue 812 MET Chi-restraints excluded: chain F residue 820 LEU Chi-restraints excluded: chain G residue 24 CYS Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 37 PHE Chi-restraints excluded: chain H residue 124 LEU Chi-restraints excluded: chain H residue 402 SER Chi-restraints excluded: chain H residue 411 LYS Chi-restraints excluded: chain M residue 273 THR Chi-restraints excluded: chain M residue 285 ASP Chi-restraints excluded: chain M residue 390 CYS Chi-restraints excluded: chain M residue 424 VAL Chi-restraints excluded: chain M residue 468 THR Chi-restraints excluded: chain M residue 470 PHE Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 180 SER Chi-restraints excluded: chain a residue 316 THR Chi-restraints excluded: chain a residue 380 THR Chi-restraints excluded: chain a residue 420 LEU Chi-restraints excluded: chain a residue 475 SER Chi-restraints excluded: chain b residue 278 VAL Chi-restraints excluded: chain b residue 339 CYS Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 53 VAL Chi-restraints excluded: chain c residue 55 SER Chi-restraints excluded: chain c residue 74 CYS Chi-restraints excluded: chain c residue 110 SER Chi-restraints excluded: chain c residue 123 CYS Chi-restraints excluded: chain c residue 129 SER Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain c residue 174 LEU Chi-restraints excluded: chain c residue 177 ASP Chi-restraints excluded: chain c residue 185 GLU Chi-restraints excluded: chain c residue 186 GLU Chi-restraints excluded: chain c residue 214 LEU Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 21 GLN Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 67 VAL Chi-restraints excluded: chain d residue 93 CYS Chi-restraints excluded: chain d residue 116 VAL Chi-restraints excluded: chain d residue 172 LEU Chi-restraints excluded: chain e residue 6 SER Chi-restraints excluded: chain e residue 15 SER Chi-restraints excluded: chain e residue 30 SER Chi-restraints excluded: chain e residue 46 THR Chi-restraints excluded: chain e residue 105 SER Chi-restraints excluded: chain e residue 116 VAL Chi-restraints excluded: chain e residue 151 LEU Chi-restraints excluded: chain e residue 165 CYS Chi-restraints excluded: chain e residue 189 THR Chi-restraints excluded: chain f residue 688 TYR Chi-restraints excluded: chain f residue 699 CYS Chi-restraints excluded: chain f residue 736 VAL Chi-restraints excluded: chain f residue 764 SER Chi-restraints excluded: chain f residue 769 THR Chi-restraints excluded: chain f residue 773 GLN Chi-restraints excluded: chain f residue 781 ILE Chi-restraints excluded: chain m residue 34 LEU Chi-restraints excluded: chain m residue 54 LYS Chi-restraints excluded: chain m residue 58 VAL Chi-restraints excluded: chain m residue 63 SER Chi-restraints excluded: chain m residue 78 GLU Chi-restraints excluded: chain m residue 84 GLU Chi-restraints excluded: chain m residue 102 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 27 optimal weight: 2.9990 chunk 399 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 310 optimal weight: 0.9980 chunk 335 optimal weight: 7.9990 chunk 239 optimal weight: 50.0000 chunk 35 optimal weight: 2.9990 chunk 39 optimal weight: 0.3980 chunk 288 optimal weight: 0.9990 chunk 210 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 243 HIS ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 229 HIS ** F 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 89 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.101290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.066895 restraints weight = 154524.795| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 4.22 r_work: 0.2955 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2965 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2965 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 45186 Z= 0.128 Angle : 0.620 14.987 61660 Z= 0.311 Chirality : 0.041 0.455 6845 Planarity : 0.004 0.097 7415 Dihedral : 16.321 152.943 7190 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.97 % Allowed : 24.81 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.83 % 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: 1.52 (0.12), residues: 5048 helix: 2.55 (0.12), residues: 2077 sheet: 0.47 (0.18), residues: 819 loop : -0.31 (0.13), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG M 85 TYR 0.032 0.001 TYR d 129 PHE 0.048 0.001 PHE m 46 TRP 0.046 0.001 TRP m 82 HIS 0.004 0.001 HIS M 365 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (45186) covalent geometry : angle 0.61952 / 0.31 (61660) hydrogen bonds : bond 0.03488 / 2.29 ( 2239) hydrogen bonds : angle 4.01404 / 2.81 ( 6265) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10096 Ramachandran restraints generated. 5048 Oldfield, 0 Emsley, 5048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10096 Ramachandran restraints generated. 5048 Oldfield, 0 Emsley, 5048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 4521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 324 time to evaluate : 1.074 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: A 409 TYR cc_start: 0.8991 (OUTLIER) cc_final: 0.8160 (t80) REVERT: A 462 MET cc_start: 0.9446 (tpt) cc_final: 0.9214 (tpp) REVERT: B 137 ASP cc_start: 0.8907 (t0) cc_final: 0.8663 (t0) REVERT: C 108 VAL cc_start: 0.9170 (OUTLIER) cc_final: 0.8918 (m) REVERT: C 165 GLN cc_start: 0.8015 (tp-100) cc_final: 0.7551 (tp-100) REVERT: D 192 ARG cc_start: 0.8979 (mmm160) cc_final: 0.8121 (tpm170) REVERT: D 193 SER cc_start: 0.9295 (OUTLIER) cc_final: 0.8991 (p) REVERT: E 29 GLU cc_start: 0.9343 (OUTLIER) cc_final: 0.9050 (mp0) REVERT: E 153 ARG cc_start: 0.8888 (mtm110) cc_final: 0.8618 (mtm-85) REVERT: E 177 TYR cc_start: 0.8226 (OUTLIER) cc_final: 0.7694 (t80) REVERT: F 51 ASP cc_start: 0.9428 (t70) cc_final: 0.9205 (p0) REVERT: F 68 MET cc_start: 0.9576 (tpp) cc_final: 0.9055 (tpp) REVERT: F 80 MET cc_start: 0.8554 (mmt) cc_final: 0.8352 (mmm) REVERT: F 201 GLN cc_start: 0.9444 (tt0) cc_final: 0.9143 (tm-30) REVERT: F 220 ASP cc_start: 0.7733 (OUTLIER) cc_final: 0.7389 (p0) REVERT: F 241 THR cc_start: 0.9173 (OUTLIER) cc_final: 0.8891 (p) REVERT: F 263 MET cc_start: 0.7731 (pmm) cc_final: 0.5195 (pp-130) REVERT: F 268 PHE cc_start: 0.6377 (p90) cc_final: 0.6101 (OUTLIER) REVERT: F 275 ASP cc_start: 0.7558 (OUTLIER) cc_final: 0.6862 (p0) REVERT: F 279 MET cc_start: 0.7105 (mmp) cc_final: 0.6727 (mmp) REVERT: F 371 MET cc_start: 0.7651 (ttt) cc_final: 0.6697 (tmm) REVERT: F 792 MET cc_start: 0.9551 (tpp) cc_final: 0.9311 (tpt) REVERT: F 812 MET cc_start: 0.8966 (OUTLIER) cc_final: 0.8687 (ppp) REVERT: F 820 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8195 (tm) REVERT: H 37 PHE cc_start: 0.7630 (OUTLIER) cc_final: 0.5942 (t80) REVERT: H 401 GLU cc_start: 0.8133 (tp30) cc_final: 0.7628 (tp30) REVERT: H 409 LYS cc_start: 0.9251 (tppt) cc_final: 0.8755 (tppt) REVERT: M 39 MET cc_start: 0.8115 (ttm) cc_final: 0.7751 (ttm) REVERT: M 73 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7879 (tm-30) REVERT: M 285 ASP cc_start: 0.8818 (OUTLIER) cc_final: 0.8471 (t0) REVERT: a 135 MET cc_start: 0.8919 (tpp) cc_final: 0.8366 (mmt) REVERT: a 315 ASP cc_start: 0.9264 (t0) cc_final: 0.9041 (t0) REVERT: a 316 THR cc_start: 0.8761 (OUTLIER) cc_final: 0.8539 (m) REVERT: c 185 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7471 (tm-30) REVERT: c 186 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.8692 (pm20) REVERT: c 192 GLN cc_start: 0.8823 (tp40) cc_final: 0.8595 (tp-100) REVERT: c 197 LYS cc_start: 0.9103 (mttp) cc_final: 0.8831 (mtpp) REVERT: c 214 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9014 (pp) REVERT: d 93 CYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8491 (t) REVERT: d 145 GLN cc_start: 0.9197 (tm-30) cc_final: 0.8713 (tm-30) REVERT: d 175 ASP cc_start: 0.9293 (t0) cc_final: 0.9064 (t0) REVERT: d 192 ARG cc_start: 0.8943 (mmm160) cc_final: 0.8470 (tpm170) REVERT: e 54 GLN cc_start: 0.8357 (tm-30) cc_final: 0.8081 (tm-30) REVERT: e 59 MET cc_start: 0.7906 (mmm) cc_final: 0.7434 (tpp) REVERT: e 105 SER cc_start: 0.7959 (OUTLIER) cc_final: 0.7603 (p) REVERT: e 151 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8499 (tt) REVERT: f 688 TYR cc_start: 0.8101 (OUTLIER) cc_final: 0.7663 (t80) REVERT: f 773 GLN cc_start: 0.9435 (OUTLIER) cc_final: 0.8962 (mp10) REVERT: f 875 PHE cc_start: 0.8649 (m-80) cc_final: 0.7943 (m-80) REVERT: m 36 GLU cc_start: 0.8636 (mp0) cc_final: 0.8090 (mp0) REVERT: m 59 LEU cc_start: 0.7198 (pt) cc_final: 0.6838 (pp) REVERT: m 107 GLU cc_start: 0.9501 (tp30) cc_final: 0.9183 (tm-30) outliers start: 89 outliers final: 58 residues processed: 394 average time/residue: 0.4809 time to fit residues: 235.7970 Evaluate side-chains 394 residues out of total 4521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 316 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 177 TYR Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 220 ASP Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 275 ASP Chi-restraints excluded: chain F residue 662 VAL Chi-restraints excluded: chain F residue 700 VAL Chi-restraints excluded: chain F residue 754 PHE Chi-restraints excluded: chain F residue 812 MET Chi-restraints excluded: chain F residue 820 LEU Chi-restraints excluded: chain G residue 24 CYS Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 37 PHE Chi-restraints excluded: chain H residue 124 LEU Chi-restraints excluded: chain M residue 285 ASP Chi-restraints excluded: chain M residue 390 CYS Chi-restraints excluded: chain M residue 424 VAL Chi-restraints excluded: chain M residue 468 THR Chi-restraints excluded: chain M residue 470 PHE Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 316 THR Chi-restraints excluded: chain a residue 420 LEU Chi-restraints excluded: chain b residue 278 VAL Chi-restraints excluded: chain b residue 339 CYS Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 53 VAL Chi-restraints excluded: chain c residue 74 CYS Chi-restraints excluded: chain c residue 123 CYS Chi-restraints excluded: chain c residue 129 SER Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain c residue 174 LEU Chi-restraints excluded: chain c residue 177 ASP Chi-restraints excluded: chain c residue 185 GLU Chi-restraints excluded: chain c residue 186 GLU Chi-restraints excluded: chain c residue 214 LEU Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 67 VAL Chi-restraints excluded: chain d residue 93 CYS Chi-restraints excluded: chain d residue 116 VAL Chi-restraints excluded: chain d residue 128 CYS Chi-restraints excluded: chain d residue 172 LEU Chi-restraints excluded: chain e residue 6 SER Chi-restraints excluded: chain e residue 15 SER Chi-restraints excluded: chain e residue 30 SER Chi-restraints excluded: chain e residue 46 THR Chi-restraints excluded: chain e residue 105 SER Chi-restraints excluded: chain e residue 151 LEU Chi-restraints excluded: chain e residue 165 CYS Chi-restraints excluded: chain e residue 189 THR Chi-restraints excluded: chain f residue 688 TYR Chi-restraints excluded: chain f residue 769 THR Chi-restraints excluded: chain f residue 773 GLN Chi-restraints excluded: chain m residue 34 LEU Chi-restraints excluded: chain m residue 43 ARG Chi-restraints excluded: chain m residue 54 LYS Chi-restraints excluded: chain m residue 78 GLU Chi-restraints excluded: chain m residue 84 GLU Chi-restraints excluded: chain m residue 102 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 142 optimal weight: 0.2980 chunk 364 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 385 optimal weight: 10.0000 chunk 57 optimal weight: 0.6980 chunk 310 optimal weight: 1.9990 chunk 432 optimal weight: 2.9990 chunk 333 optimal weight: 1.9990 chunk 207 optimal weight: 0.6980 chunk 423 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 243 HIS F 57 HIS ** F 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.101642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.065827 restraints weight = 142099.734| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 3.90 r_work: 0.2998 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3003 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3003 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 45186 Z= 0.124 Angle : 0.606 15.633 61660 Z= 0.306 Chirality : 0.040 0.447 6845 Planarity : 0.004 0.059 7415 Dihedral : 16.258 153.046 7190 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.06 % Allowed : 24.74 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.83 % 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: 1.54 (0.12), residues: 5048 helix: 2.59 (0.12), residues: 2076 sheet: 0.50 (0.18), residues: 819 loop : -0.32 (0.13), residues: 2153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 192 TYR 0.020 0.001 TYR M 362 PHE 0.041 0.001 PHE m 46 TRP 0.046 0.001 TRP m 82 HIS 0.007 0.001 HIS F 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (45186) covalent geometry : angle 0.60565 / 0.31 (61660) hydrogen bonds : bond 0.03397 / 2.22 ( 2239) hydrogen bonds : angle 3.96321 / 2.77 ( 6265) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21883.58 seconds wall clock time: 371 minutes 5.01 seconds (22265.01 seconds total)