Starting phenix.real_space_refine on Thu Mar 5 04:31:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vqh_21350/03_2026/6vqh_21350.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vqh_21350/03_2026/6vqh_21350.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6vqh_21350/03_2026/6vqh_21350.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vqh_21350/03_2026/6vqh_21350.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vqh_21350/03_2026/6vqh_21350.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vqh_21350/03_2026/6vqh_21350.map" } resolution = 4.4 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= -0.002 sd= 0.056 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 109 5.16 5 C 12438 2.51 5 N 3246 2.21 5 O 3545 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 83 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19338 Number of models: 1 Model: "" Number of chains: 18 Chain: "H" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 803 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 1, 'TRANS': 102} Chain: "L" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 875 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "a" Number of atoms: 2173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 2173 Classifications: {'peptide': 441} Incomplete info: {'truncation_to_alanine': 386} Link IDs: {'PTRANS': 18, 'TRANS': 422} Chain breaks: 2 Unresolved chain link angles: 18 Unresolved non-hydrogen bonds: 1513 Unresolved non-hydrogen angles: 1961 Unresolved non-hydrogen dihedrals: 1323 Unresolved non-hydrogen chiralities: 140 Planarities with less than four sites: {'GLU:plan': 17, 'PHE:plan': 45, 'ARG:plan': 13, 'ASN:plan1': 21, 'GLN:plan1': 10, 'TYR:plan': 19, 'HIS:plan': 15, 'ASP:plan': 7, 'TRP:plan': 9} Unresolved non-hydrogen planarities: 816 Chain: "b" Number of atoms: 1503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1503 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 5, 'TRANS': 197} Chain: "c" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 337 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "d" Number of atoms: 2833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2833 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 13, 'TRANS': 336} Chain: "e" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 384 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 6, 'TRANS': 71} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 361 Unresolved non-hydrogen dihedrals: 242 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'HIS:plan': 1, 'PHE:plan': 7, 'TRP:plan': 5, 'ASN:plan1': 3, 'ARG:plan': 2, 'TYR:plan': 2, 'GLN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 137 Chain: "f" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 412 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 3, 'TRANS': 80} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 259 Unresolved non-hydrogen angles: 337 Unresolved non-hydrogen dihedrals: 219 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'TRP:plan': 1, 'PHE:plan': 7, 'ASN:plan1': 6, 'HIS:plan': 1, 'GLU:plan': 4, 'ASP:plan': 2, 'GLN:plan1': 3, 'TYR:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 141 Chain: "g" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "h" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "i" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "j" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "k" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "l" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "m" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "n" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "o" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "p" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 406 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 50} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 17 Time building chain proxies: 4.30, per 1000 atoms: 0.22 Number of scatterers: 19338 At special positions: 0 Unit cell: (120.84, 119.78, 162.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 109 16.00 O 3545 8.00 N 3246 7.00 C 12438 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: 1.80 Conformation dependent library (CDL) restraints added in 935.8 milliseconds 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5030 Finding SS restraints... Secondary structure from input PDB file: 121 helices and 3 sheets defined 81.5% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'H' and resid 50 through 77 Processing helix chain 'H' and resid 79 through 86 Processing helix chain 'H' and resid 127 through 153 removed outlier: 3.622A pdb=" N THR H 153 " --> pdb=" O ALA H 149 " (cutoff:3.500A) Processing helix chain 'L' and resid 13 through 23 Processing helix chain 'L' and resid 44 through 57 Processing helix chain 'L' and resid 68 through 74 Processing helix chain 'L' and resid 74 through 81 removed outlier: 3.804A pdb=" N LEU L 78 " --> pdb=" O VAL L 74 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N HIS L 81 " --> pdb=" O ALA L 77 " (cutoff:3.500A) Processing helix chain 'L' and resid 103 through 109 Processing helix chain 'a' and resid 370 through 380 removed outlier: 4.462A pdb=" N PHE a 374 " --> pdb=" O PHE a 370 " (cutoff:3.500A) Processing helix chain 'a' and resid 391 through 407 removed outlier: 4.686A pdb=" N ILE a 397 " --> pdb=" O PRO a 393 " (cutoff:3.500A) Proline residue: a 400 - end of helix Processing helix chain 'a' and resid 409 through 426 Processing helix chain 'a' and resid 426 through 432 Processing helix chain 'a' and resid 437 through 446 Processing helix chain 'a' and resid 446 through 465 Processing helix chain 'a' and resid 481 through 488 removed outlier: 3.631A pdb=" N ILE a 487 " --> pdb=" O PRO a 483 " (cutoff:3.500A) Processing helix chain 'a' and resid 492 through 497 removed outlier: 4.320A pdb=" N LEU a 496 " --> pdb=" O GLU a 492 " (cutoff:3.500A) Processing helix chain 'a' and resid 498 through 500 No H-bonds generated for 'chain 'a' and resid 498 through 500' Processing helix chain 'a' and resid 520 through 526 Processing helix chain 'a' and resid 528 through 563 removed outlier: 4.577A pdb=" N ASN a 534 " --> pdb=" O LEU a 530 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER a 556 " --> pdb=" O GLY a 552 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU a 557 " --> pdb=" O VAL a 553 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE a 558 " --> pdb=" O SER a 554 " (cutoff:3.500A) Processing helix chain 'a' and resid 565 through 571 removed outlier: 3.812A pdb=" N ILE a 569 " --> pdb=" O LYS a 565 " (cutoff:3.500A) Processing helix chain 'a' and resid 572 through 598 removed outlier: 4.228A pdb=" N TYR a 586 " --> pdb=" O SER a 582 " (cutoff:3.500A) Processing helix chain 'a' and resid 599 through 603 Processing helix chain 'a' and resid 608 through 619 Processing helix chain 'a' and resid 632 through 647 Processing helix chain 'a' and resid 647 through 667 removed outlier: 3.560A pdb=" N MET a 651 " --> pdb=" O CYS a 647 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N LYS a 655 " --> pdb=" O MET a 651 " (cutoff:3.500A) Proline residue: a 656 - end of helix Processing helix chain 'a' and resid 713 through 739 removed outlier: 3.572A pdb=" N ILE a 733 " --> pdb=" O CYS a 729 " (cutoff:3.500A) Processing helix chain 'a' and resid 739 through 759 removed outlier: 4.259A pdb=" N TRP a 743 " --> pdb=" O TYR a 739 " (cutoff:3.500A) Processing helix chain 'a' and resid 761 through 765 Processing helix chain 'a' and resid 768 through 791 Processing helix chain 'a' and resid 793 through 810 Processing helix chain 'a' and resid 811 through 815 Processing helix chain 'b' and resid 3 through 29 Processing helix chain 'b' and resid 36 through 44 Processing helix chain 'b' and resid 45 through 80 removed outlier: 3.602A pdb=" N TRP b 49 " --> pdb=" O SER b 45 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER b 61 " --> pdb=" O ALA b 57 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER b 75 " --> pdb=" O ILE b 71 " (cutoff:3.500A) Processing helix chain 'b' and resid 81 through 82 No H-bonds generated for 'chain 'b' and resid 81 through 82' Processing helix chain 'b' and resid 83 through 84 No H-bonds generated for 'chain 'b' and resid 83 through 84' Processing helix chain 'b' and resid 85 through 90 removed outlier: 4.085A pdb=" N LYS b 89 " --> pdb=" O ARG b 85 " (cutoff:3.500A) Processing helix chain 'b' and resid 91 through 113 Processing helix chain 'b' and resid 127 through 169 removed outlier: 3.928A pdb=" N GLN b 168 " --> pdb=" O LEU b 164 " (cutoff:3.500A) Processing helix chain 'b' and resid 172 through 198 removed outlier: 4.197A pdb=" N ILE b 178 " --> pdb=" O VAL b 174 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N VAL b 179 " --> pdb=" O LYS b 175 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU b 180 " --> pdb=" O ILE b 176 " (cutoff:3.500A) Processing helix chain 'c' and resid 416 through 442 Processing helix chain 'd' and resid 8 through 25 removed outlier: 4.126A pdb=" N ASP d 12 " --> pdb=" O TYR d 8 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N TYR d 15 " --> pdb=" O VAL d 11 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N LEU d 16 " --> pdb=" O ASP d 12 " (cutoff:3.500A) Processing helix chain 'd' and resid 29 through 38 Processing helix chain 'd' and resid 41 through 50 Processing helix chain 'd' and resid 66 through 88 Processing helix chain 'd' and resid 90 through 116 removed outlier: 4.899A pdb=" N PHE d 96 " --> pdb=" O PRO d 92 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE d 100 " --> pdb=" O PHE d 96 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TYR d 104 " --> pdb=" O ILE d 100 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP d 107 " --> pdb=" O SER d 103 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N THR d 114 " --> pdb=" O ILE d 110 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY d 115 " --> pdb=" O LEU d 111 " (cutoff:3.500A) Processing helix chain 'd' and resid 121 through 126 Processing helix chain 'd' and resid 127 through 129 No H-bonds generated for 'chain 'd' and resid 127 through 129' Processing helix chain 'd' and resid 146 through 157 Processing helix chain 'd' and resid 158 through 167 removed outlier: 4.100A pdb=" N ALA d 162 " --> pdb=" O PRO d 159 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP d 166 " --> pdb=" O PHE d 163 " (cutoff:3.500A) Processing helix chain 'd' and resid 170 through 176 Processing helix chain 'd' and resid 177 through 200 Processing helix chain 'd' and resid 202 through 227 Proline residue: d 210 - end of helix Processing helix chain 'd' and resid 228 through 230 No H-bonds generated for 'chain 'd' and resid 228 through 230' Processing helix chain 'd' and resid 233 through 240 removed outlier: 3.636A pdb=" N LEU d 240 " --> pdb=" O ASP d 236 " (cutoff:3.500A) Processing helix chain 'd' and resid 251 through 258 Processing helix chain 'd' and resid 260 through 269 Processing helix chain 'd' and resid 271 through 281 removed outlier: 4.438A pdb=" N LEU d 277 " --> pdb=" O GLU d 273 " (cutoff:3.500A) Processing helix chain 'd' and resid 289 through 305 Processing helix chain 'd' and resid 306 through 308 No H-bonds generated for 'chain 'd' and resid 306 through 308' Processing helix chain 'd' and resid 312 through 338 removed outlier: 3.708A pdb=" N TYR d 316 " --> pdb=" O PHE d 312 " (cutoff:3.500A) Processing helix chain 'd' and resid 340 through 344 Processing helix chain 'e' and resid 6 through 23 Processing helix chain 'e' and resid 24 through 27 Processing helix chain 'e' and resid 33 through 58 Processing helix chain 'e' and resid 69 through 78 removed outlier: 3.575A pdb=" N ARG e 77 " --> pdb=" O ILE e 73 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE e 78 " --> pdb=" O TRP e 74 " (cutoff:3.500A) Processing helix chain 'f' and resid 8 through 36 Processing helix chain 'f' and resid 54 through 90 removed outlier: 3.967A pdb=" N ILE f 58 " --> pdb=" O GLY f 54 " (cutoff:3.500A) Processing helix chain 'g' and resid 10 through 46 removed outlier: 3.614A pdb=" N PHE g 14 " --> pdb=" O TYR g 10 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLY g 15 " --> pdb=" O SER g 11 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET g 23 " --> pdb=" O ALA g 19 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER g 26 " --> pdb=" O ALA g 22 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL g 46 " --> pdb=" O ALA g 42 " (cutoff:3.500A) Processing helix chain 'g' and resid 48 through 52 Processing helix chain 'g' and resid 53 through 55 No H-bonds generated for 'chain 'g' and resid 53 through 55' Processing helix chain 'g' and resid 56 through 78 Processing helix chain 'g' and resid 86 through 124 Processing helix chain 'g' and resid 127 through 153 removed outlier: 3.838A pdb=" N SER g 153 " --> pdb=" O ALA g 149 " (cutoff:3.500A) Processing helix chain 'h' and resid 11 through 46 removed outlier: 4.421A pdb=" N GLY h 15 " --> pdb=" O SER h 11 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL h 46 " --> pdb=" O ALA h 42 " (cutoff:3.500A) Processing helix chain 'h' and resid 48 through 52 Processing helix chain 'h' and resid 56 through 78 Processing helix chain 'h' and resid 86 through 124 Processing helix chain 'h' and resid 126 through 154 removed outlier: 4.454A pdb=" N GLY h 130 " --> pdb=" O ARG h 126 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY h 145 " --> pdb=" O LEU h 141 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR h 154 " --> pdb=" O LEU h 150 " (cutoff:3.500A) Processing helix chain 'i' and resid 10 through 48 removed outlier: 4.083A pdb=" N PHE i 14 " --> pdb=" O TYR i 10 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLY i 15 " --> pdb=" O SER i 11 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N MET i 23 " --> pdb=" O ALA i 19 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER i 26 " --> pdb=" O ALA i 22 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET i 47 " --> pdb=" O ALA i 43 " (cutoff:3.500A) Processing helix chain 'i' and resid 49 through 52 Processing helix chain 'i' and resid 56 through 78 Processing helix chain 'i' and resid 86 through 124 removed outlier: 3.900A pdb=" N GLN i 123 " --> pdb=" O ARG i 119 " (cutoff:3.500A) Processing helix chain 'i' and resid 126 through 154 removed outlier: 4.604A pdb=" N GLY i 130 " --> pdb=" O ARG i 126 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY i 145 " --> pdb=" O LEU i 141 " (cutoff:3.500A) Processing helix chain 'j' and resid 11 through 48 removed outlier: 4.302A pdb=" N GLY j 15 " --> pdb=" O SER j 11 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET j 23 " --> pdb=" O ALA j 19 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL j 46 " --> pdb=" O ALA j 42 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N MET j 47 " --> pdb=" O ALA j 43 " (cutoff:3.500A) Processing helix chain 'j' and resid 49 through 52 Processing helix chain 'j' and resid 53 through 55 No H-bonds generated for 'chain 'j' and resid 53 through 55' Processing helix chain 'j' and resid 56 through 78 removed outlier: 3.614A pdb=" N ILE j 64 " --> pdb=" O VAL j 60 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE j 65 " --> pdb=" O MET j 61 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA j 66 " --> pdb=" O ALA j 62 " (cutoff:3.500A) Processing helix chain 'j' and resid 86 through 124 Processing helix chain 'j' and resid 126 through 154 removed outlier: 4.483A pdb=" N GLY j 130 " --> pdb=" O ARG j 126 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY j 145 " --> pdb=" O LEU j 141 " (cutoff:3.500A) Processing helix chain 'k' and resid 10 through 48 removed outlier: 3.898A pdb=" N PHE k 14 " --> pdb=" O TYR k 10 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLY k 15 " --> pdb=" O SER k 11 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET k 23 " --> pdb=" O ALA k 19 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL k 46 " --> pdb=" O ALA k 42 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N MET k 47 " --> pdb=" O ALA k 43 " (cutoff:3.500A) Processing helix chain 'k' and resid 49 through 52 Processing helix chain 'k' and resid 53 through 55 No H-bonds generated for 'chain 'k' and resid 53 through 55' Processing helix chain 'k' and resid 56 through 80 Processing helix chain 'k' and resid 86 through 124 Processing helix chain 'k' and resid 127 through 154 Processing helix chain 'l' and resid 11 through 48 removed outlier: 4.417A pdb=" N GLY l 15 " --> pdb=" O SER l 11 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA l 43 " --> pdb=" O THR l 39 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL l 46 " --> pdb=" O ALA l 42 " (cutoff:3.500A) Processing helix chain 'l' and resid 49 through 52 Processing helix chain 'l' and resid 53 through 55 No H-bonds generated for 'chain 'l' and resid 53 through 55' Processing helix chain 'l' and resid 56 through 80 Processing helix chain 'l' and resid 86 through 124 removed outlier: 3.737A pdb=" N GLN l 123 " --> pdb=" O ARG l 119 " (cutoff:3.500A) Processing helix chain 'l' and resid 126 through 155 removed outlier: 4.390A pdb=" N GLY l 130 " --> pdb=" O ARG l 126 " (cutoff:3.500A) Processing helix chain 'm' and resid 10 through 45 removed outlier: 3.641A pdb=" N SER m 26 " --> pdb=" O ALA m 22 " (cutoff:3.500A) Processing helix chain 'm' and resid 46 through 47 No H-bonds generated for 'chain 'm' and resid 46 through 47' Processing helix chain 'm' and resid 48 through 55 removed outlier: 4.732A pdb=" N MET m 53 " --> pdb=" O GLU m 50 " (cutoff:3.500A) Processing helix chain 'm' and resid 56 through 80 Processing helix chain 'm' and resid 86 through 124 removed outlier: 3.989A pdb=" N GLN m 123 " --> pdb=" O ARG m 119 " (cutoff:3.500A) Processing helix chain 'm' and resid 126 through 154 removed outlier: 4.365A pdb=" N GLY m 130 " --> pdb=" O ARG m 126 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY m 145 " --> pdb=" O LEU m 141 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR m 154 " --> pdb=" O LEU m 150 " (cutoff:3.500A) Processing helix chain 'n' and resid 11 through 46 removed outlier: 4.512A pdb=" N GLY n 15 " --> pdb=" O SER n 11 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET n 23 " --> pdb=" O ALA n 19 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL n 46 " --> pdb=" O ALA n 42 " (cutoff:3.500A) Processing helix chain 'n' and resid 48 through 52 Processing helix chain 'n' and resid 56 through 79 removed outlier: 3.567A pdb=" N SER n 79 " --> pdb=" O LEU n 75 " (cutoff:3.500A) Processing helix chain 'n' and resid 86 through 124 removed outlier: 3.590A pdb=" N ARG n 119 " --> pdb=" O ASP n 115 " (cutoff:3.500A) Processing helix chain 'n' and resid 126 through 154 removed outlier: 4.631A pdb=" N GLY n 130 " --> pdb=" O ARG n 126 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY n 145 " --> pdb=" O LEU n 141 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR n 154 " --> pdb=" O LEU n 150 " (cutoff:3.500A) Processing helix chain 'o' and resid 10 through 48 removed outlier: 4.311A pdb=" N PHE o 14 " --> pdb=" O TYR o 10 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLY o 15 " --> pdb=" O SER o 11 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N MET o 47 " --> pdb=" O ALA o 43 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 52 Processing helix chain 'o' and resid 53 through 55 No H-bonds generated for 'chain 'o' and resid 53 through 55' Processing helix chain 'o' and resid 56 through 80 removed outlier: 3.527A pdb=" N VAL o 60 " --> pdb=" O ILE o 56 " (cutoff:3.500A) Processing helix chain 'o' and resid 86 through 124 Processing helix chain 'o' and resid 127 through 154 removed outlier: 3.662A pdb=" N THR o 154 " --> pdb=" O LEU o 150 " (cutoff:3.500A) Processing helix chain 'p' and resid 302 through 330 Processing helix chain 'p' and resid 338 through 343 Processing sheet with id=AA1, first strand: chain 'H' and resid 93 through 99 Processing sheet with id=AA2, first strand: chain 'L' and resid 36 through 38 removed outlier: 8.550A pdb=" N LEU L 37 " --> pdb=" O ILE L 8 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL L 10 " --> pdb=" O LEU L 37 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ALA L 9 " --> pdb=" O LEU L 65 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N ASN L 67 " --> pdb=" O ALA L 9 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ILE L 11 " --> pdb=" O ASN L 67 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE L 64 " --> pdb=" O LEU L 89 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ILE L 91 " --> pdb=" O ILE L 64 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE L 66 " --> pdb=" O ILE L 91 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'a' and resid 362 through 363 1741 hydrogen bonds defined for protein. 5118 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.51 Time building geometry restraints manager: 2.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3210 1.30 - 1.43: 4702 1.43 - 1.56: 11493 1.56 - 1.68: 0 1.68 - 1.81: 205 Bond restraints: 19610 Sorted by residual: bond pdb=" C PRO H 107 " pdb=" O PRO H 107 " ideal model delta sigma weight residual 1.233 1.171 0.062 1.13e-02 7.83e+03 3.06e+01 bond pdb=" N PRO c 417 " pdb=" CD PRO c 417 " ideal model delta sigma weight residual 1.473 1.543 -0.070 1.40e-02 5.10e+03 2.52e+01 bond pdb=" N PRO L 86 " pdb=" CD PRO L 86 " ideal model delta sigma weight residual 1.473 1.534 -0.061 1.40e-02 5.10e+03 1.87e+01 bond pdb=" CA ALA L 109 " pdb=" CB ALA L 109 " ideal model delta sigma weight residual 1.529 1.473 0.056 1.38e-02 5.25e+03 1.67e+01 bond pdb=" N GLN h 124 " pdb=" CA GLN h 124 " ideal model delta sigma weight residual 1.462 1.419 0.043 1.06e-02 8.90e+03 1.63e+01 ... (remaining 19605 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 25089 2.17 - 4.34: 1422 4.34 - 6.52: 109 6.52 - 8.69: 21 8.69 - 10.86: 6 Bond angle restraints: 26647 Sorted by residual: angle pdb=" C ILE L 91 " pdb=" N PRO L 92 " pdb=" CA PRO L 92 " ideal model delta sigma weight residual 119.76 127.74 -7.98 1.00e+00 1.00e+00 6.37e+01 angle pdb=" C ARG L 108 " pdb=" N ALA L 109 " pdb=" CA ALA L 109 " ideal model delta sigma weight residual 123.05 112.32 10.73 1.40e+00 5.10e-01 5.88e+01 angle pdb=" N SER L 104 " pdb=" CA SER L 104 " pdb=" C SER L 104 " ideal model delta sigma weight residual 111.82 103.06 8.76 1.16e+00 7.43e-01 5.70e+01 angle pdb=" C ASN m 7 " pdb=" N PRO m 8 " pdb=" CA PRO m 8 " ideal model delta sigma weight residual 119.76 127.31 -7.55 1.03e+00 9.43e-01 5.37e+01 angle pdb=" N GLN d 171 " pdb=" CA GLN d 171 " pdb=" C GLN d 171 " ideal model delta sigma weight residual 111.33 102.55 8.78 1.21e+00 6.83e-01 5.26e+01 ... (remaining 26642 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 11062 17.93 - 35.87: 285 35.87 - 53.80: 87 53.80 - 71.73: 18 71.73 - 89.67: 23 Dihedral angle restraints: 11475 sinusoidal: 3573 harmonic: 7902 Sorted by residual: dihedral pdb=" CA ILE a 793 " pdb=" C ILE a 793 " pdb=" N MET a 794 " pdb=" CA MET a 794 " ideal model delta harmonic sigma weight residual 180.00 -160.57 -19.43 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA PRO p 292 " pdb=" C PRO p 292 " pdb=" N TYR p 293 " pdb=" CA TYR p 293 " ideal model delta harmonic sigma weight residual 180.00 161.43 18.57 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA GLN d 119 " pdb=" C GLN d 119 " pdb=" N ARG d 120 " pdb=" CA ARG d 120 " ideal model delta harmonic sigma weight residual 180.00 162.07 17.93 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 11472 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2210 0.063 - 0.125: 878 0.125 - 0.188: 99 0.188 - 0.250: 75 0.250 - 0.313: 6 Chirality restraints: 3268 Sorted by residual: chirality pdb=" CA TYR o 68 " pdb=" N TYR o 68 " pdb=" C TYR o 68 " pdb=" CB TYR o 68 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CA TYR l 68 " pdb=" N TYR l 68 " pdb=" C TYR l 68 " pdb=" CB TYR l 68 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CA TYR m 68 " pdb=" N TYR m 68 " pdb=" C TYR m 68 " pdb=" CB TYR m 68 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 3265 not shown) Planarity restraints: 3401 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU o 86 " -0.023 2.00e-02 2.50e+03 4.59e-02 2.10e+01 pdb=" C LEU o 86 " 0.079 2.00e-02 2.50e+03 pdb=" O LEU o 86 " -0.030 2.00e-02 2.50e+03 pdb=" N TYR o 87 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN k 7 " -0.022 2.00e-02 2.50e+03 4.30e-02 1.85e+01 pdb=" C ASN k 7 " 0.074 2.00e-02 2.50e+03 pdb=" O ASN k 7 " -0.028 2.00e-02 2.50e+03 pdb=" N PRO k 8 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU d 160 " 0.019 2.00e-02 2.50e+03 3.99e-02 1.60e+01 pdb=" C LEU d 160 " -0.069 2.00e-02 2.50e+03 pdb=" O LEU d 160 " 0.026 2.00e-02 2.50e+03 pdb=" N ALA d 161 " 0.023 2.00e-02 2.50e+03 ... (remaining 3398 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 7273 2.85 - 3.36: 21816 3.36 - 3.87: 32693 3.87 - 4.39: 38695 4.39 - 4.90: 61389 Nonbonded interactions: 161866 Sorted by model distance: nonbonded pdb=" NZ LYS H 55 " pdb=" OD2 ASP L 99 " model vdw 2.336 3.120 nonbonded pdb=" OD1 ASP d 12 " pdb=" NZ LYS g 36 " model vdw 2.341 3.120 nonbonded pdb=" O LEU n 86 " pdb=" OG SER n 89 " model vdw 2.354 3.040 nonbonded pdb=" O PRO d 249 " pdb=" NE2 GLN m 123 " model vdw 2.355 3.120 nonbonded pdb=" O PRO i 8 " pdb=" OG SER i 11 " model vdw 2.357 3.040 ... (remaining 161861 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 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.790 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 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 : 0.008 0.070 19610 Z= 0.532 Angle : 1.001 10.860 26647 Z= 0.763 Chirality : 0.068 0.313 3268 Planarity : 0.005 0.046 3401 Dihedral : 11.127 89.669 6445 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.60 % Favored : 97.19 % Rotamer: Outliers : 2.06 % Allowed : 1.18 % Favored : 96.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.15), residues: 2771 helix: 0.86 (0.10), residues: 2122 sheet: -0.93 (0.97), residues: 18 loop : -0.78 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG l 48 TYR 0.011 0.000 TYR d 33 PHE 0.010 0.000 PHE d 96 TRP 0.001 0.000 TRP c 420 HIS 0.001 0.000 HIS L 96 Details of bonding type rmsd covalent geometry : bond 0.00819 (19610) covalent geometry : angle 1.00069 (26647) hydrogen bonds : bond 0.18719 ( 1741) hydrogen bonds : angle 6.81688 ( 5118) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1294 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 1259 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 52 ILE cc_start: 0.9510 (tp) cc_final: 0.9101 (tp) REVERT: H 55 LYS cc_start: 0.9579 (tttp) cc_final: 0.9166 (tmtt) REVERT: H 56 MET cc_start: 0.8992 (mmp) cc_final: 0.8748 (mmm) REVERT: H 60 GLU cc_start: 0.9371 (mm-30) cc_final: 0.8840 (mp0) REVERT: H 64 GLU cc_start: 0.9401 (tp30) cc_final: 0.8567 (tm-30) REVERT: H 81 THR cc_start: 0.9562 (m) cc_final: 0.9333 (p) REVERT: H 85 GLN cc_start: 0.9340 (mm-40) cc_final: 0.9078 (mm-40) REVERT: H 143 GLU cc_start: 0.9468 (mt-10) cc_final: 0.9074 (mm-30) REVERT: H 147 GLU cc_start: 0.8961 (mt-10) cc_final: 0.8639 (mt-10) REVERT: H 153 THR cc_start: 0.6257 (m) cc_final: 0.5824 (m) REVERT: L 11 ILE cc_start: 0.9595 (mt) cc_final: 0.9349 (mp) REVERT: L 15 ASP cc_start: 0.9095 (m-30) cc_final: 0.8695 (m-30) REVERT: L 31 ASN cc_start: 0.8771 (m-40) cc_final: 0.8549 (m-40) REVERT: L 46 ASN cc_start: 0.9452 (m-40) cc_final: 0.8903 (t0) REVERT: L 53 ARG cc_start: 0.8595 (ttp-110) cc_final: 0.8264 (ttp-110) REVERT: L 61 ILE cc_start: 0.8898 (mm) cc_final: 0.8674 (mm) REVERT: L 67 ASN cc_start: 0.9043 (m110) cc_final: 0.8295 (m110) REVERT: L 70 ILE cc_start: 0.9747 (mt) cc_final: 0.9414 (mt) REVERT: L 73 MET cc_start: 0.8630 (mtp) cc_final: 0.8425 (mtt) REVERT: L 78 LEU cc_start: 0.9212 (mp) cc_final: 0.8917 (tt) REVERT: L 94 LYS cc_start: 0.9236 (ttpt) cc_final: 0.8644 (tptt) REVERT: L 98 TYR cc_start: 0.6897 (t80) cc_final: 0.6394 (t80) REVERT: L 106 LEU cc_start: 0.9527 (mt) cc_final: 0.9079 (mm) REVERT: b 5 GLU cc_start: 0.9123 (mp0) cc_final: 0.8853 (pt0) REVERT: b 8 TYR cc_start: 0.8823 (m-80) cc_final: 0.8540 (m-80) REVERT: b 43 GLU cc_start: 0.8467 (mm-30) cc_final: 0.8072 (mm-30) REVERT: b 48 MET cc_start: 0.8901 (tmm) cc_final: 0.8634 (tmm) REVERT: b 51 ASN cc_start: 0.9483 (m-40) cc_final: 0.9108 (t0) REVERT: b 74 SER cc_start: 0.9870 (m) cc_final: 0.9640 (p) REVERT: b 75 SER cc_start: 0.9704 (m) cc_final: 0.9471 (p) REVERT: b 90 ASN cc_start: 0.9039 (m110) cc_final: 0.8776 (m110) REVERT: b 103 TYR cc_start: 0.8615 (m-10) cc_final: 0.8351 (m-10) REVERT: b 107 MET cc_start: 0.9327 (mmm) cc_final: 0.9064 (mmm) REVERT: b 114 MET cc_start: 0.8505 (mmm) cc_final: 0.8038 (mmm) REVERT: b 116 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7309 (mp0) REVERT: b 135 TYR cc_start: 0.9130 (m-80) cc_final: 0.8876 (m-80) REVERT: b 137 MET cc_start: 0.9194 (mtp) cc_final: 0.8627 (mtp) REVERT: b 164 LEU cc_start: 0.9597 (mt) cc_final: 0.9164 (mp) REVERT: b 169 ASN cc_start: 0.9087 (t0) cc_final: 0.8677 (t0) REVERT: b 172 LEU cc_start: 0.9245 (mt) cc_final: 0.8587 (mt) REVERT: b 186 ILE cc_start: 0.9635 (mt) cc_final: 0.9236 (mt) REVERT: b 189 PHE cc_start: 0.8175 (m-10) cc_final: 0.7850 (m-80) REVERT: b 193 VAL cc_start: 0.9649 (t) cc_final: 0.9418 (t) REVERT: b 202 LYS cc_start: 0.8601 (tttt) cc_final: 0.8378 (tmmt) REVERT: c 421 MET cc_start: 0.9068 (mtm) cc_final: 0.8749 (mtp) REVERT: c 442 SER cc_start: 0.9276 (m) cc_final: 0.8860 (p) REVERT: d 7 LEU cc_start: 0.9492 (mt) cc_final: 0.8867 (mp) REVERT: d 34 LEU cc_start: 0.9474 (mt) cc_final: 0.9241 (mt) REVERT: d 39 CYS cc_start: 0.3445 (m) cc_final: 0.2944 (m) REVERT: d 40 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7479 (mm-30) REVERT: d 63 SER cc_start: 0.9046 (m) cc_final: 0.8804 (p) REVERT: d 76 GLU cc_start: 0.9246 (mt-10) cc_final: 0.8711 (mt-10) REVERT: d 97 LEU cc_start: 0.9521 (mt) cc_final: 0.9281 (mt) REVERT: d 105 MET cc_start: 0.9039 (mtt) cc_final: 0.8815 (mmm) REVERT: d 135 PHE cc_start: 0.8626 (m-80) cc_final: 0.8070 (m-80) REVERT: d 170 GLU cc_start: 0.8919 (mt-10) cc_final: 0.8627 (mt-10) REVERT: d 197 CYS cc_start: 0.9579 (m) cc_final: 0.9315 (m) REVERT: d 208 MET cc_start: 0.9058 (tpt) cc_final: 0.8773 (tpt) REVERT: d 226 ASN cc_start: 0.8965 (m-40) cc_final: 0.8582 (m-40) REVERT: d 241 PHE cc_start: 0.9034 (m-10) cc_final: 0.8656 (m-10) REVERT: d 262 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8412 (tm-30) REVERT: d 276 LEU cc_start: 0.9339 (mt) cc_final: 0.9060 (tt) REVERT: d 315 PHE cc_start: 0.9470 (m-80) cc_final: 0.9115 (m-80) REVERT: d 324 GLN cc_start: 0.8741 (tp40) cc_final: 0.7981 (tp40) REVERT: d 339 ARG cc_start: 0.9155 (mmm160) cc_final: 0.8400 (mmp-170) REVERT: d 348 ILE cc_start: 0.8826 (mm) cc_final: 0.8408 (mp) REVERT: g 8 PRO cc_start: 0.8768 (Cg_exo) cc_final: 0.8309 (Cg_endo) REVERT: g 28 MET cc_start: 0.9585 (mtp) cc_final: 0.9334 (mtp) REVERT: g 32 TYR cc_start: 0.8811 (t80) cc_final: 0.8364 (t80) REVERT: g 53 MET cc_start: 0.8621 (mtm) cc_final: 0.8344 (ttp) REVERT: g 57 ILE cc_start: 0.9609 (mt) cc_final: 0.9233 (mt) REVERT: g 108 PHE cc_start: 0.8308 (m-10) cc_final: 0.7932 (m-10) REVERT: g 118 VAL cc_start: 0.9695 (t) cc_final: 0.9387 (p) REVERT: g 124 GLN cc_start: 0.8399 (tp-100) cc_final: 0.7735 (tm-30) REVERT: g 136 ILE cc_start: 0.9813 (OUTLIER) cc_final: 0.9561 (mt) REVERT: g 143 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8619 (tp) REVERT: g 144 TYR cc_start: 0.9278 (m-80) cc_final: 0.8827 (m-80) REVERT: h 8 PRO cc_start: 0.8196 (Cg_exo) cc_final: 0.7855 (Cg_endo) REVERT: h 28 MET cc_start: 0.8937 (mtp) cc_final: 0.8580 (mtm) REVERT: h 45 SER cc_start: 0.7970 (m) cc_final: 0.7765 (p) REVERT: h 52 ILE cc_start: 0.8686 (tt) cc_final: 0.8391 (pt) REVERT: h 54 LYS cc_start: 0.7853 (mttt) cc_final: 0.7370 (mttt) REVERT: h 57 ILE cc_start: 0.9794 (mt) cc_final: 0.9529 (mt) REVERT: h 88 ARG cc_start: 0.8128 (mtp-110) cc_final: 0.7831 (mmm-85) REVERT: h 112 ILE cc_start: 0.9458 (mm) cc_final: 0.9009 (tp) REVERT: h 128 PHE cc_start: 0.8879 (t80) cc_final: 0.8622 (t80) REVERT: h 137 PHE cc_start: 0.9287 (m-80) cc_final: 0.8789 (m-80) REVERT: h 139 GLU cc_start: 0.9348 (OUTLIER) cc_final: 0.9105 (tp30) REVERT: h 144 TYR cc_start: 0.9664 (m-10) cc_final: 0.9282 (m-10) REVERT: i 16 VAL cc_start: 0.9593 (t) cc_final: 0.9386 (t) REVERT: i 17 MET cc_start: 0.9332 (mmp) cc_final: 0.8839 (mmm) REVERT: i 65 ILE cc_start: 0.9687 (OUTLIER) cc_final: 0.9393 (mm) REVERT: i 68 TYR cc_start: 0.9551 (m-10) cc_final: 0.8903 (m-80) REVERT: i 82 ASP cc_start: 0.9064 (p0) cc_final: 0.8753 (p0) REVERT: i 90 PHE cc_start: 0.9271 (m-80) cc_final: 0.8862 (m-10) REVERT: i 124 GLN cc_start: 0.8524 (tp-100) cc_final: 0.8195 (tm-30) REVERT: i 127 LEU cc_start: 0.7538 (tp) cc_final: 0.7251 (tp) REVERT: i 131 MET cc_start: 0.9075 (ttp) cc_final: 0.8701 (ttt) REVERT: i 152 LEU cc_start: 0.9728 (mt) cc_final: 0.9487 (mt) REVERT: j 28 MET cc_start: 0.9037 (mtp) cc_final: 0.8553 (mmt) REVERT: j 84 ILE cc_start: 0.7365 (mt) cc_final: 0.7000 (mt) REVERT: j 101 LEU cc_start: 0.9310 (mt) cc_final: 0.9019 (mt) REVERT: j 108 PHE cc_start: 0.9246 (m-80) cc_final: 0.8743 (m-80) REVERT: j 121 THR cc_start: 0.8949 (m) cc_final: 0.8748 (p) REVERT: j 124 GLN cc_start: 0.7864 (tp-100) cc_final: 0.7161 (tm-30) REVERT: j 127 LEU cc_start: 0.9330 (tp) cc_final: 0.8779 (tp) REVERT: j 140 VAL cc_start: 0.9417 (OUTLIER) cc_final: 0.8955 (t) REVERT: j 141 LEU cc_start: 0.9528 (OUTLIER) cc_final: 0.9014 (mt) REVERT: j 144 TYR cc_start: 0.9428 (m-10) cc_final: 0.9218 (m-80) REVERT: j 152 LEU cc_start: 0.9421 (tp) cc_final: 0.9156 (tp) REVERT: k 6 ASN cc_start: 0.8804 (m-40) cc_final: 0.8550 (p0) REVERT: k 17 MET cc_start: 0.8981 (mtm) cc_final: 0.8695 (mtm) REVERT: k 23 MET cc_start: 0.9047 (tpt) cc_final: 0.8831 (mmm) REVERT: k 28 MET cc_start: 0.9018 (mtp) cc_final: 0.8755 (mtt) REVERT: k 41 ILE cc_start: 0.9440 (mt) cc_final: 0.8999 (mm) REVERT: k 51 LEU cc_start: 0.8826 (mt) cc_final: 0.8602 (mt) REVERT: k 57 ILE cc_start: 0.9296 (mt) cc_final: 0.8855 (mm) REVERT: k 61 MET cc_start: 0.8291 (mmp) cc_final: 0.8077 (mmm) REVERT: k 91 LEU cc_start: 0.9308 (mt) cc_final: 0.8829 (mt) REVERT: k 118 VAL cc_start: 0.9502 (t) cc_final: 0.9195 (p) REVERT: k 121 THR cc_start: 0.8210 (m) cc_final: 0.7766 (p) REVERT: k 152 LEU cc_start: 0.9581 (mt) cc_final: 0.9349 (mt) REVERT: l 68 TYR cc_start: 0.8076 (m-10) cc_final: 0.7028 (m-80) REVERT: l 74 VAL cc_start: 0.9407 (t) cc_final: 0.8946 (t) REVERT: l 113 VAL cc_start: 0.9668 (t) cc_final: 0.9467 (p) REVERT: l 124 GLN cc_start: 0.8191 (tp-100) cc_final: 0.7587 (tm-30) REVERT: l 131 MET cc_start: 0.9296 (ttp) cc_final: 0.8995 (ttm) REVERT: m 11 SER cc_start: 0.8224 (p) cc_final: 0.7698 (t) REVERT: m 21 SER cc_start: 0.9270 (m) cc_final: 0.8977 (p) REVERT: m 47 MET cc_start: 0.9111 (mmm) cc_final: 0.8479 (mmm) REVERT: m 53 MET cc_start: 0.8741 (mmm) cc_final: 0.7810 (tmm) REVERT: m 89 SER cc_start: 0.9387 (m) cc_final: 0.8731 (p) REVERT: m 92 GLN cc_start: 0.9161 (mt0) cc_final: 0.8856 (mt0) REVERT: m 118 VAL cc_start: 0.9297 (t) cc_final: 0.9034 (m) REVERT: n 13 PHE cc_start: 0.8986 (t80) cc_final: 0.8709 (t80) REVERT: n 23 MET cc_start: 0.9362 (tpt) cc_final: 0.8632 (tpp) REVERT: n 32 TYR cc_start: 0.7907 (t80) cc_final: 0.7705 (t80) REVERT: n 47 MET cc_start: 0.9257 (mmm) cc_final: 0.8996 (mmm) REVERT: n 64 ILE cc_start: 0.9143 (mt) cc_final: 0.8849 (mt) REVERT: n 68 TYR cc_start: 0.8374 (m-10) cc_final: 0.8158 (m-80) REVERT: n 70 LEU cc_start: 0.9123 (tp) cc_final: 0.8748 (tp) REVERT: n 72 VAL cc_start: 0.9505 (t) cc_final: 0.9282 (p) REVERT: n 99 VAL cc_start: 0.9736 (p) cc_final: 0.9424 (m) REVERT: n 119 ARG cc_start: 0.8532 (mtm-85) cc_final: 0.8325 (ptp90) REVERT: o 13 PHE cc_start: 0.9059 (t80) cc_final: 0.8445 (t80) REVERT: o 17 MET cc_start: 0.9340 (mmp) cc_final: 0.8906 (mmp) REVERT: o 21 SER cc_start: 0.9109 (m) cc_final: 0.8659 (p) REVERT: o 48 ARG cc_start: 0.8827 (ptm160) cc_final: 0.8519 (ptp-170) REVERT: o 51 LEU cc_start: 0.8960 (mt) cc_final: 0.8752 (mt) REVERT: o 64 ILE cc_start: 0.9337 (mt) cc_final: 0.9061 (mt) REVERT: o 68 TYR cc_start: 0.8631 (m-10) cc_final: 0.8392 (m-80) REVERT: o 82 ASP cc_start: 0.8543 (p0) cc_final: 0.8334 (m-30) REVERT: o 91 LEU cc_start: 0.9728 (mt) cc_final: 0.9493 (mp) REVERT: o 97 LEU cc_start: 0.9479 (mt) cc_final: 0.9250 (mt) REVERT: o 112 ILE cc_start: 0.9307 (mm) cc_final: 0.9080 (mm) REVERT: o 119 ARG cc_start: 0.9207 (mtm-85) cc_final: 0.8973 (mpp80) REVERT: o 132 ILE cc_start: 0.9254 (mm) cc_final: 0.8492 (mt) REVERT: o 135 LEU cc_start: 0.9813 (mt) cc_final: 0.9484 (mt) REVERT: o 144 TYR cc_start: 0.9146 (m-10) cc_final: 0.8840 (m-10) REVERT: p 303 TYR cc_start: 0.9001 (t80) cc_final: 0.8356 (t80) REVERT: p 328 ILE cc_start: 0.9633 (mt) cc_final: 0.9417 (tp) REVERT: p 338 ILE cc_start: 0.8323 (pt) cc_final: 0.7673 (pt) outliers start: 35 outliers final: 15 residues processed: 1265 average time/residue: 0.1236 time to fit residues: 246.4137 Evaluate side-chains 970 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 949 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 152 GLN L 82 GLN L 96 HIS d 38 GLN ** d 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 340 HIS h 92 GLN i 6 ASN ** j 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 92 GLN n 123 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.090953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.071454 restraints weight = 65913.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.074138 restraints weight = 39407.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.076076 restraints weight = 26383.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.077517 restraints weight = 19244.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.078546 restraints weight = 14604.070| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 19610 Z= 0.197 Angle : 0.679 11.962 26647 Z= 0.369 Chirality : 0.043 0.229 3268 Planarity : 0.005 0.058 3401 Dihedral : 3.960 17.647 2941 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.24 % Allowed : 2.30 % Favored : 97.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.45 (0.15), residues: 2771 helix: 2.27 (0.11), residues: 2053 sheet: -1.05 (0.99), residues: 18 loop : -0.25 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 63 TYR 0.025 0.002 TYR o 32 PHE 0.028 0.002 PHE k 90 TRP 0.025 0.001 TRP b 67 HIS 0.008 0.001 HIS d 311 Details of bonding type rmsd covalent geometry : bond 0.00387 (19610) covalent geometry : angle 0.67923 (26647) hydrogen bonds : bond 0.07014 ( 1741) hydrogen bonds : angle 4.75458 ( 5118) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1091 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 1087 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 55 LYS cc_start: 0.9508 (tttp) cc_final: 0.9155 (tptp) REVERT: H 60 GLU cc_start: 0.9090 (mm-30) cc_final: 0.8854 (mm-30) REVERT: H 62 MET cc_start: 0.9398 (mmm) cc_final: 0.9081 (ttm) REVERT: H 64 GLU cc_start: 0.9340 (tp30) cc_final: 0.8565 (tm-30) REVERT: H 84 ILE cc_start: 0.9522 (mt) cc_final: 0.9229 (mt) REVERT: H 85 GLN cc_start: 0.9153 (mm-40) cc_final: 0.8946 (mm-40) REVERT: H 119 TYR cc_start: 0.7311 (p90) cc_final: 0.6811 (p90) REVERT: H 143 GLU cc_start: 0.9471 (mt-10) cc_final: 0.9183 (mm-30) REVERT: H 144 LEU cc_start: 0.9497 (mm) cc_final: 0.9107 (mm) REVERT: H 147 GLU cc_start: 0.9036 (mt-10) cc_final: 0.8752 (mt-10) REVERT: L 14 GLU cc_start: 0.8839 (pm20) cc_final: 0.8612 (pm20) REVERT: L 15 ASP cc_start: 0.8791 (m-30) cc_final: 0.8146 (m-30) REVERT: L 22 LEU cc_start: 0.9403 (mt) cc_final: 0.9147 (mt) REVERT: L 43 THR cc_start: 0.8304 (p) cc_final: 0.7943 (p) REVERT: L 53 ARG cc_start: 0.8835 (ttp-110) cc_final: 0.8554 (ttp-110) REVERT: L 67 ASN cc_start: 0.9045 (m110) cc_final: 0.8206 (m110) REVERT: L 70 ILE cc_start: 0.9533 (mt) cc_final: 0.9079 (mt) REVERT: L 91 ILE cc_start: 0.9467 (pt) cc_final: 0.9156 (pt) REVERT: b 4 LEU cc_start: 0.9481 (mm) cc_final: 0.9104 (mm) REVERT: b 5 GLU cc_start: 0.9076 (mp0) cc_final: 0.8842 (pt0) REVERT: b 8 TYR cc_start: 0.8953 (m-80) cc_final: 0.8615 (m-80) REVERT: b 19 MET cc_start: 0.8704 (mtp) cc_final: 0.8336 (mtp) REVERT: b 43 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8200 (mm-30) REVERT: b 48 MET cc_start: 0.9014 (tmm) cc_final: 0.8435 (tmm) REVERT: b 90 ASN cc_start: 0.8990 (m110) cc_final: 0.8681 (m110) REVERT: b 91 LEU cc_start: 0.9647 (tp) cc_final: 0.9393 (tp) REVERT: b 102 ILE cc_start: 0.9710 (mm) cc_final: 0.9468 (mm) REVERT: b 103 TYR cc_start: 0.8558 (m-10) cc_final: 0.8142 (m-10) REVERT: b 114 MET cc_start: 0.8354 (mmm) cc_final: 0.7473 (mmm) REVERT: b 116 GLU cc_start: 0.8141 (mm-30) cc_final: 0.6976 (mp0) REVERT: b 126 ILE cc_start: 0.8252 (mm) cc_final: 0.8023 (mm) REVERT: b 131 TYR cc_start: 0.9227 (m-80) cc_final: 0.8252 (m-80) REVERT: b 135 TYR cc_start: 0.8915 (m-80) cc_final: 0.8080 (m-80) REVERT: b 137 MET cc_start: 0.9045 (mtp) cc_final: 0.8812 (mtp) REVERT: b 164 LEU cc_start: 0.9550 (mt) cc_final: 0.9171 (mp) REVERT: b 169 ASN cc_start: 0.9396 (t0) cc_final: 0.8954 (t0) REVERT: b 172 LEU cc_start: 0.9394 (mt) cc_final: 0.8758 (mt) REVERT: b 186 ILE cc_start: 0.9662 (mt) cc_final: 0.9240 (mt) REVERT: b 189 PHE cc_start: 0.8747 (m-10) cc_final: 0.8398 (m-80) REVERT: b 197 GLN cc_start: 0.8771 (mt0) cc_final: 0.8055 (mt0) REVERT: b 202 LYS cc_start: 0.8962 (tttt) cc_final: 0.8737 (tmmt) REVERT: b 203 MET cc_start: 0.8164 (mmm) cc_final: 0.7800 (ttm) REVERT: c 421 MET cc_start: 0.9228 (mtm) cc_final: 0.8856 (mtp) REVERT: c 430 LEU cc_start: 0.9752 (tp) cc_final: 0.9449 (tp) REVERT: c 442 SER cc_start: 0.9306 (m) cc_final: 0.8796 (p) REVERT: d 30 GLN cc_start: 0.9186 (tm-30) cc_final: 0.8806 (tm-30) REVERT: d 76 GLU cc_start: 0.9063 (mt-10) cc_final: 0.8781 (mt-10) REVERT: d 81 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8608 (tp30) REVERT: d 93 LEU cc_start: 0.9674 (tt) cc_final: 0.9201 (tt) REVERT: d 135 PHE cc_start: 0.8805 (m-80) cc_final: 0.7133 (m-80) REVERT: d 158 THR cc_start: 0.9014 (m) cc_final: 0.8568 (p) REVERT: d 181 ILE cc_start: 0.9142 (mt) cc_final: 0.8900 (mt) REVERT: d 197 CYS cc_start: 0.9593 (m) cc_final: 0.9367 (m) REVERT: d 208 MET cc_start: 0.8821 (tpt) cc_final: 0.8413 (tpt) REVERT: d 215 GLU cc_start: 0.9192 (mm-30) cc_final: 0.8914 (mm-30) REVERT: d 241 PHE cc_start: 0.8958 (m-10) cc_final: 0.8701 (m-10) REVERT: d 244 CYS cc_start: 0.8731 (m) cc_final: 0.8134 (m) REVERT: d 262 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8262 (tm-30) REVERT: d 276 LEU cc_start: 0.9413 (mt) cc_final: 0.9184 (tt) REVERT: d 302 ASN cc_start: 0.9694 (m-40) cc_final: 0.9452 (m110) REVERT: d 308 ASN cc_start: 0.8198 (m-40) cc_final: 0.7944 (m-40) REVERT: d 312 PHE cc_start: 0.8600 (m-80) cc_final: 0.7712 (m-80) REVERT: d 315 PHE cc_start: 0.9692 (m-80) cc_final: 0.9176 (m-80) REVERT: d 325 GLU cc_start: 0.9275 (tt0) cc_final: 0.8884 (tm-30) REVERT: d 334 GLU cc_start: 0.9364 (tp30) cc_final: 0.9163 (mm-30) REVERT: d 339 ARG cc_start: 0.9127 (mmm160) cc_final: 0.8809 (mmm160) REVERT: d 348 ILE cc_start: 0.9209 (mm) cc_final: 0.8966 (mp) REVERT: g 8 PRO cc_start: 0.9019 (Cg_exo) cc_final: 0.8510 (Cg_endo) REVERT: g 24 VAL cc_start: 0.9715 (t) cc_final: 0.9515 (t) REVERT: g 32 TYR cc_start: 0.8979 (t80) cc_final: 0.8314 (t80) REVERT: g 48 ARG cc_start: 0.8603 (mtp180) cc_final: 0.8159 (mtp85) REVERT: g 53 MET cc_start: 0.8655 (mtm) cc_final: 0.8167 (ttp) REVERT: g 54 LYS cc_start: 0.8271 (ptpt) cc_final: 0.7978 (pttt) REVERT: g 57 ILE cc_start: 0.9580 (mt) cc_final: 0.9346 (mt) REVERT: g 70 LEU cc_start: 0.9479 (tp) cc_final: 0.9167 (tp) REVERT: g 78 ASN cc_start: 0.8674 (p0) cc_final: 0.8432 (p0) REVERT: g 93 LEU cc_start: 0.9308 (pp) cc_final: 0.9071 (pp) REVERT: g 112 ILE cc_start: 0.9580 (mm) cc_final: 0.9342 (mm) REVERT: g 140 VAL cc_start: 0.9346 (t) cc_final: 0.8776 (t) REVERT: g 141 LEU cc_start: 0.9465 (mt) cc_final: 0.9214 (mt) REVERT: g 144 TYR cc_start: 0.8981 (m-80) cc_final: 0.8756 (m-80) REVERT: h 8 PRO cc_start: 0.8556 (Cg_exo) cc_final: 0.8316 (Cg_endo) REVERT: h 11 SER cc_start: 0.8809 (p) cc_final: 0.8550 (m) REVERT: h 44 MET cc_start: 0.7882 (tmm) cc_final: 0.7677 (tmm) REVERT: h 45 SER cc_start: 0.8304 (m) cc_final: 0.7294 (m) REVERT: h 48 ARG cc_start: 0.8081 (ttm170) cc_final: 0.7458 (ttm170) REVERT: h 54 LYS cc_start: 0.7706 (mttt) cc_final: 0.7247 (mttt) REVERT: h 112 ILE cc_start: 0.9543 (mm) cc_final: 0.9103 (tp) REVERT: h 115 ASP cc_start: 0.9437 (t70) cc_final: 0.9109 (p0) REVERT: h 127 LEU cc_start: 0.8840 (tt) cc_final: 0.8364 (tt) REVERT: h 128 PHE cc_start: 0.8919 (t80) cc_final: 0.8643 (t80) REVERT: h 137 PHE cc_start: 0.9298 (m-80) cc_final: 0.8853 (m-80) REVERT: h 144 TYR cc_start: 0.9666 (m-10) cc_final: 0.9191 (m-10) REVERT: i 10 TYR cc_start: 0.7059 (m-80) cc_final: 0.6580 (m-80) REVERT: i 13 PHE cc_start: 0.8715 (t80) cc_final: 0.8269 (t80) REVERT: i 23 MET cc_start: 0.8758 (tpt) cc_final: 0.8545 (tpp) REVERT: i 25 PHE cc_start: 0.9027 (m-80) cc_final: 0.8815 (m-80) REVERT: i 68 TYR cc_start: 0.9498 (m-10) cc_final: 0.9288 (m-80) REVERT: i 115 ASP cc_start: 0.8546 (t70) cc_final: 0.7881 (t0) REVERT: i 131 MET cc_start: 0.9041 (ttp) cc_final: 0.8638 (ttt) REVERT: i 135 LEU cc_start: 0.9577 (mm) cc_final: 0.9229 (mm) REVERT: i 152 LEU cc_start: 0.9707 (mt) cc_final: 0.9479 (mt) REVERT: j 17 MET cc_start: 0.9271 (mtm) cc_final: 0.8755 (mtp) REVERT: j 28 MET cc_start: 0.9069 (mtp) cc_final: 0.8454 (mmt) REVERT: j 47 MET cc_start: 0.8825 (mmm) cc_final: 0.8061 (mmm) REVERT: j 86 LEU cc_start: 0.9103 (tp) cc_final: 0.8836 (tt) REVERT: j 90 PHE cc_start: 0.8922 (m-10) cc_final: 0.8582 (m-10) REVERT: j 91 LEU cc_start: 0.9267 (mt) cc_final: 0.9005 (mt) REVERT: j 104 LEU cc_start: 0.9457 (tp) cc_final: 0.9161 (tp) REVERT: j 108 PHE cc_start: 0.9140 (m-80) cc_final: 0.8665 (m-80) REVERT: j 121 THR cc_start: 0.9024 (m) cc_final: 0.8543 (m) REVERT: j 124 GLN cc_start: 0.8391 (tp-100) cc_final: 0.7475 (tm-30) REVERT: j 127 LEU cc_start: 0.9253 (tp) cc_final: 0.8470 (tp) REVERT: j 131 MET cc_start: 0.8253 (ttp) cc_final: 0.8042 (ttp) REVERT: j 140 VAL cc_start: 0.9414 (t) cc_final: 0.9185 (t) REVERT: j 141 LEU cc_start: 0.9284 (mt) cc_final: 0.9021 (mt) REVERT: j 143 LEU cc_start: 0.9414 (tp) cc_final: 0.9182 (tp) REVERT: j 152 LEU cc_start: 0.9389 (tp) cc_final: 0.9019 (tp) REVERT: k 13 PHE cc_start: 0.9339 (t80) cc_final: 0.9078 (t80) REVERT: k 28 MET cc_start: 0.9120 (mtp) cc_final: 0.8804 (mtt) REVERT: k 44 MET cc_start: 0.8997 (ppp) cc_final: 0.8528 (ppp) REVERT: k 53 MET cc_start: 0.8823 (tmm) cc_final: 0.8030 (mtt) REVERT: k 57 ILE cc_start: 0.9268 (mt) cc_final: 0.8769 (mm) REVERT: k 59 VAL cc_start: 0.9329 (t) cc_final: 0.8950 (t) REVERT: k 61 MET cc_start: 0.8339 (mmp) cc_final: 0.8128 (mmm) REVERT: k 64 ILE cc_start: 0.8821 (mm) cc_final: 0.8577 (mm) REVERT: k 65 ILE cc_start: 0.9607 (mm) cc_final: 0.9160 (mm) REVERT: k 68 TYR cc_start: 0.7725 (m-10) cc_final: 0.7150 (m-80) REVERT: k 91 LEU cc_start: 0.9330 (mt) cc_final: 0.8904 (mt) REVERT: k 92 GLN cc_start: 0.9409 (mm-40) cc_final: 0.9194 (mm-40) REVERT: k 118 VAL cc_start: 0.9571 (t) cc_final: 0.9358 (p) REVERT: k 131 MET cc_start: 0.8318 (mtm) cc_final: 0.7969 (mtp) REVERT: l 17 MET cc_start: 0.9316 (mmp) cc_final: 0.8553 (mmt) REVERT: l 24 VAL cc_start: 0.9427 (t) cc_final: 0.9105 (t) REVERT: l 28 MET cc_start: 0.8807 (mtp) cc_final: 0.8562 (mtp) REVERT: l 53 MET cc_start: 0.7897 (mtp) cc_final: 0.7489 (ttp) REVERT: l 68 TYR cc_start: 0.8454 (m-10) cc_final: 0.7625 (m-80) REVERT: l 97 LEU cc_start: 0.9442 (mt) cc_final: 0.9224 (mm) REVERT: l 124 GLN cc_start: 0.8620 (tp-100) cc_final: 0.8218 (tm-30) REVERT: l 127 LEU cc_start: 0.7538 (tp) cc_final: 0.7127 (tp) REVERT: l 131 MET cc_start: 0.9286 (ttp) cc_final: 0.9008 (ttm) REVERT: l 135 LEU cc_start: 0.9307 (mt) cc_final: 0.8938 (pp) REVERT: l 136 ILE cc_start: 0.9007 (mm) cc_final: 0.8509 (mm) REVERT: l 137 PHE cc_start: 0.8837 (m-80) cc_final: 0.8549 (m-10) REVERT: l 152 LEU cc_start: 0.9752 (mt) cc_final: 0.9545 (mt) REVERT: m 10 TYR cc_start: 0.4899 (m-80) cc_final: 0.4663 (m-80) REVERT: m 11 SER cc_start: 0.8320 (p) cc_final: 0.7991 (t) REVERT: m 14 PHE cc_start: 0.9231 (m-80) cc_final: 0.8915 (m-80) REVERT: m 21 SER cc_start: 0.9510 (m) cc_final: 0.9234 (p) REVERT: m 48 ARG cc_start: 0.8933 (mmm160) cc_final: 0.8602 (mmm160) REVERT: m 51 LEU cc_start: 0.8521 (mt) cc_final: 0.8256 (mt) REVERT: m 53 MET cc_start: 0.8848 (mmm) cc_final: 0.7972 (tmm) REVERT: m 61 MET cc_start: 0.9088 (mtt) cc_final: 0.8731 (mmm) REVERT: m 70 LEU cc_start: 0.8932 (mt) cc_final: 0.8725 (mt) REVERT: m 86 LEU cc_start: 0.9531 (tp) cc_final: 0.9324 (tp) REVERT: m 89 SER cc_start: 0.9165 (m) cc_final: 0.8832 (p) REVERT: m 92 GLN cc_start: 0.9236 (mt0) cc_final: 0.8937 (mt0) REVERT: m 97 LEU cc_start: 0.9126 (mt) cc_final: 0.8894 (mt) REVERT: m 135 LEU cc_start: 0.9150 (mt) cc_final: 0.8934 (mp) REVERT: m 139 GLU cc_start: 0.8603 (mm-30) cc_final: 0.8339 (mm-30) REVERT: m 144 TYR cc_start: 0.9435 (m-10) cc_final: 0.9082 (m-10) REVERT: n 13 PHE cc_start: 0.9116 (t80) cc_final: 0.8560 (t80) REVERT: n 17 MET cc_start: 0.9350 (mmt) cc_final: 0.9087 (mmm) REVERT: n 23 MET cc_start: 0.9146 (tpt) cc_final: 0.8645 (tpp) REVERT: n 47 MET cc_start: 0.9234 (mmm) cc_final: 0.8836 (mmm) REVERT: n 48 ARG cc_start: 0.9086 (mmm-85) cc_final: 0.8857 (mmm-85) REVERT: n 61 MET cc_start: 0.9159 (mmp) cc_final: 0.8379 (mmm) REVERT: n 68 TYR cc_start: 0.8664 (m-10) cc_final: 0.8301 (m-10) REVERT: n 70 LEU cc_start: 0.9236 (tp) cc_final: 0.8702 (tp) REVERT: n 124 GLN cc_start: 0.8761 (tp-100) cc_final: 0.8376 (tm-30) REVERT: n 135 LEU cc_start: 0.9642 (mt) cc_final: 0.9397 (mt) REVERT: o 13 PHE cc_start: 0.9090 (t80) cc_final: 0.8272 (t80) REVERT: o 17 MET cc_start: 0.9280 (mmp) cc_final: 0.8784 (mmt) REVERT: o 21 SER cc_start: 0.9055 (m) cc_final: 0.8829 (p) REVERT: o 47 MET cc_start: 0.8583 (tmm) cc_final: 0.7036 (tmm) REVERT: o 48 ARG cc_start: 0.9042 (ptm160) cc_final: 0.8660 (mtm-85) REVERT: o 57 ILE cc_start: 0.9166 (mt) cc_final: 0.8614 (tt) REVERT: o 64 ILE cc_start: 0.9315 (mt) cc_final: 0.8867 (mt) REVERT: o 68 TYR cc_start: 0.8939 (m-10) cc_final: 0.8430 (m-80) REVERT: o 112 ILE cc_start: 0.9407 (mm) cc_final: 0.9155 (mm) REVERT: o 119 ARG cc_start: 0.9413 (mtm-85) cc_final: 0.8456 (mtm110) REVERT: o 128 PHE cc_start: 0.8549 (t80) cc_final: 0.7988 (t80) REVERT: o 132 ILE cc_start: 0.9081 (mm) cc_final: 0.8545 (tp) REVERT: o 144 TYR cc_start: 0.9158 (m-10) cc_final: 0.8789 (m-10) REVERT: o 151 ILE cc_start: 0.9367 (mt) cc_final: 0.9127 (mt) REVERT: p 303 TYR cc_start: 0.8591 (t80) cc_final: 0.8025 (t80) REVERT: p 328 ILE cc_start: 0.9745 (mt) cc_final: 0.9303 (tp) REVERT: p 330 ASN cc_start: 0.9048 (t0) cc_final: 0.8774 (t0) outliers start: 4 outliers final: 1 residues processed: 1087 average time/residue: 0.1103 time to fit residues: 193.8990 Evaluate side-chains 924 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 923 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 91 optimal weight: 0.7980 chunk 260 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 127 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 101 optimal weight: 0.0040 chunk 224 optimal weight: 2.9990 chunk 68 optimal weight: 0.3980 chunk 179 optimal weight: 0.7980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 137 ASN ** b 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 148 ASN ** d 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 48 HIS d 56 ASN d 88 HIS d 338 GLN d 346 ASN ** g 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 123 GLN n 123 GLN ** o 7 ASN ** 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 = 0.3632 r_free = 0.3632 target = 0.097000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.077027 restraints weight = 63907.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.079608 restraints weight = 39117.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.081571 restraints weight = 26700.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.083021 restraints weight = 19698.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.084046 restraints weight = 15520.943| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.4367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 19610 Z= 0.166 Angle : 0.634 9.604 26647 Z= 0.339 Chirality : 0.042 0.215 3268 Planarity : 0.004 0.040 3401 Dihedral : 3.957 23.830 2941 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.53 % Allowed : 1.83 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.40 (0.15), residues: 2771 helix: 2.26 (0.11), residues: 2064 sheet: -1.68 (0.94), residues: 18 loop : -0.39 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG d 86 TYR 0.038 0.002 TYR H 138 PHE 0.037 0.002 PHE j 13 TRP 0.013 0.002 TRP p 312 HIS 0.006 0.001 HIS d 48 Details of bonding type rmsd covalent geometry : bond 0.00333 (19610) covalent geometry : angle 0.63381 (26647) hydrogen bonds : bond 0.05934 ( 1741) hydrogen bonds : angle 4.47415 ( 5118) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1076 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 1067 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 55 LYS cc_start: 0.9532 (tttp) cc_final: 0.9211 (tptp) REVERT: H 64 GLU cc_start: 0.9267 (tp30) cc_final: 0.8764 (tp30) REVERT: H 84 ILE cc_start: 0.9487 (mt) cc_final: 0.9157 (mt) REVERT: H 85 GLN cc_start: 0.9131 (mm-40) cc_final: 0.8816 (mm-40) REVERT: H 119 TYR cc_start: 0.7454 (p90) cc_final: 0.6899 (p90) REVERT: H 143 GLU cc_start: 0.9468 (mt-10) cc_final: 0.9216 (mm-30) REVERT: H 144 LEU cc_start: 0.9506 (mm) cc_final: 0.9247 (mm) REVERT: H 147 GLU cc_start: 0.8991 (mt-10) cc_final: 0.8665 (mt-10) REVERT: L 14 GLU cc_start: 0.8959 (pm20) cc_final: 0.8688 (pm20) REVERT: L 15 ASP cc_start: 0.8871 (m-30) cc_final: 0.8217 (m-30) REVERT: L 22 LEU cc_start: 0.9293 (mt) cc_final: 0.9077 (mt) REVERT: L 66 ILE cc_start: 0.9215 (tp) cc_final: 0.8877 (tp) REVERT: L 67 ASN cc_start: 0.9092 (m110) cc_final: 0.8124 (m110) REVERT: L 69 TYR cc_start: 0.8394 (p90) cc_final: 0.8084 (p90) REVERT: L 72 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8665 (mm-30) REVERT: L 79 ASP cc_start: 0.9140 (m-30) cc_final: 0.8878 (m-30) REVERT: b 4 LEU cc_start: 0.9551 (mm) cc_final: 0.9178 (mm) REVERT: b 5 GLU cc_start: 0.9006 (mp0) cc_final: 0.8783 (pt0) REVERT: b 8 TYR cc_start: 0.9015 (m-80) cc_final: 0.8744 (m-80) REVERT: b 19 MET cc_start: 0.8751 (mtp) cc_final: 0.8247 (mtp) REVERT: b 48 MET cc_start: 0.9077 (tmm) cc_final: 0.8381 (tmm) REVERT: b 90 ASN cc_start: 0.8983 (m110) cc_final: 0.8629 (m110) REVERT: b 91 LEU cc_start: 0.9645 (tp) cc_final: 0.9315 (tp) REVERT: b 102 ILE cc_start: 0.9719 (mm) cc_final: 0.9481 (mm) REVERT: b 103 TYR cc_start: 0.8617 (m-10) cc_final: 0.8140 (m-10) REVERT: b 114 MET cc_start: 0.8347 (mmm) cc_final: 0.7634 (mmm) REVERT: b 116 GLU cc_start: 0.8187 (mm-30) cc_final: 0.6949 (mp0) REVERT: b 126 ILE cc_start: 0.8083 (mm) cc_final: 0.7876 (mm) REVERT: b 131 TYR cc_start: 0.9168 (m-80) cc_final: 0.8274 (m-80) REVERT: b 135 TYR cc_start: 0.8866 (m-80) cc_final: 0.8204 (m-80) REVERT: b 137 MET cc_start: 0.9070 (mtp) cc_final: 0.8867 (mtp) REVERT: b 164 LEU cc_start: 0.9573 (mt) cc_final: 0.9275 (mp) REVERT: b 169 ASN cc_start: 0.9229 (t0) cc_final: 0.8677 (t0) REVERT: b 172 LEU cc_start: 0.9358 (mt) cc_final: 0.8806 (mt) REVERT: b 186 ILE cc_start: 0.9678 (mt) cc_final: 0.9198 (mt) REVERT: b 189 PHE cc_start: 0.8874 (m-10) cc_final: 0.8404 (m-80) REVERT: b 197 GLN cc_start: 0.8738 (mt0) cc_final: 0.8238 (mt0) REVERT: b 202 LYS cc_start: 0.9082 (tttt) cc_final: 0.8830 (tmmt) REVERT: c 425 THR cc_start: 0.9771 (p) cc_final: 0.9401 (p) REVERT: c 439 MET cc_start: 0.9527 (mtt) cc_final: 0.9270 (mtp) REVERT: c 442 SER cc_start: 0.9288 (m) cc_final: 0.8861 (p) REVERT: d 30 GLN cc_start: 0.9106 (tm-30) cc_final: 0.8805 (tm-30) REVERT: d 35 ASN cc_start: 0.9335 (m-40) cc_final: 0.9018 (t0) REVERT: d 36 LEU cc_start: 0.9527 (mt) cc_final: 0.9323 (mt) REVERT: d 48 HIS cc_start: 0.9002 (m90) cc_final: 0.8401 (m170) REVERT: d 76 GLU cc_start: 0.9105 (mt-10) cc_final: 0.8847 (mt-10) REVERT: d 81 GLU cc_start: 0.8966 (mm-30) cc_final: 0.8571 (tp30) REVERT: d 93 LEU cc_start: 0.9666 (tt) cc_final: 0.9276 (tt) REVERT: d 128 LYS cc_start: 0.9388 (mmtt) cc_final: 0.8872 (mmmt) REVERT: d 129 CYS cc_start: 0.8542 (m) cc_final: 0.7887 (m) REVERT: d 135 PHE cc_start: 0.8657 (m-80) cc_final: 0.8220 (m-80) REVERT: d 158 THR cc_start: 0.9021 (m) cc_final: 0.8575 (p) REVERT: d 181 ILE cc_start: 0.9120 (mt) cc_final: 0.8867 (mt) REVERT: d 197 CYS cc_start: 0.9599 (m) cc_final: 0.9398 (m) REVERT: d 208 MET cc_start: 0.8790 (tpt) cc_final: 0.8389 (tpt) REVERT: d 215 GLU cc_start: 0.9186 (mm-30) cc_final: 0.8899 (mm-30) REVERT: d 233 SER cc_start: 0.8865 (p) cc_final: 0.8622 (p) REVERT: d 241 PHE cc_start: 0.9028 (m-10) cc_final: 0.8781 (m-10) REVERT: d 262 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8185 (tm-30) REVERT: d 276 LEU cc_start: 0.9391 (mt) cc_final: 0.9151 (tt) REVERT: d 287 ASP cc_start: 0.7780 (t0) cc_final: 0.6645 (m-30) REVERT: d 312 PHE cc_start: 0.8631 (m-80) cc_final: 0.7736 (m-80) REVERT: d 315 PHE cc_start: 0.9713 (m-80) cc_final: 0.9199 (m-80) REVERT: d 325 GLU cc_start: 0.9281 (tt0) cc_final: 0.8794 (tm-30) REVERT: d 327 ARG cc_start: 0.9566 (mtt90) cc_final: 0.9311 (mpp80) REVERT: d 348 ILE cc_start: 0.9275 (mm) cc_final: 0.8974 (mp) REVERT: g 7 ASN cc_start: 0.8012 (p0) cc_final: 0.7490 (p0) REVERT: g 13 PHE cc_start: 0.8840 (t80) cc_final: 0.8364 (t80) REVERT: g 28 MET cc_start: 0.9781 (mtm) cc_final: 0.9422 (mtm) REVERT: g 32 TYR cc_start: 0.9024 (t80) cc_final: 0.8325 (t80) REVERT: g 48 ARG cc_start: 0.8765 (mtp180) cc_final: 0.8546 (mtp180) REVERT: g 53 MET cc_start: 0.8612 (mtm) cc_final: 0.8214 (ttp) REVERT: g 57 ILE cc_start: 0.9561 (mt) cc_final: 0.9174 (mt) REVERT: g 70 LEU cc_start: 0.9536 (tp) cc_final: 0.9176 (tp) REVERT: g 78 ASN cc_start: 0.8569 (p0) cc_final: 0.8359 (m110) REVERT: g 140 VAL cc_start: 0.9221 (t) cc_final: 0.8491 (t) REVERT: g 141 LEU cc_start: 0.9375 (mt) cc_final: 0.9076 (mt) REVERT: g 143 LEU cc_start: 0.9124 (tp) cc_final: 0.8916 (tp) REVERT: g 144 TYR cc_start: 0.8854 (m-80) cc_final: 0.8651 (m-80) REVERT: h 44 MET cc_start: 0.7958 (tmm) cc_final: 0.7583 (tmm) REVERT: h 45 SER cc_start: 0.8463 (m) cc_final: 0.7599 (m) REVERT: h 48 ARG cc_start: 0.8314 (ttm170) cc_final: 0.7398 (ttm-80) REVERT: h 51 LEU cc_start: 0.8532 (mt) cc_final: 0.8184 (mt) REVERT: h 54 LYS cc_start: 0.7586 (mttt) cc_final: 0.7141 (mttt) REVERT: h 57 ILE cc_start: 0.9739 (mt) cc_final: 0.9475 (mt) REVERT: h 86 LEU cc_start: 0.9286 (tt) cc_final: 0.8887 (tt) REVERT: h 90 PHE cc_start: 0.8767 (m-10) cc_final: 0.8048 (m-80) REVERT: h 112 ILE cc_start: 0.9529 (mm) cc_final: 0.9066 (tp) REVERT: h 115 ASP cc_start: 0.9336 (t70) cc_final: 0.9135 (p0) REVERT: h 135 LEU cc_start: 0.9549 (mp) cc_final: 0.9291 (mp) REVERT: h 137 PHE cc_start: 0.9286 (m-80) cc_final: 0.8864 (m-80) REVERT: h 144 TYR cc_start: 0.9661 (m-10) cc_final: 0.9100 (m-10) REVERT: h 152 LEU cc_start: 0.9664 (mt) cc_final: 0.9408 (mt) REVERT: i 10 TYR cc_start: 0.7054 (m-80) cc_final: 0.6716 (m-80) REVERT: i 13 PHE cc_start: 0.9091 (t80) cc_final: 0.8158 (t80) REVERT: i 17 MET cc_start: 0.9480 (mmt) cc_final: 0.9174 (mmt) REVERT: i 32 TYR cc_start: 0.8546 (t80) cc_final: 0.8137 (t80) REVERT: i 61 MET cc_start: 0.9360 (mtp) cc_final: 0.8898 (mtp) REVERT: i 115 ASP cc_start: 0.8550 (t70) cc_final: 0.8231 (t0) REVERT: i 131 MET cc_start: 0.9015 (ttp) cc_final: 0.8578 (ttt) REVERT: i 135 LEU cc_start: 0.9574 (mm) cc_final: 0.9220 (mm) REVERT: i 152 LEU cc_start: 0.9676 (mt) cc_final: 0.9437 (mt) REVERT: j 28 MET cc_start: 0.8996 (mtp) cc_final: 0.8401 (mmt) REVERT: j 84 ILE cc_start: 0.8188 (mm) cc_final: 0.7671 (pt) REVERT: j 86 LEU cc_start: 0.8968 (tp) cc_final: 0.8612 (tt) REVERT: j 90 PHE cc_start: 0.8971 (m-10) cc_final: 0.8567 (m-10) REVERT: j 91 LEU cc_start: 0.9192 (mt) cc_final: 0.8904 (mt) REVERT: j 108 PHE cc_start: 0.9021 (m-80) cc_final: 0.8618 (m-80) REVERT: j 121 THR cc_start: 0.9005 (m) cc_final: 0.8578 (p) REVERT: j 124 GLN cc_start: 0.8675 (tp-100) cc_final: 0.7766 (tm-30) REVERT: j 127 LEU cc_start: 0.9339 (tp) cc_final: 0.8592 (tp) REVERT: j 140 VAL cc_start: 0.9381 (t) cc_final: 0.8921 (t) REVERT: j 141 LEU cc_start: 0.9251 (mt) cc_final: 0.8783 (mt) REVERT: j 143 LEU cc_start: 0.9337 (tp) cc_final: 0.9123 (tp) REVERT: j 152 LEU cc_start: 0.9332 (tp) cc_final: 0.8953 (tp) REVERT: k 44 MET cc_start: 0.9007 (ppp) cc_final: 0.8554 (ppp) REVERT: k 53 MET cc_start: 0.8680 (tmm) cc_final: 0.7998 (mtt) REVERT: k 57 ILE cc_start: 0.9159 (mt) cc_final: 0.8683 (mm) REVERT: k 59 VAL cc_start: 0.9318 (t) cc_final: 0.8996 (t) REVERT: k 65 ILE cc_start: 0.9611 (mm) cc_final: 0.9078 (mm) REVERT: k 67 ILE cc_start: 0.8660 (mt) cc_final: 0.8270 (mt) REVERT: k 68 TYR cc_start: 0.7902 (m-10) cc_final: 0.7298 (m-80) REVERT: k 70 LEU cc_start: 0.9233 (tp) cc_final: 0.8716 (pp) REVERT: k 90 PHE cc_start: 0.8811 (m-80) cc_final: 0.8497 (m-80) REVERT: k 91 LEU cc_start: 0.9174 (mt) cc_final: 0.8805 (mt) REVERT: k 131 MET cc_start: 0.8327 (mtm) cc_final: 0.8024 (mtp) REVERT: l 17 MET cc_start: 0.9332 (mmp) cc_final: 0.8845 (mmp) REVERT: l 24 VAL cc_start: 0.9422 (t) cc_final: 0.9120 (t) REVERT: l 28 MET cc_start: 0.8867 (mtp) cc_final: 0.8596 (mtp) REVERT: l 32 TYR cc_start: 0.8239 (t80) cc_final: 0.7640 (t80) REVERT: l 53 MET cc_start: 0.7905 (mtp) cc_final: 0.7536 (ttp) REVERT: l 97 LEU cc_start: 0.9462 (mt) cc_final: 0.9246 (mm) REVERT: l 108 PHE cc_start: 0.8306 (t80) cc_final: 0.7819 (t80) REVERT: l 113 VAL cc_start: 0.9724 (p) cc_final: 0.9524 (p) REVERT: l 124 GLN cc_start: 0.8636 (tp-100) cc_final: 0.8314 (tm-30) REVERT: l 131 MET cc_start: 0.9260 (ttp) cc_final: 0.8899 (ttm) REVERT: l 137 PHE cc_start: 0.8826 (m-80) cc_final: 0.8569 (m-10) REVERT: m 11 SER cc_start: 0.8388 (p) cc_final: 0.8045 (t) REVERT: m 21 SER cc_start: 0.9391 (m) cc_final: 0.9137 (p) REVERT: m 51 LEU cc_start: 0.8495 (mt) cc_final: 0.8174 (mt) REVERT: m 53 MET cc_start: 0.8775 (mmm) cc_final: 0.8115 (tmm) REVERT: m 86 LEU cc_start: 0.9519 (tp) cc_final: 0.8855 (tp) REVERT: m 89 SER cc_start: 0.9385 (m) cc_final: 0.8799 (p) REVERT: m 90 PHE cc_start: 0.9077 (m-10) cc_final: 0.8702 (m-80) REVERT: m 92 GLN cc_start: 0.9253 (mt0) cc_final: 0.8901 (mt0) REVERT: m 128 PHE cc_start: 0.8528 (t80) cc_final: 0.7749 (t80) REVERT: m 144 TYR cc_start: 0.9475 (m-10) cc_final: 0.9026 (m-10) REVERT: n 13 PHE cc_start: 0.9154 (t80) cc_final: 0.8470 (t80) REVERT: n 17 MET cc_start: 0.9289 (mmt) cc_final: 0.8965 (mmm) REVERT: n 47 MET cc_start: 0.9223 (mmm) cc_final: 0.8815 (mmm) REVERT: n 61 MET cc_start: 0.9206 (mmp) cc_final: 0.8423 (mmm) REVERT: n 68 TYR cc_start: 0.8875 (m-10) cc_final: 0.8458 (m-10) REVERT: n 86 LEU cc_start: 0.9279 (tp) cc_final: 0.9062 (tp) REVERT: n 90 PHE cc_start: 0.9154 (m-80) cc_final: 0.8852 (m-80) REVERT: n 124 GLN cc_start: 0.8779 (tp-100) cc_final: 0.8376 (tm-30) REVERT: n 133 LEU cc_start: 0.9384 (mt) cc_final: 0.9169 (mt) REVERT: n 135 LEU cc_start: 0.9614 (mt) cc_final: 0.9386 (mt) REVERT: n 146 LEU cc_start: 0.8988 (mt) cc_final: 0.8742 (mt) REVERT: o 13 PHE cc_start: 0.9084 (t80) cc_final: 0.8252 (t80) REVERT: o 17 MET cc_start: 0.9243 (mmp) cc_final: 0.8731 (mmt) REVERT: o 21 SER cc_start: 0.8889 (m) cc_final: 0.8451 (p) REVERT: o 25 PHE cc_start: 0.8152 (m-10) cc_final: 0.7949 (m-10) REVERT: o 51 LEU cc_start: 0.8890 (mt) cc_final: 0.8598 (mt) REVERT: o 54 LYS cc_start: 0.8027 (mttt) cc_final: 0.7708 (mttp) REVERT: o 57 ILE cc_start: 0.9178 (mt) cc_final: 0.8868 (mm) REVERT: o 64 ILE cc_start: 0.9330 (mt) cc_final: 0.9125 (mt) REVERT: o 68 TYR cc_start: 0.9126 (m-10) cc_final: 0.8905 (m-10) REVERT: o 70 LEU cc_start: 0.9412 (tp) cc_final: 0.9133 (tp) REVERT: o 91 LEU cc_start: 0.9703 (mm) cc_final: 0.9450 (mp) REVERT: o 97 LEU cc_start: 0.9555 (mt) cc_final: 0.9342 (mt) REVERT: o 112 ILE cc_start: 0.9402 (mm) cc_final: 0.9196 (mm) REVERT: o 128 PHE cc_start: 0.8404 (t80) cc_final: 0.8153 (t80) REVERT: o 144 TYR cc_start: 0.9105 (m-10) cc_final: 0.8786 (m-10) REVERT: o 152 LEU cc_start: 0.9515 (mt) cc_final: 0.9137 (mt) REVERT: p 303 TYR cc_start: 0.8758 (t80) cc_final: 0.8303 (t80) REVERT: p 307 PHE cc_start: 0.8734 (t80) cc_final: 0.8524 (t80) REVERT: p 311 LEU cc_start: 0.9521 (tt) cc_final: 0.9312 (tt) REVERT: p 314 MET cc_start: 0.8754 (mtt) cc_final: 0.8374 (tmm) REVERT: p 328 ILE cc_start: 0.9618 (mt) cc_final: 0.9367 (tp) REVERT: p 330 ASN cc_start: 0.8892 (t0) cc_final: 0.8588 (t0) REVERT: p 338 ILE cc_start: 0.8404 (pt) cc_final: 0.8116 (pt) outliers start: 9 outliers final: 1 residues processed: 1069 average time/residue: 0.1121 time to fit residues: 193.5688 Evaluate side-chains 907 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 906 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 157 optimal weight: 2.9990 chunk 169 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 270 optimal weight: 0.9980 chunk 148 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 159 optimal weight: 0.9990 chunk 166 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 135 optimal weight: 0.0570 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 88 HIS d 183 ASN d 338 GLN ** h 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.098038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.078227 restraints weight = 63126.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.080841 restraints weight = 38746.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.082742 restraints weight = 26433.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.084172 restraints weight = 19482.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.085273 restraints weight = 15334.265| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.4876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19610 Z= 0.157 Angle : 0.640 9.689 26647 Z= 0.337 Chirality : 0.041 0.183 3268 Planarity : 0.004 0.075 3401 Dihedral : 3.932 20.225 2941 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.35 % Allowed : 1.65 % Favored : 98.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.16), residues: 2771 helix: 2.09 (0.11), residues: 2114 sheet: -1.50 (0.93), residues: 16 loop : -0.53 (0.25), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG o 119 TYR 0.035 0.002 TYR b 70 PHE 0.023 0.002 PHE k 108 TRP 0.014 0.001 TRP p 329 HIS 0.007 0.001 HIS d 311 Details of bonding type rmsd covalent geometry : bond 0.00317 (19610) covalent geometry : angle 0.63964 (26647) hydrogen bonds : bond 0.05451 ( 1741) hydrogen bonds : angle 4.41132 ( 5118) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1042 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 1036 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 55 LYS cc_start: 0.9471 (tttp) cc_final: 0.9180 (tptp) REVERT: H 64 GLU cc_start: 0.9261 (tp30) cc_final: 0.8612 (tm-30) REVERT: H 84 ILE cc_start: 0.9473 (mt) cc_final: 0.9107 (mt) REVERT: H 85 GLN cc_start: 0.9093 (mm-40) cc_final: 0.8791 (mm-40) REVERT: H 119 TYR cc_start: 0.7733 (p90) cc_final: 0.7379 (p90) REVERT: L 14 GLU cc_start: 0.8963 (pm20) cc_final: 0.8761 (pm20) REVERT: L 22 LEU cc_start: 0.9393 (mt) cc_final: 0.9125 (mt) REVERT: L 43 THR cc_start: 0.8425 (p) cc_final: 0.7659 (p) REVERT: L 47 GLU cc_start: 0.9089 (mt-10) cc_final: 0.8635 (mt-10) REVERT: L 53 ARG cc_start: 0.8834 (mtp-110) cc_final: 0.8315 (mtp-110) REVERT: L 66 ILE cc_start: 0.9201 (tp) cc_final: 0.8909 (tp) REVERT: L 67 ASN cc_start: 0.8947 (m110) cc_final: 0.8271 (m110) REVERT: L 69 TYR cc_start: 0.8376 (p90) cc_final: 0.8112 (p90) REVERT: L 70 ILE cc_start: 0.9383 (mt) cc_final: 0.9170 (mt) REVERT: L 72 GLU cc_start: 0.8912 (mm-30) cc_final: 0.8687 (mm-30) REVERT: L 79 ASP cc_start: 0.9138 (m-30) cc_final: 0.8861 (m-30) REVERT: b 5 GLU cc_start: 0.9011 (mp0) cc_final: 0.8777 (pt0) REVERT: b 19 MET cc_start: 0.8734 (mtp) cc_final: 0.8336 (mtp) REVERT: b 42 THR cc_start: 0.9114 (t) cc_final: 0.8794 (t) REVERT: b 43 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7903 (mm-30) REVERT: b 48 MET cc_start: 0.8843 (tmm) cc_final: 0.8486 (tmm) REVERT: b 51 ASN cc_start: 0.8805 (p0) cc_final: 0.7942 (p0) REVERT: b 70 TYR cc_start: 0.9572 (p90) cc_final: 0.9327 (p90) REVERT: b 90 ASN cc_start: 0.8984 (m110) cc_final: 0.8663 (m110) REVERT: b 102 ILE cc_start: 0.9684 (mm) cc_final: 0.9452 (mm) REVERT: b 103 TYR cc_start: 0.8666 (m-10) cc_final: 0.8190 (m-10) REVERT: b 116 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7575 (mm-30) REVERT: b 137 MET cc_start: 0.9064 (mtp) cc_final: 0.8702 (mtp) REVERT: b 164 LEU cc_start: 0.9651 (mt) cc_final: 0.9211 (mm) REVERT: b 169 ASN cc_start: 0.9121 (t0) cc_final: 0.8454 (t0) REVERT: b 172 LEU cc_start: 0.9269 (mt) cc_final: 0.8714 (mt) REVERT: b 186 ILE cc_start: 0.9674 (mt) cc_final: 0.9191 (mt) REVERT: b 189 PHE cc_start: 0.8952 (m-10) cc_final: 0.8255 (m-80) REVERT: b 197 GLN cc_start: 0.8662 (mt0) cc_final: 0.8286 (mt0) REVERT: b 202 LYS cc_start: 0.9090 (tttt) cc_final: 0.8700 (mptt) REVERT: c 439 MET cc_start: 0.9469 (mtt) cc_final: 0.9146 (mtp) REVERT: d 30 GLN cc_start: 0.9082 (tm-30) cc_final: 0.8767 (tm-30) REVERT: d 36 LEU cc_start: 0.9457 (mt) cc_final: 0.9225 (mt) REVERT: d 39 CYS cc_start: 0.7538 (p) cc_final: 0.7212 (p) REVERT: d 44 ASP cc_start: 0.9086 (m-30) cc_final: 0.8861 (m-30) REVERT: d 48 HIS cc_start: 0.9010 (m90) cc_final: 0.8458 (m90) REVERT: d 76 GLU cc_start: 0.9129 (mt-10) cc_final: 0.8922 (mt-10) REVERT: d 81 GLU cc_start: 0.9024 (mm-30) cc_final: 0.8668 (tp30) REVERT: d 93 LEU cc_start: 0.9682 (tt) cc_final: 0.9321 (tt) REVERT: d 105 MET cc_start: 0.8898 (mmm) cc_final: 0.8683 (tpt) REVERT: d 125 LEU cc_start: 0.9049 (mt) cc_final: 0.8699 (mt) REVERT: d 128 LYS cc_start: 0.9419 (mmtt) cc_final: 0.8942 (mmmt) REVERT: d 129 CYS cc_start: 0.8540 (m) cc_final: 0.7947 (m) REVERT: d 181 ILE cc_start: 0.9138 (mt) cc_final: 0.8768 (mt) REVERT: d 224 THR cc_start: 0.9457 (m) cc_final: 0.9139 (p) REVERT: d 241 PHE cc_start: 0.9108 (m-10) cc_final: 0.8867 (m-10) REVERT: d 254 GLN cc_start: 0.8193 (mp10) cc_final: 0.7930 (mp10) REVERT: d 262 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8128 (tm-30) REVERT: d 276 LEU cc_start: 0.9370 (mt) cc_final: 0.9168 (tt) REVERT: d 287 ASP cc_start: 0.8033 (t0) cc_final: 0.6897 (m-30) REVERT: d 291 GLU cc_start: 0.9486 (mm-30) cc_final: 0.9156 (mm-30) REVERT: d 312 PHE cc_start: 0.8586 (m-80) cc_final: 0.7836 (m-80) REVERT: d 315 PHE cc_start: 0.9697 (m-80) cc_final: 0.9262 (m-80) REVERT: d 322 LYS cc_start: 0.9592 (mtpp) cc_final: 0.9165 (mtpt) REVERT: d 323 GLU cc_start: 0.9240 (tt0) cc_final: 0.8676 (tt0) REVERT: d 325 GLU cc_start: 0.9339 (tt0) cc_final: 0.8779 (tm-30) REVERT: d 327 ARG cc_start: 0.9579 (mtt90) cc_final: 0.8921 (mtt-85) REVERT: g 28 MET cc_start: 0.9782 (mtm) cc_final: 0.9342 (mtm) REVERT: g 32 TYR cc_start: 0.9000 (t80) cc_final: 0.8342 (t80) REVERT: g 53 MET cc_start: 0.8589 (mtm) cc_final: 0.8257 (ttm) REVERT: g 57 ILE cc_start: 0.9548 (mt) cc_final: 0.9173 (mt) REVERT: g 64 ILE cc_start: 0.9445 (mt) cc_final: 0.9179 (mt) REVERT: g 68 TYR cc_start: 0.9452 (m-80) cc_final: 0.9116 (m-80) REVERT: g 70 LEU cc_start: 0.9566 (tp) cc_final: 0.9247 (tp) REVERT: g 90 PHE cc_start: 0.8969 (m-80) cc_final: 0.8730 (m-80) REVERT: g 112 ILE cc_start: 0.9487 (mm) cc_final: 0.9163 (mm) REVERT: g 118 VAL cc_start: 0.9501 (p) cc_final: 0.9287 (p) REVERT: g 140 VAL cc_start: 0.9225 (t) cc_final: 0.8588 (t) REVERT: g 141 LEU cc_start: 0.9354 (mt) cc_final: 0.9118 (mt) REVERT: h 13 PHE cc_start: 0.9243 (t80) cc_final: 0.8929 (t80) REVERT: h 17 MET cc_start: 0.9357 (mmp) cc_final: 0.9152 (mmm) REVERT: h 23 MET cc_start: 0.9477 (mmm) cc_final: 0.9267 (tpp) REVERT: h 24 VAL cc_start: 0.9603 (p) cc_final: 0.9342 (p) REVERT: h 28 MET cc_start: 0.8956 (mtp) cc_final: 0.8594 (mtm) REVERT: h 44 MET cc_start: 0.8046 (tmm) cc_final: 0.7619 (tmm) REVERT: h 45 SER cc_start: 0.8464 (m) cc_final: 0.7543 (m) REVERT: h 48 ARG cc_start: 0.8461 (ttm170) cc_final: 0.7580 (ttm170) REVERT: h 51 LEU cc_start: 0.8589 (mt) cc_final: 0.8198 (mt) REVERT: h 54 LYS cc_start: 0.7604 (mttt) cc_final: 0.7077 (tttt) REVERT: h 57 ILE cc_start: 0.9693 (mt) cc_final: 0.9307 (mt) REVERT: h 60 VAL cc_start: 0.9569 (t) cc_final: 0.9295 (p) REVERT: h 61 MET cc_start: 0.9234 (mmp) cc_final: 0.8800 (mmp) REVERT: h 112 ILE cc_start: 0.9583 (mm) cc_final: 0.9150 (tp) REVERT: h 115 ASP cc_start: 0.9327 (t70) cc_final: 0.9095 (p0) REVERT: h 137 PHE cc_start: 0.9233 (m-80) cc_final: 0.8675 (m-80) REVERT: h 144 TYR cc_start: 0.9647 (m-10) cc_final: 0.9145 (m-10) REVERT: h 152 LEU cc_start: 0.9654 (mt) cc_final: 0.9424 (mt) REVERT: i 10 TYR cc_start: 0.7041 (m-80) cc_final: 0.6769 (m-80) REVERT: i 17 MET cc_start: 0.9462 (mmt) cc_final: 0.8770 (mmm) REVERT: i 23 MET cc_start: 0.8863 (tpp) cc_final: 0.8601 (tpp) REVERT: i 32 TYR cc_start: 0.8902 (t80) cc_final: 0.8530 (t80) REVERT: i 61 MET cc_start: 0.9241 (mtp) cc_final: 0.9016 (mtp) REVERT: i 76 ILE cc_start: 0.9343 (mt) cc_final: 0.9069 (mt) REVERT: i 101 LEU cc_start: 0.9434 (mt) cc_final: 0.9212 (mt) REVERT: i 115 ASP cc_start: 0.8489 (t70) cc_final: 0.7582 (t0) REVERT: i 131 MET cc_start: 0.9026 (ttp) cc_final: 0.8574 (ttt) REVERT: i 135 LEU cc_start: 0.9532 (mm) cc_final: 0.9090 (mm) REVERT: i 152 LEU cc_start: 0.9660 (mt) cc_final: 0.9426 (mt) REVERT: j 17 MET cc_start: 0.9230 (mtm) cc_final: 0.8680 (mtt) REVERT: j 28 MET cc_start: 0.8981 (mtp) cc_final: 0.8671 (mtt) REVERT: j 91 LEU cc_start: 0.9211 (mt) cc_final: 0.8894 (mt) REVERT: j 93 LEU cc_start: 0.9270 (tt) cc_final: 0.9006 (tt) REVERT: j 108 PHE cc_start: 0.8893 (m-80) cc_final: 0.8658 (m-80) REVERT: j 119 ARG cc_start: 0.8090 (mtp-110) cc_final: 0.7520 (mtm180) REVERT: j 121 THR cc_start: 0.8952 (m) cc_final: 0.8603 (p) REVERT: j 124 GLN cc_start: 0.8746 (tp-100) cc_final: 0.7858 (tm-30) REVERT: j 127 LEU cc_start: 0.9344 (tp) cc_final: 0.8607 (tp) REVERT: j 131 MET cc_start: 0.8243 (ttp) cc_final: 0.7946 (ttp) REVERT: j 141 LEU cc_start: 0.9119 (mt) cc_final: 0.8822 (mt) REVERT: j 152 LEU cc_start: 0.9336 (tp) cc_final: 0.9003 (tp) REVERT: k 13 PHE cc_start: 0.9151 (t80) cc_final: 0.8949 (t80) REVERT: k 17 MET cc_start: 0.8887 (mtm) cc_final: 0.8505 (mtm) REVERT: k 44 MET cc_start: 0.9024 (ppp) cc_final: 0.8514 (ppp) REVERT: k 53 MET cc_start: 0.8662 (tmm) cc_final: 0.7966 (mtt) REVERT: k 57 ILE cc_start: 0.9145 (mt) cc_final: 0.8783 (mm) REVERT: k 59 VAL cc_start: 0.9285 (t) cc_final: 0.8934 (t) REVERT: k 65 ILE cc_start: 0.9606 (mm) cc_final: 0.9221 (mt) REVERT: k 68 TYR cc_start: 0.8243 (m-10) cc_final: 0.7559 (m-80) REVERT: k 91 LEU cc_start: 0.9194 (mt) cc_final: 0.8879 (mt) REVERT: k 121 THR cc_start: 0.8493 (p) cc_final: 0.8104 (p) REVERT: k 123 GLN cc_start: 0.9162 (mm-40) cc_final: 0.8749 (mm-40) REVERT: k 127 LEU cc_start: 0.8574 (mp) cc_final: 0.8312 (mp) REVERT: k 131 MET cc_start: 0.8194 (mtm) cc_final: 0.7985 (mtp) REVERT: l 13 PHE cc_start: 0.9275 (t80) cc_final: 0.8541 (t80) REVERT: l 17 MET cc_start: 0.9316 (mmp) cc_final: 0.8818 (mmp) REVERT: l 24 VAL cc_start: 0.9491 (t) cc_final: 0.9139 (t) REVERT: l 28 MET cc_start: 0.8906 (mtp) cc_final: 0.8638 (mtp) REVERT: l 32 TYR cc_start: 0.8317 (t80) cc_final: 0.7799 (t80) REVERT: l 68 TYR cc_start: 0.8847 (m-10) cc_final: 0.8308 (m-80) REVERT: l 97 LEU cc_start: 0.9484 (mt) cc_final: 0.9272 (mm) REVERT: l 113 VAL cc_start: 0.9651 (p) cc_final: 0.9374 (p) REVERT: l 124 GLN cc_start: 0.8697 (tp-100) cc_final: 0.8394 (tm-30) REVERT: l 127 LEU cc_start: 0.7492 (tp) cc_final: 0.7235 (tp) REVERT: l 131 MET cc_start: 0.9303 (ttp) cc_final: 0.8881 (ttm) REVERT: l 137 PHE cc_start: 0.8823 (m-80) cc_final: 0.8518 (m-10) REVERT: l 143 LEU cc_start: 0.9521 (mm) cc_final: 0.9219 (mm) REVERT: l 146 LEU cc_start: 0.8992 (tt) cc_final: 0.8557 (pp) REVERT: m 11 SER cc_start: 0.8620 (p) cc_final: 0.8307 (t) REVERT: m 21 SER cc_start: 0.9334 (m) cc_final: 0.9085 (p) REVERT: m 51 LEU cc_start: 0.8545 (mt) cc_final: 0.8216 (mt) REVERT: m 53 MET cc_start: 0.8750 (mmm) cc_final: 0.8040 (tmm) REVERT: m 86 LEU cc_start: 0.9518 (tp) cc_final: 0.8905 (tp) REVERT: m 89 SER cc_start: 0.9314 (m) cc_final: 0.8774 (p) REVERT: m 90 PHE cc_start: 0.9010 (m-10) cc_final: 0.8667 (m-80) REVERT: m 92 GLN cc_start: 0.9244 (mt0) cc_final: 0.8919 (mt0) REVERT: m 128 PHE cc_start: 0.8432 (t80) cc_final: 0.7788 (t80) REVERT: m 144 TYR cc_start: 0.9452 (m-10) cc_final: 0.9011 (m-10) REVERT: m 152 LEU cc_start: 0.9143 (mt) cc_final: 0.8911 (mt) REVERT: n 47 MET cc_start: 0.9152 (mmm) cc_final: 0.8682 (mmm) REVERT: n 48 ARG cc_start: 0.9148 (mmm-85) cc_final: 0.8393 (mmm-85) REVERT: n 61 MET cc_start: 0.9231 (mmp) cc_final: 0.8515 (mmm) REVERT: n 68 TYR cc_start: 0.8987 (m-10) cc_final: 0.8550 (m-10) REVERT: n 70 LEU cc_start: 0.9445 (tp) cc_final: 0.9196 (tp) REVERT: n 72 VAL cc_start: 0.9339 (t) cc_final: 0.9078 (p) REVERT: n 86 LEU cc_start: 0.9271 (tp) cc_final: 0.9021 (tp) REVERT: n 90 PHE cc_start: 0.9169 (m-80) cc_final: 0.8630 (m-80) REVERT: n 124 GLN cc_start: 0.8811 (tp-100) cc_final: 0.8371 (tm-30) REVERT: n 135 LEU cc_start: 0.9612 (mt) cc_final: 0.9388 (mt) REVERT: n 146 LEU cc_start: 0.9046 (mt) cc_final: 0.8655 (mt) REVERT: o 13 PHE cc_start: 0.9062 (t80) cc_final: 0.8317 (t80) REVERT: o 17 MET cc_start: 0.9319 (mmp) cc_final: 0.8694 (mmt) REVERT: o 21 SER cc_start: 0.8902 (m) cc_final: 0.8449 (p) REVERT: o 25 PHE cc_start: 0.8200 (m-10) cc_final: 0.7989 (m-10) REVERT: o 47 MET cc_start: 0.8518 (tmm) cc_final: 0.8150 (tmm) REVERT: o 51 LEU cc_start: 0.8797 (mt) cc_final: 0.8497 (mt) REVERT: o 54 LYS cc_start: 0.8107 (mttt) cc_final: 0.7831 (mttp) REVERT: o 57 ILE cc_start: 0.9240 (mt) cc_final: 0.8940 (mt) REVERT: o 64 ILE cc_start: 0.9359 (mt) cc_final: 0.8898 (mt) REVERT: o 65 ILE cc_start: 0.9516 (mp) cc_final: 0.9126 (mp) REVERT: o 68 TYR cc_start: 0.9243 (m-10) cc_final: 0.8642 (m-80) REVERT: o 70 LEU cc_start: 0.9444 (tp) cc_final: 0.9060 (tp) REVERT: o 80 LEU cc_start: 0.8987 (mm) cc_final: 0.8768 (mm) REVERT: o 91 LEU cc_start: 0.9708 (mm) cc_final: 0.9483 (mm) REVERT: o 97 LEU cc_start: 0.9603 (mt) cc_final: 0.9388 (mt) REVERT: o 128 PHE cc_start: 0.8600 (t80) cc_final: 0.8119 (t80) REVERT: o 131 MET cc_start: 0.8853 (ppp) cc_final: 0.8652 (ppp) REVERT: o 144 TYR cc_start: 0.9060 (m-10) cc_final: 0.8691 (m-10) REVERT: o 152 LEU cc_start: 0.9426 (mt) cc_final: 0.9039 (mt) REVERT: p 303 TYR cc_start: 0.8694 (t80) cc_final: 0.8312 (t80) REVERT: p 308 ASN cc_start: 0.8773 (p0) cc_final: 0.8491 (p0) REVERT: p 313 ILE cc_start: 0.9744 (pt) cc_final: 0.9439 (pt) outliers start: 6 outliers final: 0 residues processed: 1037 average time/residue: 0.1148 time to fit residues: 192.7965 Evaluate side-chains 898 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 898 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 95 optimal weight: 2.9990 chunk 236 optimal weight: 0.0270 chunk 28 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 109 optimal weight: 0.9990 chunk 216 optimal weight: 0.8980 chunk 204 optimal weight: 0.4980 chunk 5 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 141 optimal weight: 7.9990 chunk 36 optimal weight: 20.0000 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 92 GLN ** h 124 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 = 0.3641 r_free = 0.3641 target = 0.098326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.078480 restraints weight = 62962.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.081088 restraints weight = 39096.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.082956 restraints weight = 26895.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.084159 restraints weight = 19878.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.085464 restraints weight = 15968.237| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.5214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 19610 Z= 0.153 Angle : 0.636 10.362 26647 Z= 0.335 Chirality : 0.042 0.238 3268 Planarity : 0.004 0.042 3401 Dihedral : 3.921 23.891 2941 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.12 % Allowed : 1.71 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.16), residues: 2771 helix: 1.98 (0.11), residues: 2135 sheet: -1.65 (0.92), residues: 16 loop : -0.73 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG k 119 TYR 0.041 0.002 TYR j 144 PHE 0.053 0.002 PHE b 118 TRP 0.014 0.001 TRP c 420 HIS 0.004 0.001 HIS d 48 Details of bonding type rmsd covalent geometry : bond 0.00317 (19610) covalent geometry : angle 0.63649 (26647) hydrogen bonds : bond 0.05205 ( 1741) hydrogen bonds : angle 4.38468 ( 5118) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1027 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1025 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 55 LYS cc_start: 0.9485 (tttp) cc_final: 0.9059 (tptp) REVERT: H 64 GLU cc_start: 0.9294 (tp30) cc_final: 0.8737 (tp30) REVERT: H 84 ILE cc_start: 0.9475 (mt) cc_final: 0.9096 (mt) REVERT: H 85 GLN cc_start: 0.9115 (mm-40) cc_final: 0.8810 (mm-40) REVERT: H 119 TYR cc_start: 0.7743 (p90) cc_final: 0.7451 (p90) REVERT: L 11 ILE cc_start: 0.9633 (mm) cc_final: 0.9428 (mm) REVERT: L 14 GLU cc_start: 0.9043 (pm20) cc_final: 0.8842 (pm20) REVERT: L 22 LEU cc_start: 0.9414 (mt) cc_final: 0.9130 (mt) REVERT: L 43 THR cc_start: 0.8453 (p) cc_final: 0.7623 (p) REVERT: L 47 GLU cc_start: 0.9132 (mt-10) cc_final: 0.8726 (mt-10) REVERT: L 53 ARG cc_start: 0.8715 (mtp-110) cc_final: 0.8198 (mtp-110) REVERT: L 66 ILE cc_start: 0.9220 (tp) cc_final: 0.9016 (tp) REVERT: L 67 ASN cc_start: 0.8959 (m110) cc_final: 0.8174 (m110) REVERT: L 69 TYR cc_start: 0.8268 (p90) cc_final: 0.7834 (p90) REVERT: L 70 ILE cc_start: 0.9401 (mt) cc_final: 0.9155 (mt) REVERT: L 72 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8703 (mm-30) REVERT: L 73 MET cc_start: 0.8673 (mtm) cc_final: 0.8270 (mtt) REVERT: L 79 ASP cc_start: 0.9186 (m-30) cc_final: 0.8892 (m-30) REVERT: L 90 GLU cc_start: 0.9047 (mp0) cc_final: 0.8165 (tt0) REVERT: b 5 GLU cc_start: 0.9009 (mp0) cc_final: 0.8772 (pt0) REVERT: b 19 MET cc_start: 0.8710 (mtp) cc_final: 0.8307 (mtp) REVERT: b 42 THR cc_start: 0.9100 (t) cc_final: 0.8753 (t) REVERT: b 43 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7780 (mm-30) REVERT: b 48 MET cc_start: 0.8827 (tmm) cc_final: 0.8541 (tmm) REVERT: b 51 ASN cc_start: 0.8733 (p0) cc_final: 0.8086 (p0) REVERT: b 70 TYR cc_start: 0.9548 (p90) cc_final: 0.9058 (p90) REVERT: b 90 ASN cc_start: 0.9002 (m110) cc_final: 0.8674 (m110) REVERT: b 91 LEU cc_start: 0.9584 (tp) cc_final: 0.9275 (tp) REVERT: b 102 ILE cc_start: 0.9688 (mm) cc_final: 0.9472 (mm) REVERT: b 103 TYR cc_start: 0.8701 (m-10) cc_final: 0.8184 (m-10) REVERT: b 116 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7697 (mm-30) REVERT: b 137 MET cc_start: 0.9127 (mtp) cc_final: 0.8696 (mtp) REVERT: b 164 LEU cc_start: 0.9517 (mt) cc_final: 0.9304 (mp) REVERT: b 168 GLN cc_start: 0.9053 (mp10) cc_final: 0.8736 (mp10) REVERT: b 169 ASN cc_start: 0.8775 (t0) cc_final: 0.8089 (t0) REVERT: b 172 LEU cc_start: 0.9298 (mt) cc_final: 0.8647 (mt) REVERT: b 186 ILE cc_start: 0.9652 (mt) cc_final: 0.9175 (mt) REVERT: b 189 PHE cc_start: 0.9018 (m-10) cc_final: 0.8591 (m-80) REVERT: b 197 GLN cc_start: 0.8619 (mt0) cc_final: 0.8306 (mt0) REVERT: b 202 LYS cc_start: 0.8891 (tttt) cc_final: 0.8530 (tmmt) REVERT: c 439 MET cc_start: 0.9431 (mtt) cc_final: 0.9096 (mtp) REVERT: d 28 LEU cc_start: 0.9368 (mt) cc_final: 0.9000 (mm) REVERT: d 30 GLN cc_start: 0.9079 (tm-30) cc_final: 0.8757 (tm-30) REVERT: d 39 CYS cc_start: 0.7397 (p) cc_final: 0.7143 (p) REVERT: d 44 ASP cc_start: 0.9071 (m-30) cc_final: 0.8812 (m-30) REVERT: d 48 HIS cc_start: 0.8889 (m90) cc_final: 0.8605 (m90) REVERT: d 76 GLU cc_start: 0.9147 (mt-10) cc_final: 0.8885 (mt-10) REVERT: d 81 GLU cc_start: 0.9034 (mm-30) cc_final: 0.8453 (tp30) REVERT: d 85 MET cc_start: 0.9529 (ptp) cc_final: 0.8935 (ptp) REVERT: d 105 MET cc_start: 0.8939 (mmm) cc_final: 0.8521 (tpt) REVERT: d 125 LEU cc_start: 0.9066 (mt) cc_final: 0.8719 (mt) REVERT: d 128 LYS cc_start: 0.9419 (mmtt) cc_final: 0.8945 (mmmt) REVERT: d 129 CYS cc_start: 0.8485 (m) cc_final: 0.7875 (m) REVERT: d 181 ILE cc_start: 0.9120 (mt) cc_final: 0.8852 (mt) REVERT: d 224 THR cc_start: 0.9487 (m) cc_final: 0.9164 (p) REVERT: d 254 GLN cc_start: 0.8102 (mp10) cc_final: 0.7766 (mp10) REVERT: d 262 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8195 (tm-30) REVERT: d 276 LEU cc_start: 0.9325 (mt) cc_final: 0.9115 (tt) REVERT: d 291 GLU cc_start: 0.9508 (mm-30) cc_final: 0.9232 (mm-30) REVERT: d 302 ASN cc_start: 0.9784 (m110) cc_final: 0.9582 (m110) REVERT: d 315 PHE cc_start: 0.9721 (m-80) cc_final: 0.9300 (m-80) REVERT: d 322 LYS cc_start: 0.9618 (mtpp) cc_final: 0.9008 (mtpp) REVERT: d 323 GLU cc_start: 0.9273 (tt0) cc_final: 0.8663 (tt0) REVERT: d 325 GLU cc_start: 0.9459 (tt0) cc_final: 0.8893 (tm-30) REVERT: d 327 ARG cc_start: 0.9575 (mtt90) cc_final: 0.8751 (mtt-85) REVERT: d 338 GLN cc_start: 0.9104 (mm-40) cc_final: 0.8900 (mm110) REVERT: d 348 ILE cc_start: 0.9451 (mm) cc_final: 0.9193 (mp) REVERT: g 7 ASN cc_start: 0.8120 (p0) cc_final: 0.7859 (p0) REVERT: g 24 VAL cc_start: 0.9765 (t) cc_final: 0.9557 (t) REVERT: g 28 MET cc_start: 0.9805 (mtm) cc_final: 0.9448 (mtm) REVERT: g 32 TYR cc_start: 0.9022 (t80) cc_final: 0.8368 (t80) REVERT: g 51 LEU cc_start: 0.8571 (mm) cc_final: 0.8236 (mm) REVERT: g 53 MET cc_start: 0.8580 (mtm) cc_final: 0.8276 (ttm) REVERT: g 64 ILE cc_start: 0.9425 (mt) cc_final: 0.9210 (mt) REVERT: g 68 TYR cc_start: 0.9508 (m-80) cc_final: 0.9276 (m-80) REVERT: g 70 LEU cc_start: 0.9557 (tp) cc_final: 0.9301 (tp) REVERT: g 90 PHE cc_start: 0.9020 (m-80) cc_final: 0.8765 (m-80) REVERT: g 118 VAL cc_start: 0.9459 (p) cc_final: 0.9217 (p) REVERT: g 141 LEU cc_start: 0.9389 (mt) cc_final: 0.9130 (mt) REVERT: g 144 TYR cc_start: 0.8852 (m-80) cc_final: 0.8527 (m-80) REVERT: g 146 LEU cc_start: 0.9790 (tp) cc_final: 0.9581 (tp) REVERT: h 13 PHE cc_start: 0.9296 (t80) cc_final: 0.8865 (t80) REVERT: h 23 MET cc_start: 0.9528 (mmm) cc_final: 0.9281 (tpp) REVERT: h 24 VAL cc_start: 0.9609 (p) cc_final: 0.9353 (p) REVERT: h 28 MET cc_start: 0.8914 (mtp) cc_final: 0.8087 (tpt) REVERT: h 44 MET cc_start: 0.8090 (tmm) cc_final: 0.7579 (tmm) REVERT: h 48 ARG cc_start: 0.8512 (ttm170) cc_final: 0.7541 (ttm170) REVERT: h 51 LEU cc_start: 0.8578 (mt) cc_final: 0.8179 (mt) REVERT: h 54 LYS cc_start: 0.7507 (mttt) cc_final: 0.7028 (tttt) REVERT: h 57 ILE cc_start: 0.9680 (mt) cc_final: 0.9336 (mt) REVERT: h 60 VAL cc_start: 0.9505 (t) cc_final: 0.9271 (p) REVERT: h 112 ILE cc_start: 0.9585 (mm) cc_final: 0.9121 (tp) REVERT: h 115 ASP cc_start: 0.9336 (t70) cc_final: 0.9040 (p0) REVERT: h 137 PHE cc_start: 0.9239 (m-80) cc_final: 0.8718 (m-80) REVERT: h 144 TYR cc_start: 0.9633 (m-10) cc_final: 0.9145 (m-10) REVERT: h 152 LEU cc_start: 0.9644 (mt) cc_final: 0.9413 (mt) REVERT: i 10 TYR cc_start: 0.6952 (m-80) cc_final: 0.6748 (m-80) REVERT: i 13 PHE cc_start: 0.9012 (t80) cc_final: 0.7997 (t80) REVERT: i 14 PHE cc_start: 0.8966 (m-10) cc_final: 0.8580 (m-10) REVERT: i 17 MET cc_start: 0.9436 (mmt) cc_final: 0.9072 (mmt) REVERT: i 32 TYR cc_start: 0.9026 (t80) cc_final: 0.8709 (t80) REVERT: i 61 MET cc_start: 0.9230 (mtp) cc_final: 0.9000 (mtp) REVERT: i 76 ILE cc_start: 0.9413 (mt) cc_final: 0.9038 (mt) REVERT: i 92 GLN cc_start: 0.9167 (mt0) cc_final: 0.8792 (mt0) REVERT: i 101 LEU cc_start: 0.9407 (mt) cc_final: 0.9158 (mt) REVERT: i 115 ASP cc_start: 0.8486 (t70) cc_final: 0.7954 (t70) REVERT: i 119 ARG cc_start: 0.8967 (mtt180) cc_final: 0.8697 (mtt90) REVERT: i 124 GLN cc_start: 0.8812 (tp-100) cc_final: 0.8554 (tm-30) REVERT: i 127 LEU cc_start: 0.8320 (tp) cc_final: 0.8049 (tp) REVERT: i 131 MET cc_start: 0.8992 (ttp) cc_final: 0.8527 (ttt) REVERT: i 135 LEU cc_start: 0.9526 (mm) cc_final: 0.9119 (mm) REVERT: i 152 LEU cc_start: 0.9645 (mt) cc_final: 0.9414 (mt) REVERT: j 17 MET cc_start: 0.8963 (mtm) cc_final: 0.8703 (mtp) REVERT: j 28 MET cc_start: 0.9002 (mtp) cc_final: 0.8317 (mmt) REVERT: j 52 ILE cc_start: 0.9508 (tt) cc_final: 0.9285 (mm) REVERT: j 91 LEU cc_start: 0.9211 (mt) cc_final: 0.8927 (mt) REVERT: j 121 THR cc_start: 0.8856 (m) cc_final: 0.8455 (p) REVERT: j 124 GLN cc_start: 0.8711 (tp-100) cc_final: 0.7846 (tm-30) REVERT: j 127 LEU cc_start: 0.9338 (tp) cc_final: 0.8666 (tp) REVERT: j 131 MET cc_start: 0.8165 (ttp) cc_final: 0.7786 (ttp) REVERT: j 143 LEU cc_start: 0.9248 (tp) cc_final: 0.9036 (tp) REVERT: j 152 LEU cc_start: 0.9312 (tp) cc_final: 0.8977 (tp) REVERT: k 13 PHE cc_start: 0.9193 (t80) cc_final: 0.8945 (t80) REVERT: k 17 MET cc_start: 0.8904 (mtm) cc_final: 0.8514 (mtm) REVERT: k 23 MET cc_start: 0.9005 (mmm) cc_final: 0.8480 (mmm) REVERT: k 44 MET cc_start: 0.9037 (ppp) cc_final: 0.8509 (ppp) REVERT: k 53 MET cc_start: 0.8665 (tmm) cc_final: 0.7989 (mtt) REVERT: k 59 VAL cc_start: 0.9295 (t) cc_final: 0.8925 (t) REVERT: k 91 LEU cc_start: 0.9116 (mt) cc_final: 0.8736 (mt) REVERT: k 127 LEU cc_start: 0.8434 (mp) cc_final: 0.8111 (mp) REVERT: l 17 MET cc_start: 0.9336 (mmp) cc_final: 0.8881 (mmp) REVERT: l 24 VAL cc_start: 0.9487 (t) cc_final: 0.8844 (t) REVERT: l 32 TYR cc_start: 0.8179 (t80) cc_final: 0.7614 (t80) REVERT: l 48 ARG cc_start: 0.8501 (tmm-80) cc_final: 0.8164 (tmm-80) REVERT: l 68 TYR cc_start: 0.8889 (m-10) cc_final: 0.8439 (m-80) REVERT: l 74 VAL cc_start: 0.9067 (t) cc_final: 0.8802 (t) REVERT: l 97 LEU cc_start: 0.9416 (mt) cc_final: 0.9205 (mm) REVERT: l 113 VAL cc_start: 0.9657 (p) cc_final: 0.9379 (p) REVERT: l 124 GLN cc_start: 0.8789 (tp-100) cc_final: 0.8556 (tm-30) REVERT: l 127 LEU cc_start: 0.7739 (tp) cc_final: 0.7463 (tp) REVERT: l 131 MET cc_start: 0.9340 (ttp) cc_final: 0.8896 (ttm) REVERT: l 143 LEU cc_start: 0.9475 (mm) cc_final: 0.9145 (mm) REVERT: l 146 LEU cc_start: 0.9045 (tt) cc_final: 0.8516 (pp) REVERT: m 11 SER cc_start: 0.8648 (p) cc_final: 0.8260 (t) REVERT: m 21 SER cc_start: 0.9285 (m) cc_final: 0.9031 (p) REVERT: m 48 ARG cc_start: 0.8993 (mmm160) cc_final: 0.8503 (mmm160) REVERT: m 51 LEU cc_start: 0.8558 (mt) cc_final: 0.8234 (mt) REVERT: m 53 MET cc_start: 0.8732 (mmm) cc_final: 0.8036 (tmm) REVERT: m 86 LEU cc_start: 0.9496 (tp) cc_final: 0.8796 (tp) REVERT: m 89 SER cc_start: 0.9348 (m) cc_final: 0.8619 (t) REVERT: m 90 PHE cc_start: 0.9048 (m-10) cc_final: 0.8684 (m-80) REVERT: m 92 GLN cc_start: 0.9280 (mt0) cc_final: 0.8959 (mt0) REVERT: m 128 PHE cc_start: 0.8421 (t80) cc_final: 0.7710 (t80) REVERT: m 133 LEU cc_start: 0.8941 (tp) cc_final: 0.8464 (tt) REVERT: m 137 PHE cc_start: 0.9071 (m-80) cc_final: 0.8647 (m-80) REVERT: m 144 TYR cc_start: 0.9453 (m-10) cc_final: 0.9203 (m-10) REVERT: m 152 LEU cc_start: 0.9175 (mt) cc_final: 0.8945 (mt) REVERT: n 17 MET cc_start: 0.9199 (mmt) cc_final: 0.8848 (mmm) REVERT: n 25 PHE cc_start: 0.9037 (m-10) cc_final: 0.8804 (m-80) REVERT: n 47 MET cc_start: 0.9222 (mmm) cc_final: 0.8838 (mmm) REVERT: n 61 MET cc_start: 0.9244 (mmp) cc_final: 0.8233 (mmm) REVERT: n 68 TYR cc_start: 0.9140 (m-10) cc_final: 0.8747 (m-10) REVERT: n 72 VAL cc_start: 0.9354 (t) cc_final: 0.9093 (p) REVERT: n 90 PHE cc_start: 0.9120 (m-80) cc_final: 0.8601 (m-80) REVERT: n 124 GLN cc_start: 0.8818 (tp-100) cc_final: 0.8390 (tm-30) REVERT: n 146 LEU cc_start: 0.9030 (mt) cc_final: 0.8607 (mt) REVERT: o 13 PHE cc_start: 0.8974 (t80) cc_final: 0.8305 (t80) REVERT: o 17 MET cc_start: 0.9232 (mmp) cc_final: 0.8779 (mmt) REVERT: o 21 SER cc_start: 0.8808 (m) cc_final: 0.8410 (p) REVERT: o 47 MET cc_start: 0.8320 (tmm) cc_final: 0.7397 (tmm) REVERT: o 48 ARG cc_start: 0.9088 (ptp-170) cc_final: 0.8507 (mtm-85) REVERT: o 51 LEU cc_start: 0.8892 (mt) cc_final: 0.8661 (mt) REVERT: o 54 LYS cc_start: 0.8071 (mttt) cc_final: 0.7804 (mttp) REVERT: o 57 ILE cc_start: 0.9259 (mt) cc_final: 0.8916 (mt) REVERT: o 61 MET cc_start: 0.9478 (mmp) cc_final: 0.9272 (mmm) REVERT: o 64 ILE cc_start: 0.9366 (mt) cc_final: 0.8950 (mt) REVERT: o 65 ILE cc_start: 0.9564 (mp) cc_final: 0.9168 (mp) REVERT: o 68 TYR cc_start: 0.9359 (m-10) cc_final: 0.8626 (m-80) REVERT: o 70 LEU cc_start: 0.9444 (tp) cc_final: 0.9208 (tp) REVERT: o 90 PHE cc_start: 0.9123 (m-80) cc_final: 0.8775 (m-80) REVERT: o 91 LEU cc_start: 0.9728 (mm) cc_final: 0.9477 (mm) REVERT: o 97 LEU cc_start: 0.9565 (mt) cc_final: 0.9315 (mt) REVERT: o 128 PHE cc_start: 0.8546 (t80) cc_final: 0.8094 (t80) REVERT: o 131 MET cc_start: 0.8820 (ppp) cc_final: 0.8534 (ppp) REVERT: o 144 TYR cc_start: 0.8981 (m-10) cc_final: 0.8759 (m-10) REVERT: o 152 LEU cc_start: 0.9441 (mt) cc_final: 0.9029 (mt) REVERT: p 303 TYR cc_start: 0.8753 (t80) cc_final: 0.8308 (t80) REVERT: p 313 ILE cc_start: 0.9599 (pt) cc_final: 0.9308 (pt) outliers start: 2 outliers final: 0 residues processed: 1026 average time/residue: 0.1127 time to fit residues: 186.7911 Evaluate side-chains 921 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 921 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 219 optimal weight: 6.9990 chunk 80 optimal weight: 0.9980 chunk 230 optimal weight: 0.9990 chunk 200 optimal weight: 1.9990 chunk 35 optimal weight: 0.0980 chunk 105 optimal weight: 0.0270 chunk 186 optimal weight: 0.9980 chunk 145 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 179 optimal weight: 0.8980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 148 ASN ** d 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 88 HIS d 311 HIS ** h 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 92 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.090918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.071717 restraints weight = 65451.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.074318 restraints weight = 40058.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.076309 restraints weight = 27130.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.077681 restraints weight = 19673.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.078705 restraints weight = 15124.706| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.5444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 19610 Z= 0.151 Angle : 0.663 18.116 26647 Z= 0.341 Chirality : 0.042 0.335 3268 Planarity : 0.004 0.039 3401 Dihedral : 3.959 22.515 2941 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.16), residues: 2771 helix: 1.90 (0.11), residues: 2152 sheet: -2.00 (0.91), residues: 16 loop : -0.81 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG j 119 TYR 0.038 0.002 TYR b 135 PHE 0.038 0.002 PHE j 108 TRP 0.023 0.001 TRP b 67 HIS 0.004 0.001 HIS d 311 Details of bonding type rmsd covalent geometry : bond 0.00318 (19610) covalent geometry : angle 0.66290 (26647) hydrogen bonds : bond 0.05105 ( 1741) hydrogen bonds : angle 4.41100 ( 5118) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1020 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1020 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 55 LYS cc_start: 0.9499 (tttp) cc_final: 0.9177 (tptp) REVERT: H 64 GLU cc_start: 0.9283 (tp30) cc_final: 0.8623 (tm-30) REVERT: H 84 ILE cc_start: 0.9476 (mt) cc_final: 0.9097 (mt) REVERT: H 85 GLN cc_start: 0.9094 (mm-40) cc_final: 0.8799 (mm-40) REVERT: H 101 VAL cc_start: 0.8279 (p) cc_final: 0.7891 (p) REVERT: L 11 ILE cc_start: 0.9612 (mm) cc_final: 0.9387 (mm) REVERT: L 14 GLU cc_start: 0.9015 (pm20) cc_final: 0.8805 (pm20) REVERT: L 22 LEU cc_start: 0.9431 (mt) cc_final: 0.9116 (mt) REVERT: L 44 THR cc_start: 0.9542 (t) cc_final: 0.8872 (p) REVERT: L 47 GLU cc_start: 0.9125 (mt-10) cc_final: 0.8680 (mt-10) REVERT: L 53 ARG cc_start: 0.8745 (mtp-110) cc_final: 0.8145 (mtp-110) REVERT: L 67 ASN cc_start: 0.8978 (m110) cc_final: 0.8208 (m110) REVERT: L 69 TYR cc_start: 0.8355 (p90) cc_final: 0.7847 (p90) REVERT: L 79 ASP cc_start: 0.9126 (m-30) cc_final: 0.8862 (m-30) REVERT: L 90 GLU cc_start: 0.8969 (mp0) cc_final: 0.8158 (tt0) REVERT: b 4 LEU cc_start: 0.9532 (mm) cc_final: 0.9328 (mm) REVERT: b 19 MET cc_start: 0.8710 (mtp) cc_final: 0.8302 (mtp) REVERT: b 42 THR cc_start: 0.9068 (t) cc_final: 0.8796 (t) REVERT: b 43 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7746 (mm-30) REVERT: b 51 ASN cc_start: 0.8817 (p0) cc_final: 0.8363 (p0) REVERT: b 90 ASN cc_start: 0.8987 (m110) cc_final: 0.8648 (m110) REVERT: b 91 LEU cc_start: 0.9577 (tp) cc_final: 0.9256 (tp) REVERT: b 102 ILE cc_start: 0.9667 (mm) cc_final: 0.9426 (mm) REVERT: b 103 TYR cc_start: 0.8660 (m-10) cc_final: 0.8165 (m-10) REVERT: b 137 MET cc_start: 0.9103 (mtp) cc_final: 0.8737 (mtp) REVERT: b 164 LEU cc_start: 0.9675 (mt) cc_final: 0.9310 (mp) REVERT: b 168 GLN cc_start: 0.9057 (mp10) cc_final: 0.8685 (mp10) REVERT: b 169 ASN cc_start: 0.8867 (t0) cc_final: 0.8125 (t0) REVERT: b 172 LEU cc_start: 0.9283 (mt) cc_final: 0.8614 (mt) REVERT: b 186 ILE cc_start: 0.9638 (mt) cc_final: 0.9141 (mt) REVERT: b 189 PHE cc_start: 0.9120 (m-10) cc_final: 0.8672 (m-80) REVERT: b 197 GLN cc_start: 0.8578 (mt0) cc_final: 0.8267 (mt0) REVERT: c 439 MET cc_start: 0.9482 (mtt) cc_final: 0.9030 (mtp) REVERT: d 28 LEU cc_start: 0.9361 (mt) cc_final: 0.8937 (mm) REVERT: d 30 GLN cc_start: 0.9086 (tm-30) cc_final: 0.8764 (tm-30) REVERT: d 39 CYS cc_start: 0.7198 (p) cc_final: 0.6901 (p) REVERT: d 44 ASP cc_start: 0.9127 (m-30) cc_final: 0.8806 (m-30) REVERT: d 48 HIS cc_start: 0.8912 (m90) cc_final: 0.8553 (m90) REVERT: d 76 GLU cc_start: 0.9128 (mt-10) cc_final: 0.8831 (mt-10) REVERT: d 78 MET cc_start: 0.9367 (tpp) cc_final: 0.9061 (tpp) REVERT: d 82 PHE cc_start: 0.9438 (t80) cc_final: 0.9195 (t80) REVERT: d 85 MET cc_start: 0.9550 (ptp) cc_final: 0.9302 (ptp) REVERT: d 90 TYR cc_start: 0.7944 (m-80) cc_final: 0.7734 (m-80) REVERT: d 105 MET cc_start: 0.8967 (mmm) cc_final: 0.8491 (tpt) REVERT: d 125 LEU cc_start: 0.9023 (mt) cc_final: 0.8702 (mt) REVERT: d 128 LYS cc_start: 0.9410 (mmtt) cc_final: 0.8911 (mmmt) REVERT: d 129 CYS cc_start: 0.8498 (m) cc_final: 0.7829 (m) REVERT: d 181 ILE cc_start: 0.9039 (mt) cc_final: 0.8787 (mt) REVERT: d 183 ASN cc_start: 0.9287 (t0) cc_final: 0.9011 (t0) REVERT: d 224 THR cc_start: 0.9449 (m) cc_final: 0.9178 (p) REVERT: d 225 ILE cc_start: 0.9658 (mt) cc_final: 0.9430 (mt) REVERT: d 250 GLU cc_start: 0.8640 (tp30) cc_final: 0.7666 (tm-30) REVERT: d 262 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8198 (tm-30) REVERT: d 315 PHE cc_start: 0.9699 (m-80) cc_final: 0.9353 (m-80) REVERT: d 322 LYS cc_start: 0.9642 (mtpp) cc_final: 0.9050 (mtmm) REVERT: d 323 GLU cc_start: 0.9228 (tt0) cc_final: 0.8520 (tt0) REVERT: d 325 GLU cc_start: 0.9467 (tt0) cc_final: 0.8847 (tm-30) REVERT: d 327 ARG cc_start: 0.9557 (mtt90) cc_final: 0.8725 (mtt-85) REVERT: d 338 GLN cc_start: 0.9106 (mm-40) cc_final: 0.8828 (mm110) REVERT: d 348 ILE cc_start: 0.9507 (mm) cc_final: 0.9253 (mp) REVERT: g 7 ASN cc_start: 0.8273 (p0) cc_final: 0.7983 (p0) REVERT: g 28 MET cc_start: 0.9791 (mtm) cc_final: 0.9470 (mtm) REVERT: g 32 TYR cc_start: 0.9017 (t80) cc_final: 0.8358 (t80) REVERT: g 48 ARG cc_start: 0.8894 (mtp180) cc_final: 0.8554 (mtp180) REVERT: g 53 MET cc_start: 0.8640 (mtm) cc_final: 0.7969 (ttp) REVERT: g 57 ILE cc_start: 0.9504 (mt) cc_final: 0.9057 (mt) REVERT: g 70 LEU cc_start: 0.9546 (tp) cc_final: 0.9330 (tp) REVERT: g 90 PHE cc_start: 0.9067 (m-80) cc_final: 0.8655 (m-80) REVERT: g 118 VAL cc_start: 0.9492 (p) cc_final: 0.9261 (p) REVERT: g 141 LEU cc_start: 0.9364 (mt) cc_final: 0.9017 (mt) REVERT: g 144 TYR cc_start: 0.8799 (m-80) cc_final: 0.8470 (m-80) REVERT: g 146 LEU cc_start: 0.9795 (tp) cc_final: 0.9568 (tp) REVERT: h 23 MET cc_start: 0.9502 (mmm) cc_final: 0.9268 (tpp) REVERT: h 44 MET cc_start: 0.8071 (tmm) cc_final: 0.7513 (tmm) REVERT: h 48 ARG cc_start: 0.8555 (ttm170) cc_final: 0.7371 (ttm170) REVERT: h 51 LEU cc_start: 0.8557 (mt) cc_final: 0.7911 (mt) REVERT: h 112 ILE cc_start: 0.9563 (mm) cc_final: 0.9144 (mm) REVERT: h 115 ASP cc_start: 0.9278 (t70) cc_final: 0.9005 (p0) REVERT: h 121 THR cc_start: 0.8848 (p) cc_final: 0.8545 (p) REVERT: h 137 PHE cc_start: 0.9145 (m-80) cc_final: 0.8746 (m-80) REVERT: h 144 TYR cc_start: 0.9609 (m-10) cc_final: 0.9100 (m-10) REVERT: h 152 LEU cc_start: 0.9631 (mt) cc_final: 0.9397 (mt) REVERT: i 17 MET cc_start: 0.9547 (mmt) cc_final: 0.9046 (mmm) REVERT: i 32 TYR cc_start: 0.8783 (t80) cc_final: 0.8419 (t80) REVERT: i 61 MET cc_start: 0.9192 (mtp) cc_final: 0.8979 (mtp) REVERT: i 64 ILE cc_start: 0.9522 (mt) cc_final: 0.9304 (mt) REVERT: i 76 ILE cc_start: 0.9423 (mt) cc_final: 0.9025 (mt) REVERT: i 92 GLN cc_start: 0.9176 (mt0) cc_final: 0.8806 (mt0) REVERT: i 101 LEU cc_start: 0.9419 (mt) cc_final: 0.9165 (mt) REVERT: i 115 ASP cc_start: 0.8452 (t70) cc_final: 0.7420 (t70) REVERT: i 119 ARG cc_start: 0.8944 (mtt180) cc_final: 0.8686 (mtt90) REVERT: i 124 GLN cc_start: 0.8804 (tp-100) cc_final: 0.8581 (tm-30) REVERT: i 127 LEU cc_start: 0.8515 (tp) cc_final: 0.8185 (tt) REVERT: i 131 MET cc_start: 0.8972 (ttp) cc_final: 0.8561 (ttt) REVERT: i 135 LEU cc_start: 0.9505 (mm) cc_final: 0.9114 (mm) REVERT: i 141 LEU cc_start: 0.9587 (mp) cc_final: 0.9302 (mp) REVERT: i 144 TYR cc_start: 0.8901 (m-10) cc_final: 0.8620 (m-10) REVERT: i 152 LEU cc_start: 0.9628 (mt) cc_final: 0.9406 (mt) REVERT: j 17 MET cc_start: 0.9185 (mtm) cc_final: 0.8548 (ptp) REVERT: j 28 MET cc_start: 0.8991 (mtp) cc_final: 0.8235 (mmm) REVERT: j 47 MET cc_start: 0.9172 (mmm) cc_final: 0.8563 (mmm) REVERT: j 52 ILE cc_start: 0.9575 (tt) cc_final: 0.9268 (mm) REVERT: j 61 MET cc_start: 0.8665 (ttp) cc_final: 0.8210 (ttm) REVERT: j 91 LEU cc_start: 0.9239 (mt) cc_final: 0.8834 (pp) REVERT: j 108 PHE cc_start: 0.8980 (m-80) cc_final: 0.8603 (m-80) REVERT: j 121 THR cc_start: 0.8862 (m) cc_final: 0.8468 (p) REVERT: j 124 GLN cc_start: 0.8735 (tp-100) cc_final: 0.7874 (tm-30) REVERT: j 127 LEU cc_start: 0.9365 (tp) cc_final: 0.8609 (tp) REVERT: j 131 MET cc_start: 0.8178 (ttp) cc_final: 0.7783 (ttp) REVERT: j 152 LEU cc_start: 0.9335 (tp) cc_final: 0.9059 (tp) REVERT: k 13 PHE cc_start: 0.9152 (t80) cc_final: 0.8843 (t80) REVERT: k 17 MET cc_start: 0.8890 (mtm) cc_final: 0.8659 (mtm) REVERT: k 23 MET cc_start: 0.8931 (mmm) cc_final: 0.8444 (mmm) REVERT: k 44 MET cc_start: 0.9006 (ppp) cc_final: 0.8460 (ppp) REVERT: k 53 MET cc_start: 0.8641 (tmm) cc_final: 0.7925 (mtt) REVERT: k 59 VAL cc_start: 0.9354 (t) cc_final: 0.9138 (t) REVERT: k 65 ILE cc_start: 0.9526 (mt) cc_final: 0.9215 (mt) REVERT: k 68 TYR cc_start: 0.8615 (m-10) cc_final: 0.8080 (m-80) REVERT: k 90 PHE cc_start: 0.9055 (m-10) cc_final: 0.8752 (m-80) REVERT: k 91 LEU cc_start: 0.9225 (mt) cc_final: 0.8892 (mt) REVERT: k 119 ARG cc_start: 0.8048 (tpt90) cc_final: 0.7643 (tpt90) REVERT: k 121 THR cc_start: 0.8639 (p) cc_final: 0.8354 (p) REVERT: k 123 GLN cc_start: 0.9141 (mm-40) cc_final: 0.8702 (mm-40) REVERT: l 17 MET cc_start: 0.9321 (mmp) cc_final: 0.8821 (mmp) REVERT: l 32 TYR cc_start: 0.8289 (t80) cc_final: 0.7675 (t80) REVERT: l 47 MET cc_start: 0.8317 (mmt) cc_final: 0.8059 (mmt) REVERT: l 48 ARG cc_start: 0.8533 (tmm-80) cc_final: 0.8222 (tmm-80) REVERT: l 113 VAL cc_start: 0.9663 (p) cc_final: 0.9360 (p) REVERT: l 124 GLN cc_start: 0.8809 (tp-100) cc_final: 0.8597 (tm-30) REVERT: l 131 MET cc_start: 0.9351 (ttp) cc_final: 0.8920 (ttm) REVERT: l 143 LEU cc_start: 0.9449 (mm) cc_final: 0.9076 (mm) REVERT: l 146 LEU cc_start: 0.9081 (tt) cc_final: 0.8533 (pp) REVERT: m 11 SER cc_start: 0.8541 (p) cc_final: 0.8212 (p) REVERT: m 21 SER cc_start: 0.9247 (m) cc_final: 0.9008 (p) REVERT: m 47 MET cc_start: 0.8844 (mmm) cc_final: 0.7640 (mmm) REVERT: m 48 ARG cc_start: 0.9026 (mmm160) cc_final: 0.8502 (mmm160) REVERT: m 51 LEU cc_start: 0.8581 (mt) cc_final: 0.8252 (mt) REVERT: m 53 MET cc_start: 0.8724 (mmm) cc_final: 0.8042 (tmm) REVERT: m 61 MET cc_start: 0.9352 (mmm) cc_final: 0.9140 (mmm) REVERT: m 86 LEU cc_start: 0.9494 (tp) cc_final: 0.8971 (tp) REVERT: m 90 PHE cc_start: 0.9008 (m-10) cc_final: 0.8621 (m-80) REVERT: m 92 GLN cc_start: 0.9289 (mt0) cc_final: 0.8902 (mt0) REVERT: m 128 PHE cc_start: 0.8441 (t80) cc_final: 0.7744 (t80) REVERT: m 133 LEU cc_start: 0.8903 (tp) cc_final: 0.8457 (tp) REVERT: m 137 PHE cc_start: 0.9033 (m-80) cc_final: 0.8659 (m-80) REVERT: n 47 MET cc_start: 0.9222 (mmm) cc_final: 0.8790 (mmm) REVERT: n 61 MET cc_start: 0.9272 (mmp) cc_final: 0.8284 (mmm) REVERT: n 68 TYR cc_start: 0.9206 (m-10) cc_final: 0.8824 (m-10) REVERT: n 72 VAL cc_start: 0.9315 (t) cc_final: 0.9062 (p) REVERT: n 86 LEU cc_start: 0.9333 (tp) cc_final: 0.9082 (tp) REVERT: n 90 PHE cc_start: 0.9081 (m-10) cc_final: 0.8572 (m-80) REVERT: n 146 LEU cc_start: 0.8982 (mt) cc_final: 0.8548 (mt) REVERT: o 13 PHE cc_start: 0.8831 (t80) cc_final: 0.8161 (t80) REVERT: o 17 MET cc_start: 0.9198 (mmp) cc_final: 0.8621 (ptm) REVERT: o 21 SER cc_start: 0.8884 (m) cc_final: 0.8212 (p) REVERT: o 25 PHE cc_start: 0.8320 (m-10) cc_final: 0.8058 (m-10) REVERT: o 51 LEU cc_start: 0.8885 (mt) cc_final: 0.8510 (mt) REVERT: o 54 LYS cc_start: 0.8202 (mttt) cc_final: 0.7952 (mttp) REVERT: o 57 ILE cc_start: 0.9294 (mt) cc_final: 0.9049 (mt) REVERT: o 61 MET cc_start: 0.9530 (mmp) cc_final: 0.9311 (mmm) REVERT: o 64 ILE cc_start: 0.9331 (mt) cc_final: 0.8933 (mt) REVERT: o 65 ILE cc_start: 0.9586 (mp) cc_final: 0.9174 (mp) REVERT: o 68 TYR cc_start: 0.9380 (m-10) cc_final: 0.8734 (m-80) REVERT: o 70 LEU cc_start: 0.9488 (tp) cc_final: 0.9282 (tp) REVERT: o 76 ILE cc_start: 0.9510 (mp) cc_final: 0.9121 (tt) REVERT: o 90 PHE cc_start: 0.9173 (m-80) cc_final: 0.8785 (m-80) REVERT: o 97 LEU cc_start: 0.9520 (mt) cc_final: 0.9234 (mt) REVERT: o 128 PHE cc_start: 0.8541 (t80) cc_final: 0.7724 (t80) REVERT: o 131 MET cc_start: 0.8847 (ppp) cc_final: 0.8318 (ppp) REVERT: o 132 ILE cc_start: 0.8918 (tp) cc_final: 0.8259 (mt) REVERT: o 144 TYR cc_start: 0.9015 (m-10) cc_final: 0.8755 (m-10) REVERT: o 152 LEU cc_start: 0.9431 (mt) cc_final: 0.9216 (mt) REVERT: p 303 TYR cc_start: 0.8719 (t80) cc_final: 0.8391 (t80) REVERT: p 313 ILE cc_start: 0.9692 (pt) cc_final: 0.9291 (pt) outliers start: 0 outliers final: 0 residues processed: 1020 average time/residue: 0.1126 time to fit residues: 186.1162 Evaluate side-chains 908 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 908 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 0 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 156 optimal weight: 0.9990 chunk 88 optimal weight: 9.9990 chunk 232 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 134 optimal weight: 20.0000 chunk 149 optimal weight: 0.6980 chunk 269 optimal weight: 0.9990 chunk 22 optimal weight: 20.0000 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 111 HIS ** b 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 88 HIS ** h 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 123 GLN ** o 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.090565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.071354 restraints weight = 66130.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.073971 restraints weight = 40399.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.075972 restraints weight = 27420.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.077357 restraints weight = 19800.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.078448 restraints weight = 15213.176| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.5703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 19610 Z= 0.166 Angle : 0.674 15.097 26647 Z= 0.353 Chirality : 0.042 0.261 3268 Planarity : 0.004 0.040 3401 Dihedral : 3.992 25.019 2941 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.16), residues: 2771 helix: 1.85 (0.11), residues: 2157 sheet: -2.29 (0.94), residues: 16 loop : -0.82 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG j 119 TYR 0.053 0.002 TYR k 144 PHE 0.060 0.002 PHE j 90 TRP 0.021 0.002 TRP c 420 HIS 0.004 0.001 HIS d 297 Details of bonding type rmsd covalent geometry : bond 0.00355 (19610) covalent geometry : angle 0.67386 (26647) hydrogen bonds : bond 0.04981 ( 1741) hydrogen bonds : angle 4.45296 ( 5118) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1008 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1008 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 55 LYS cc_start: 0.9516 (tttp) cc_final: 0.9156 (tptp) REVERT: H 64 GLU cc_start: 0.9270 (tp30) cc_final: 0.8682 (tp30) REVERT: H 85 GLN cc_start: 0.9112 (mm-40) cc_final: 0.8753 (mm-40) REVERT: H 119 TYR cc_start: 0.7840 (p90) cc_final: 0.7609 (p90) REVERT: L 11 ILE cc_start: 0.9626 (mm) cc_final: 0.9267 (mm) REVERT: L 14 GLU cc_start: 0.9051 (pm20) cc_final: 0.8818 (pm20) REVERT: L 22 LEU cc_start: 0.9374 (mt) cc_final: 0.9172 (mt) REVERT: L 29 ASN cc_start: 0.8974 (p0) cc_final: 0.8339 (p0) REVERT: L 44 THR cc_start: 0.9566 (t) cc_final: 0.8910 (p) REVERT: L 47 GLU cc_start: 0.9111 (mt-10) cc_final: 0.8643 (mt-10) REVERT: L 49 GLU cc_start: 0.9071 (tp30) cc_final: 0.8606 (tm-30) REVERT: L 67 ASN cc_start: 0.8889 (m110) cc_final: 0.8065 (m110) REVERT: L 69 TYR cc_start: 0.8206 (p90) cc_final: 0.7940 (p90) REVERT: L 79 ASP cc_start: 0.9151 (m-30) cc_final: 0.8893 (m-30) REVERT: L 89 LEU cc_start: 0.8912 (mt) cc_final: 0.8668 (mt) REVERT: L 90 GLU cc_start: 0.8976 (mp0) cc_final: 0.8115 (tt0) REVERT: b 5 GLU cc_start: 0.8773 (pt0) cc_final: 0.8383 (pm20) REVERT: b 19 MET cc_start: 0.8736 (mtp) cc_final: 0.8345 (mtp) REVERT: b 43 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7662 (mm-30) REVERT: b 51 ASN cc_start: 0.8974 (p0) cc_final: 0.8493 (p0) REVERT: b 90 ASN cc_start: 0.9015 (m110) cc_final: 0.8677 (m110) REVERT: b 91 LEU cc_start: 0.9571 (tp) cc_final: 0.9269 (tp) REVERT: b 102 ILE cc_start: 0.9666 (mm) cc_final: 0.9421 (mm) REVERT: b 103 TYR cc_start: 0.8720 (m-10) cc_final: 0.8271 (m-10) REVERT: b 137 MET cc_start: 0.9119 (mtp) cc_final: 0.8757 (mtp) REVERT: b 164 LEU cc_start: 0.9684 (mt) cc_final: 0.9380 (mp) REVERT: b 169 ASN cc_start: 0.8731 (t0) cc_final: 0.7992 (t0) REVERT: b 172 LEU cc_start: 0.9314 (mt) cc_final: 0.8635 (mt) REVERT: b 186 ILE cc_start: 0.9613 (mt) cc_final: 0.9116 (mt) REVERT: b 189 PHE cc_start: 0.9106 (m-10) cc_final: 0.8774 (m-80) REVERT: b 197 GLN cc_start: 0.8585 (mt0) cc_final: 0.8309 (mt0) REVERT: c 421 MET cc_start: 0.8459 (mtt) cc_final: 0.8183 (mmt) REVERT: c 439 MET cc_start: 0.9457 (mtt) cc_final: 0.8989 (mtp) REVERT: d 28 LEU cc_start: 0.9358 (mt) cc_final: 0.8881 (mm) REVERT: d 30 GLN cc_start: 0.9139 (tm-30) cc_final: 0.8835 (tm-30) REVERT: d 39 CYS cc_start: 0.7265 (p) cc_final: 0.6951 (p) REVERT: d 44 ASP cc_start: 0.9137 (m-30) cc_final: 0.8809 (m-30) REVERT: d 48 HIS cc_start: 0.8921 (m90) cc_final: 0.8554 (m90) REVERT: d 76 GLU cc_start: 0.9106 (mt-10) cc_final: 0.8801 (mt-10) REVERT: d 78 MET cc_start: 0.9423 (tpp) cc_final: 0.9124 (tpp) REVERT: d 105 MET cc_start: 0.8996 (mmm) cc_final: 0.8581 (tpt) REVERT: d 125 LEU cc_start: 0.9078 (mt) cc_final: 0.8786 (mt) REVERT: d 128 LYS cc_start: 0.9447 (mmtt) cc_final: 0.8942 (mmmt) REVERT: d 129 CYS cc_start: 0.8580 (m) cc_final: 0.7911 (m) REVERT: d 181 ILE cc_start: 0.9080 (mt) cc_final: 0.8825 (mt) REVERT: d 213 GLU cc_start: 0.8568 (pp20) cc_final: 0.8019 (tt0) REVERT: d 224 THR cc_start: 0.9468 (m) cc_final: 0.9170 (p) REVERT: d 250 GLU cc_start: 0.8477 (tp30) cc_final: 0.8248 (tp30) REVERT: d 262 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8079 (tm-30) REVERT: d 315 PHE cc_start: 0.9715 (m-80) cc_final: 0.9365 (m-80) REVERT: d 322 LYS cc_start: 0.9624 (mtpp) cc_final: 0.9146 (mtmm) REVERT: d 325 GLU cc_start: 0.9486 (tt0) cc_final: 0.8817 (tm-30) REVERT: d 326 CYS cc_start: 0.9654 (t) cc_final: 0.9422 (t) REVERT: d 338 GLN cc_start: 0.9085 (mm-40) cc_final: 0.8831 (mm110) REVERT: d 348 ILE cc_start: 0.9545 (mm) cc_final: 0.9291 (mp) REVERT: g 7 ASN cc_start: 0.8342 (p0) cc_final: 0.8031 (p0) REVERT: g 28 MET cc_start: 0.9805 (mtm) cc_final: 0.9438 (mtm) REVERT: g 32 TYR cc_start: 0.9036 (t80) cc_final: 0.8388 (t80) REVERT: g 48 ARG cc_start: 0.8940 (mtp180) cc_final: 0.8575 (mtp180) REVERT: g 51 LEU cc_start: 0.8621 (mm) cc_final: 0.7870 (mm) REVERT: g 53 MET cc_start: 0.8716 (mtm) cc_final: 0.7978 (ttp) REVERT: g 54 LYS cc_start: 0.8342 (pttm) cc_final: 0.7472 (ptmt) REVERT: g 57 ILE cc_start: 0.9497 (mt) cc_final: 0.9044 (mt) REVERT: g 70 LEU cc_start: 0.9555 (tp) cc_final: 0.9348 (tp) REVERT: g 90 PHE cc_start: 0.9130 (m-80) cc_final: 0.8835 (m-80) REVERT: g 141 LEU cc_start: 0.9354 (mt) cc_final: 0.8963 (mt) REVERT: g 144 TYR cc_start: 0.8843 (m-80) cc_final: 0.8484 (m-80) REVERT: g 146 LEU cc_start: 0.9783 (tp) cc_final: 0.9566 (tp) REVERT: h 23 MET cc_start: 0.9547 (mmm) cc_final: 0.9339 (tpp) REVERT: h 24 VAL cc_start: 0.9575 (p) cc_final: 0.9348 (p) REVERT: h 28 MET cc_start: 0.8897 (mtp) cc_final: 0.8063 (tpt) REVERT: h 44 MET cc_start: 0.8156 (tmm) cc_final: 0.7639 (tmm) REVERT: h 48 ARG cc_start: 0.8589 (ttm170) cc_final: 0.7559 (ttm170) REVERT: h 51 LEU cc_start: 0.8541 (mt) cc_final: 0.8012 (mt) REVERT: h 54 LYS cc_start: 0.7360 (mttt) cc_final: 0.6507 (tttp) REVERT: h 57 ILE cc_start: 0.9620 (mt) cc_final: 0.9251 (mt) REVERT: h 90 PHE cc_start: 0.8847 (m-10) cc_final: 0.8248 (m-80) REVERT: h 112 ILE cc_start: 0.9568 (mm) cc_final: 0.9124 (mm) REVERT: h 115 ASP cc_start: 0.9297 (t70) cc_final: 0.9024 (p0) REVERT: h 128 PHE cc_start: 0.9125 (t80) cc_final: 0.8663 (t80) REVERT: h 137 PHE cc_start: 0.9152 (m-80) cc_final: 0.8697 (m-80) REVERT: h 144 TYR cc_start: 0.9581 (m-10) cc_final: 0.9089 (m-10) REVERT: h 152 LEU cc_start: 0.9639 (mt) cc_final: 0.9416 (mt) REVERT: i 13 PHE cc_start: 0.8834 (t80) cc_final: 0.8183 (t80) REVERT: i 17 MET cc_start: 0.9475 (mmt) cc_final: 0.9084 (mmm) REVERT: i 32 TYR cc_start: 0.8886 (t80) cc_final: 0.8575 (t80) REVERT: i 44 MET cc_start: 0.8826 (mmp) cc_final: 0.8408 (mmt) REVERT: i 64 ILE cc_start: 0.9512 (mt) cc_final: 0.9281 (mt) REVERT: i 76 ILE cc_start: 0.9472 (mt) cc_final: 0.9005 (mt) REVERT: i 92 GLN cc_start: 0.9179 (mt0) cc_final: 0.8915 (mt0) REVERT: i 101 LEU cc_start: 0.9411 (mt) cc_final: 0.9165 (mt) REVERT: i 115 ASP cc_start: 0.8434 (t70) cc_final: 0.7891 (t70) REVERT: i 127 LEU cc_start: 0.8539 (tp) cc_final: 0.8302 (tp) REVERT: i 131 MET cc_start: 0.8925 (ttp) cc_final: 0.8457 (ttt) REVERT: i 135 LEU cc_start: 0.9416 (mm) cc_final: 0.9018 (mm) REVERT: i 141 LEU cc_start: 0.9590 (mp) cc_final: 0.9279 (mp) REVERT: i 144 TYR cc_start: 0.8909 (m-10) cc_final: 0.8638 (m-10) REVERT: i 152 LEU cc_start: 0.9617 (mt) cc_final: 0.9386 (mt) REVERT: j 7 ASN cc_start: 0.8205 (p0) cc_final: 0.7919 (p0) REVERT: j 17 MET cc_start: 0.8958 (mtm) cc_final: 0.8610 (mmm) REVERT: j 28 MET cc_start: 0.8959 (mtp) cc_final: 0.8297 (mmm) REVERT: j 47 MET cc_start: 0.8892 (mmm) cc_final: 0.8451 (mmm) REVERT: j 52 ILE cc_start: 0.9559 (tt) cc_final: 0.9250 (mm) REVERT: j 108 PHE cc_start: 0.8887 (m-80) cc_final: 0.8508 (m-80) REVERT: j 121 THR cc_start: 0.8794 (m) cc_final: 0.8339 (p) REVERT: j 123 GLN cc_start: 0.8110 (mp10) cc_final: 0.7560 (mp10) REVERT: j 124 GLN cc_start: 0.8773 (tp-100) cc_final: 0.7890 (tm-30) REVERT: j 127 LEU cc_start: 0.9356 (tp) cc_final: 0.8600 (tp) REVERT: j 131 MET cc_start: 0.8173 (ttp) cc_final: 0.7826 (ttp) REVERT: j 150 LEU cc_start: 0.9727 (mt) cc_final: 0.9501 (mt) REVERT: j 152 LEU cc_start: 0.9399 (tp) cc_final: 0.9091 (tp) REVERT: k 13 PHE cc_start: 0.9178 (t80) cc_final: 0.8834 (t80) REVERT: k 17 MET cc_start: 0.9023 (mtm) cc_final: 0.8627 (mtm) REVERT: k 23 MET cc_start: 0.9039 (mmm) cc_final: 0.8586 (mmm) REVERT: k 32 TYR cc_start: 0.8159 (t80) cc_final: 0.7840 (t80) REVERT: k 44 MET cc_start: 0.9034 (ppp) cc_final: 0.8566 (ppp) REVERT: k 53 MET cc_start: 0.8616 (tmm) cc_final: 0.7917 (mtt) REVERT: k 59 VAL cc_start: 0.9434 (t) cc_final: 0.9137 (t) REVERT: k 65 ILE cc_start: 0.9472 (mt) cc_final: 0.9143 (mt) REVERT: k 68 TYR cc_start: 0.8769 (m-10) cc_final: 0.8204 (m-80) REVERT: k 91 LEU cc_start: 0.9213 (mt) cc_final: 0.8893 (mt) REVERT: l 17 MET cc_start: 0.9341 (mmp) cc_final: 0.8854 (mmp) REVERT: l 47 MET cc_start: 0.8237 (mmt) cc_final: 0.7975 (mmt) REVERT: l 48 ARG cc_start: 0.8506 (tmm-80) cc_final: 0.8181 (tmm-80) REVERT: l 108 PHE cc_start: 0.8364 (t80) cc_final: 0.8108 (t80) REVERT: l 113 VAL cc_start: 0.9664 (p) cc_final: 0.9386 (p) REVERT: l 127 LEU cc_start: 0.7962 (tp) cc_final: 0.7692 (tp) REVERT: l 131 MET cc_start: 0.9388 (ttp) cc_final: 0.8943 (ttm) REVERT: m 11 SER cc_start: 0.8546 (p) cc_final: 0.8227 (p) REVERT: m 17 MET cc_start: 0.9233 (mtt) cc_final: 0.8851 (mtm) REVERT: m 21 SER cc_start: 0.9260 (m) cc_final: 0.9011 (p) REVERT: m 48 ARG cc_start: 0.9016 (mmm160) cc_final: 0.8612 (mmm160) REVERT: m 51 LEU cc_start: 0.8587 (mt) cc_final: 0.8328 (mt) REVERT: m 53 MET cc_start: 0.8736 (mmm) cc_final: 0.8031 (tmm) REVERT: m 86 LEU cc_start: 0.9496 (tp) cc_final: 0.8984 (tp) REVERT: m 90 PHE cc_start: 0.9005 (m-10) cc_final: 0.8617 (m-80) REVERT: m 92 GLN cc_start: 0.9290 (mt0) cc_final: 0.8914 (mt0) REVERT: m 128 PHE cc_start: 0.8426 (t80) cc_final: 0.7996 (t80) REVERT: m 133 LEU cc_start: 0.8860 (tp) cc_final: 0.8432 (tp) REVERT: m 137 PHE cc_start: 0.9049 (m-80) cc_final: 0.8680 (m-80) REVERT: n 25 PHE cc_start: 0.8957 (m-80) cc_final: 0.8683 (m-80) REVERT: n 47 MET cc_start: 0.9217 (mmm) cc_final: 0.8753 (mmm) REVERT: n 61 MET cc_start: 0.9300 (mmp) cc_final: 0.8355 (mmm) REVERT: n 68 TYR cc_start: 0.9249 (m-10) cc_final: 0.8904 (m-10) REVERT: n 72 VAL cc_start: 0.9340 (t) cc_final: 0.9088 (p) REVERT: n 86 LEU cc_start: 0.9343 (tp) cc_final: 0.9085 (tp) REVERT: n 90 PHE cc_start: 0.9011 (m-10) cc_final: 0.8446 (m-80) REVERT: n 146 LEU cc_start: 0.8932 (mt) cc_final: 0.8493 (mt) REVERT: o 13 PHE cc_start: 0.8851 (t80) cc_final: 0.8241 (t80) REVERT: o 17 MET cc_start: 0.9197 (mmp) cc_final: 0.8679 (ptm) REVERT: o 21 SER cc_start: 0.8877 (m) cc_final: 0.8260 (p) REVERT: o 23 MET cc_start: 0.9130 (tpp) cc_final: 0.8630 (ttp) REVERT: o 25 PHE cc_start: 0.8317 (m-10) cc_final: 0.8063 (m-10) REVERT: o 47 MET cc_start: 0.8289 (tmm) cc_final: 0.7980 (tmm) REVERT: o 48 ARG cc_start: 0.9092 (ptp-170) cc_final: 0.8846 (ptp-170) REVERT: o 51 LEU cc_start: 0.8897 (mt) cc_final: 0.8500 (mt) REVERT: o 57 ILE cc_start: 0.9292 (mt) cc_final: 0.9080 (mt) REVERT: o 64 ILE cc_start: 0.9323 (mt) cc_final: 0.8989 (mt) REVERT: o 65 ILE cc_start: 0.9636 (mp) cc_final: 0.9357 (mp) REVERT: o 68 TYR cc_start: 0.9378 (m-10) cc_final: 0.8830 (m-80) REVERT: o 76 ILE cc_start: 0.9534 (mp) cc_final: 0.9215 (tt) REVERT: o 82 ASP cc_start: 0.8474 (p0) cc_final: 0.7626 (t0) REVERT: o 90 PHE cc_start: 0.9212 (m-80) cc_final: 0.8834 (m-80) REVERT: o 97 LEU cc_start: 0.9547 (mt) cc_final: 0.9265 (mt) REVERT: o 128 PHE cc_start: 0.8584 (t80) cc_final: 0.8158 (t80) REVERT: o 131 MET cc_start: 0.8882 (ppp) cc_final: 0.8562 (ppp) REVERT: o 144 TYR cc_start: 0.9003 (m-10) cc_final: 0.8712 (m-10) REVERT: o 152 LEU cc_start: 0.9459 (mt) cc_final: 0.9240 (mt) REVERT: p 303 TYR cc_start: 0.8833 (t80) cc_final: 0.8447 (t80) REVERT: p 341 ARG cc_start: 0.8892 (tpt90) cc_final: 0.8673 (tpt90) outliers start: 0 outliers final: 0 residues processed: 1008 average time/residue: 0.1145 time to fit residues: 186.7575 Evaluate side-chains 880 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 880 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 78 optimal weight: 10.0000 chunk 270 optimal weight: 0.9980 chunk 226 optimal weight: 4.9990 chunk 157 optimal weight: 1.9990 chunk 275 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 141 optimal weight: 0.8980 chunk 154 optimal weight: 0.0370 chunk 252 optimal weight: 1.9990 overall best weight: 1.1862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 111 HIS ** b 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 302 ASN d 311 HIS h 124 GLN ** l 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 123 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.089820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.070825 restraints weight = 65918.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.073411 restraints weight = 40291.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.075411 restraints weight = 27303.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.076749 restraints weight = 19830.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.077820 restraints weight = 15290.891| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.5912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 19610 Z= 0.167 Angle : 0.694 13.816 26647 Z= 0.360 Chirality : 0.043 0.236 3268 Planarity : 0.004 0.094 3401 Dihedral : 4.090 27.601 2941 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.16), residues: 2771 helix: 1.84 (0.11), residues: 2164 sheet: -2.46 (0.98), residues: 16 loop : -0.75 (0.26), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG h 126 TYR 0.061 0.002 TYR l 68 PHE 0.052 0.002 PHE j 90 TRP 0.023 0.002 TRP c 420 HIS 0.006 0.001 HIS b 128 Details of bonding type rmsd covalent geometry : bond 0.00364 (19610) covalent geometry : angle 0.69437 (26647) hydrogen bonds : bond 0.04953 ( 1741) hydrogen bonds : angle 4.49132 ( 5118) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1012 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1012 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 55 LYS cc_start: 0.9521 (tttp) cc_final: 0.9175 (tptp) REVERT: H 64 GLU cc_start: 0.9282 (tp30) cc_final: 0.8640 (tm-30) REVERT: H 84 ILE cc_start: 0.9471 (mt) cc_final: 0.9220 (mt) REVERT: H 85 GLN cc_start: 0.9119 (mm-40) cc_final: 0.8742 (mm-40) REVERT: H 119 TYR cc_start: 0.7773 (p90) cc_final: 0.7470 (p90) REVERT: L 11 ILE cc_start: 0.9596 (mm) cc_final: 0.9184 (mm) REVERT: L 14 GLU cc_start: 0.9044 (pm20) cc_final: 0.8815 (pm20) REVERT: L 22 LEU cc_start: 0.9374 (mt) cc_final: 0.9173 (mt) REVERT: L 40 GLU cc_start: 0.8864 (pm20) cc_final: 0.8645 (pm20) REVERT: L 44 THR cc_start: 0.9567 (t) cc_final: 0.8756 (p) REVERT: L 47 GLU cc_start: 0.9130 (mt-10) cc_final: 0.8556 (mt-10) REVERT: L 49 GLU cc_start: 0.9019 (tp30) cc_final: 0.8540 (tm-30) REVERT: L 67 ASN cc_start: 0.8853 (m110) cc_final: 0.7921 (m110) REVERT: L 69 TYR cc_start: 0.8243 (p90) cc_final: 0.7632 (p90) REVERT: L 72 GLU cc_start: 0.8836 (mm-30) cc_final: 0.8488 (mm-30) REVERT: L 79 ASP cc_start: 0.9135 (m-30) cc_final: 0.8894 (m-30) REVERT: L 89 LEU cc_start: 0.8987 (mt) cc_final: 0.8760 (mt) REVERT: L 90 GLU cc_start: 0.8925 (mp0) cc_final: 0.8136 (tt0) REVERT: b 5 GLU cc_start: 0.8825 (pt0) cc_final: 0.8395 (pm20) REVERT: b 19 MET cc_start: 0.8682 (mtp) cc_final: 0.8312 (mtp) REVERT: b 71 ILE cc_start: 0.9644 (mm) cc_final: 0.9436 (mm) REVERT: b 90 ASN cc_start: 0.9008 (m110) cc_final: 0.8658 (m110) REVERT: b 91 LEU cc_start: 0.9565 (tp) cc_final: 0.9262 (tp) REVERT: b 102 ILE cc_start: 0.9695 (mm) cc_final: 0.9446 (mm) REVERT: b 103 TYR cc_start: 0.8741 (m-10) cc_final: 0.8400 (m-10) REVERT: b 116 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7375 (mp0) REVERT: b 137 MET cc_start: 0.9124 (mtp) cc_final: 0.8757 (mtp) REVERT: b 164 LEU cc_start: 0.9669 (mt) cc_final: 0.9364 (mp) REVERT: b 168 GLN cc_start: 0.9076 (mp10) cc_final: 0.8836 (mp10) REVERT: b 169 ASN cc_start: 0.8626 (t0) cc_final: 0.7854 (t0) REVERT: b 172 LEU cc_start: 0.9312 (mt) cc_final: 0.8645 (mt) REVERT: b 186 ILE cc_start: 0.9594 (mt) cc_final: 0.9083 (mt) REVERT: b 189 PHE cc_start: 0.9124 (m-10) cc_final: 0.8755 (m-80) REVERT: b 197 GLN cc_start: 0.8536 (mt0) cc_final: 0.8194 (mt0) REVERT: c 435 TYR cc_start: 0.9434 (t80) cc_final: 0.8988 (t80) REVERT: c 439 MET cc_start: 0.9442 (mtt) cc_final: 0.8964 (mtp) REVERT: d 28 LEU cc_start: 0.9353 (mt) cc_final: 0.8881 (mm) REVERT: d 30 GLN cc_start: 0.9107 (tm-30) cc_final: 0.8797 (tm-30) REVERT: d 39 CYS cc_start: 0.7520 (p) cc_final: 0.7181 (p) REVERT: d 44 ASP cc_start: 0.9141 (m-30) cc_final: 0.8807 (m-30) REVERT: d 48 HIS cc_start: 0.8947 (m90) cc_final: 0.8574 (m90) REVERT: d 76 GLU cc_start: 0.9086 (mt-10) cc_final: 0.8748 (mt-10) REVERT: d 78 MET cc_start: 0.9455 (tpp) cc_final: 0.9167 (tpp) REVERT: d 81 GLU cc_start: 0.8816 (pp20) cc_final: 0.8612 (pp20) REVERT: d 105 MET cc_start: 0.9006 (mmm) cc_final: 0.8587 (tpt) REVERT: d 125 LEU cc_start: 0.9069 (mt) cc_final: 0.8771 (mt) REVERT: d 128 LYS cc_start: 0.9426 (mmtt) cc_final: 0.8943 (mmmt) REVERT: d 129 CYS cc_start: 0.8612 (m) cc_final: 0.7978 (m) REVERT: d 176 MET cc_start: 0.8147 (mmm) cc_final: 0.7723 (mmp) REVERT: d 181 ILE cc_start: 0.9070 (mt) cc_final: 0.8832 (mt) REVERT: d 183 ASN cc_start: 0.9375 (t0) cc_final: 0.8780 (t0) REVERT: d 240 LEU cc_start: 0.9188 (mt) cc_final: 0.8915 (mt) REVERT: d 262 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8198 (tm-30) REVERT: d 315 PHE cc_start: 0.9705 (m-80) cc_final: 0.9359 (m-80) REVERT: d 322 LYS cc_start: 0.9639 (mtpp) cc_final: 0.9129 (mtmm) REVERT: d 325 GLU cc_start: 0.9490 (tt0) cc_final: 0.8813 (tm-30) REVERT: d 338 GLN cc_start: 0.9079 (mm-40) cc_final: 0.8847 (mm110) REVERT: d 348 ILE cc_start: 0.9554 (mm) cc_final: 0.9294 (mp) REVERT: g 7 ASN cc_start: 0.8426 (p0) cc_final: 0.7959 (t0) REVERT: g 28 MET cc_start: 0.9833 (mtm) cc_final: 0.9425 (mtm) REVERT: g 32 TYR cc_start: 0.9028 (t80) cc_final: 0.8324 (t80) REVERT: g 48 ARG cc_start: 0.8932 (mtp180) cc_final: 0.8540 (mtp180) REVERT: g 51 LEU cc_start: 0.8717 (mm) cc_final: 0.8210 (mm) REVERT: g 53 MET cc_start: 0.8764 (mtm) cc_final: 0.8351 (ttm) REVERT: g 57 ILE cc_start: 0.9486 (mt) cc_final: 0.9066 (mt) REVERT: g 64 ILE cc_start: 0.9399 (mt) cc_final: 0.9125 (mt) REVERT: g 68 TYR cc_start: 0.9637 (m-80) cc_final: 0.9232 (m-80) REVERT: g 112 ILE cc_start: 0.9436 (mm) cc_final: 0.9059 (mm) REVERT: g 141 LEU cc_start: 0.9347 (mt) cc_final: 0.8925 (mt) REVERT: g 144 TYR cc_start: 0.8805 (m-80) cc_final: 0.8487 (m-80) REVERT: g 146 LEU cc_start: 0.9776 (tp) cc_final: 0.9527 (tp) REVERT: h 13 PHE cc_start: 0.9461 (t80) cc_final: 0.8726 (t80) REVERT: h 17 MET cc_start: 0.9518 (mtt) cc_final: 0.8970 (mtt) REVERT: h 23 MET cc_start: 0.9536 (mmm) cc_final: 0.9089 (tpp) REVERT: h 24 VAL cc_start: 0.9557 (p) cc_final: 0.9324 (p) REVERT: h 28 MET cc_start: 0.8907 (mtp) cc_final: 0.8065 (tpt) REVERT: h 44 MET cc_start: 0.8189 (tmm) cc_final: 0.7697 (tmm) REVERT: h 48 ARG cc_start: 0.8617 (ttm170) cc_final: 0.7557 (ttm170) REVERT: h 51 LEU cc_start: 0.8522 (mt) cc_final: 0.8001 (mt) REVERT: h 54 LYS cc_start: 0.7143 (mttt) cc_final: 0.6269 (tttp) REVERT: h 57 ILE cc_start: 0.9641 (mt) cc_final: 0.9171 (mt) REVERT: h 90 PHE cc_start: 0.8926 (m-10) cc_final: 0.8374 (m-80) REVERT: h 112 ILE cc_start: 0.9580 (mm) cc_final: 0.9140 (tp) REVERT: h 121 THR cc_start: 0.8932 (p) cc_final: 0.8641 (p) REVERT: h 128 PHE cc_start: 0.9142 (t80) cc_final: 0.8756 (t80) REVERT: h 137 PHE cc_start: 0.9067 (m-80) cc_final: 0.8642 (m-80) REVERT: h 144 TYR cc_start: 0.9564 (m-10) cc_final: 0.9089 (m-10) REVERT: h 152 LEU cc_start: 0.9636 (mt) cc_final: 0.9413 (mt) REVERT: i 13 PHE cc_start: 0.8882 (t80) cc_final: 0.8016 (t80) REVERT: i 17 MET cc_start: 0.9549 (mmt) cc_final: 0.9186 (mmm) REVERT: i 64 ILE cc_start: 0.9490 (mt) cc_final: 0.9259 (mt) REVERT: i 76 ILE cc_start: 0.9349 (mt) cc_final: 0.8926 (mt) REVERT: i 90 PHE cc_start: 0.8900 (m-10) cc_final: 0.8257 (m-80) REVERT: i 92 GLN cc_start: 0.9222 (mt0) cc_final: 0.8861 (mt0) REVERT: i 101 LEU cc_start: 0.9439 (mt) cc_final: 0.9192 (mt) REVERT: i 115 ASP cc_start: 0.8743 (t70) cc_final: 0.8280 (t70) REVERT: i 119 ARG cc_start: 0.9133 (mtt90) cc_final: 0.8761 (mtt90) REVERT: i 127 LEU cc_start: 0.8721 (tp) cc_final: 0.8430 (tp) REVERT: i 131 MET cc_start: 0.8947 (ttp) cc_final: 0.8400 (ttt) REVERT: i 135 LEU cc_start: 0.9517 (mm) cc_final: 0.9067 (mm) REVERT: i 141 LEU cc_start: 0.9589 (mp) cc_final: 0.9294 (mp) REVERT: i 144 TYR cc_start: 0.8888 (m-10) cc_final: 0.8581 (m-10) REVERT: i 152 LEU cc_start: 0.9629 (mt) cc_final: 0.9384 (mt) REVERT: j 17 MET cc_start: 0.9185 (mtm) cc_final: 0.8580 (mtp) REVERT: j 28 MET cc_start: 0.8969 (mtp) cc_final: 0.8277 (mmm) REVERT: j 47 MET cc_start: 0.8913 (mmm) cc_final: 0.8475 (mmm) REVERT: j 61 MET cc_start: 0.8480 (ttp) cc_final: 0.8220 (ttm) REVERT: j 108 PHE cc_start: 0.8798 (m-80) cc_final: 0.8468 (m-80) REVERT: j 121 THR cc_start: 0.8792 (m) cc_final: 0.8372 (p) REVERT: j 124 GLN cc_start: 0.8783 (tp-100) cc_final: 0.7906 (tm-30) REVERT: j 127 LEU cc_start: 0.9336 (tp) cc_final: 0.8585 (tp) REVERT: j 131 MET cc_start: 0.8267 (ttp) cc_final: 0.7952 (ttp) REVERT: j 150 LEU cc_start: 0.9722 (mt) cc_final: 0.9508 (mt) REVERT: j 152 LEU cc_start: 0.9419 (tp) cc_final: 0.9153 (tp) REVERT: k 13 PHE cc_start: 0.9172 (t80) cc_final: 0.8813 (t80) REVERT: k 17 MET cc_start: 0.9005 (mtm) cc_final: 0.8629 (mtm) REVERT: k 23 MET cc_start: 0.8990 (mmm) cc_final: 0.8533 (mmm) REVERT: k 32 TYR cc_start: 0.8138 (t80) cc_final: 0.7799 (t80) REVERT: k 44 MET cc_start: 0.9022 (ppp) cc_final: 0.8526 (ppp) REVERT: k 53 MET cc_start: 0.8617 (tmm) cc_final: 0.7916 (mtt) REVERT: k 59 VAL cc_start: 0.9441 (t) cc_final: 0.9159 (t) REVERT: k 65 ILE cc_start: 0.9436 (mt) cc_final: 0.9093 (mt) REVERT: k 68 TYR cc_start: 0.8836 (m-10) cc_final: 0.8302 (m-80) REVERT: k 91 LEU cc_start: 0.9239 (mt) cc_final: 0.8933 (mt) REVERT: k 118 VAL cc_start: 0.9553 (t) cc_final: 0.9256 (t) REVERT: k 131 MET cc_start: 0.8247 (mtt) cc_final: 0.7596 (mtt) REVERT: l 17 MET cc_start: 0.9319 (mmp) cc_final: 0.8834 (mmp) REVERT: l 47 MET cc_start: 0.8203 (mmt) cc_final: 0.7929 (mmt) REVERT: l 48 ARG cc_start: 0.8481 (tmm-80) cc_final: 0.8177 (tmm-80) REVERT: l 92 GLN cc_start: 0.8993 (mt0) cc_final: 0.8412 (mt0) REVERT: l 108 PHE cc_start: 0.8393 (t80) cc_final: 0.8099 (t80) REVERT: l 131 MET cc_start: 0.9405 (ttp) cc_final: 0.8963 (ttm) REVERT: m 11 SER cc_start: 0.8540 (p) cc_final: 0.8241 (p) REVERT: m 21 SER cc_start: 0.9273 (m) cc_final: 0.9024 (p) REVERT: m 48 ARG cc_start: 0.8883 (mmm160) cc_final: 0.8512 (mmm160) REVERT: m 51 LEU cc_start: 0.8560 (mt) cc_final: 0.8280 (mt) REVERT: m 53 MET cc_start: 0.8735 (mmm) cc_final: 0.8063 (tmm) REVERT: m 86 LEU cc_start: 0.9473 (tp) cc_final: 0.8945 (tp) REVERT: m 90 PHE cc_start: 0.9002 (m-10) cc_final: 0.8640 (m-80) REVERT: m 92 GLN cc_start: 0.9312 (mt0) cc_final: 0.8933 (mt0) REVERT: m 128 PHE cc_start: 0.8265 (t80) cc_final: 0.8043 (t80) REVERT: m 133 LEU cc_start: 0.8767 (tp) cc_final: 0.8324 (tp) REVERT: m 137 PHE cc_start: 0.9033 (m-80) cc_final: 0.8661 (m-80) REVERT: m 144 TYR cc_start: 0.9535 (m-10) cc_final: 0.9059 (m-10) REVERT: n 13 PHE cc_start: 0.9113 (t80) cc_final: 0.8400 (t80) REVERT: n 17 MET cc_start: 0.9205 (mmt) cc_final: 0.8823 (mmm) REVERT: n 25 PHE cc_start: 0.8995 (m-80) cc_final: 0.8704 (m-80) REVERT: n 47 MET cc_start: 0.9178 (mmm) cc_final: 0.8723 (mmm) REVERT: n 61 MET cc_start: 0.9314 (mmp) cc_final: 0.8370 (mmm) REVERT: n 68 TYR cc_start: 0.9254 (m-10) cc_final: 0.8864 (m-10) REVERT: n 72 VAL cc_start: 0.9326 (t) cc_final: 0.9067 (p) REVERT: n 86 LEU cc_start: 0.9360 (tp) cc_final: 0.9085 (tp) REVERT: n 90 PHE cc_start: 0.8822 (m-10) cc_final: 0.8193 (m-80) REVERT: n 133 LEU cc_start: 0.9365 (mt) cc_final: 0.9151 (mt) REVERT: n 146 LEU cc_start: 0.8890 (mt) cc_final: 0.8400 (mt) REVERT: o 13 PHE cc_start: 0.8951 (t80) cc_final: 0.8211 (t80) REVERT: o 17 MET cc_start: 0.9205 (mmp) cc_final: 0.8771 (mmt) REVERT: o 21 SER cc_start: 0.8874 (m) cc_final: 0.8247 (p) REVERT: o 23 MET cc_start: 0.9177 (tpp) cc_final: 0.8705 (ttp) REVERT: o 25 PHE cc_start: 0.8476 (m-10) cc_final: 0.8175 (m-10) REVERT: o 57 ILE cc_start: 0.9308 (mt) cc_final: 0.8855 (mm) REVERT: o 64 ILE cc_start: 0.9317 (mt) cc_final: 0.8995 (mt) REVERT: o 65 ILE cc_start: 0.9657 (mp) cc_final: 0.9365 (mp) REVERT: o 68 TYR cc_start: 0.9350 (m-10) cc_final: 0.8846 (m-80) REVERT: o 82 ASP cc_start: 0.8505 (p0) cc_final: 0.7698 (t0) REVERT: o 91 LEU cc_start: 0.9694 (mm) cc_final: 0.9492 (pp) REVERT: o 97 LEU cc_start: 0.9547 (mt) cc_final: 0.9257 (mt) REVERT: o 115 ASP cc_start: 0.9253 (t0) cc_final: 0.9022 (t0) REVERT: o 128 PHE cc_start: 0.8568 (t80) cc_final: 0.8150 (t80) REVERT: o 131 MET cc_start: 0.8875 (ppp) cc_final: 0.8567 (ppp) REVERT: o 144 TYR cc_start: 0.8999 (m-10) cc_final: 0.8675 (m-10) REVERT: o 152 LEU cc_start: 0.9440 (mt) cc_final: 0.9112 (mt) REVERT: p 303 TYR cc_start: 0.8832 (t80) cc_final: 0.8443 (t80) REVERT: p 313 ILE cc_start: 0.9737 (pt) cc_final: 0.9374 (pt) REVERT: p 338 ILE cc_start: 0.7219 (pt) cc_final: 0.6866 (pt) outliers start: 0 outliers final: 0 residues processed: 1012 average time/residue: 0.1109 time to fit residues: 181.8431 Evaluate side-chains 893 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 893 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 252 optimal weight: 0.1980 chunk 230 optimal weight: 0.9990 chunk 10 optimal weight: 8.9990 chunk 83 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 212 optimal weight: 2.9990 chunk 182 optimal weight: 0.8980 chunk 268 optimal weight: 3.9990 chunk 272 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 111 HIS L 81 HIS ** b 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 148 ASN b 168 GLN d 302 ASN ** h 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.090462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.071345 restraints weight = 65199.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.073958 restraints weight = 39995.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.075954 restraints weight = 27134.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.077353 restraints weight = 19698.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.078363 restraints weight = 15189.341| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.6109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 19610 Z= 0.159 Angle : 0.700 12.839 26647 Z= 0.363 Chirality : 0.044 0.265 3268 Planarity : 0.004 0.040 3401 Dihedral : 4.122 24.967 2941 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.06 % Allowed : 0.53 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.16), residues: 2771 helix: 1.84 (0.11), residues: 2150 sheet: -2.43 (1.04), residues: 16 loop : -0.65 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG j 119 TYR 0.060 0.002 TYR l 68 PHE 0.070 0.002 PHE j 90 TRP 0.031 0.003 TRP b 67 HIS 0.005 0.001 HIS b 128 Details of bonding type rmsd covalent geometry : bond 0.00346 (19610) covalent geometry : angle 0.70033 (26647) hydrogen bonds : bond 0.04911 ( 1741) hydrogen bonds : angle 4.47884 ( 5118) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1031 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1030 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 52 ILE cc_start: 0.9130 (tp) cc_final: 0.8916 (tp) REVERT: H 55 LYS cc_start: 0.9441 (tttp) cc_final: 0.9170 (tptp) REVERT: H 84 ILE cc_start: 0.9458 (mt) cc_final: 0.9209 (mt) REVERT: H 85 GLN cc_start: 0.9062 (mm-40) cc_final: 0.8679 (mm-40) REVERT: H 119 TYR cc_start: 0.7651 (p90) cc_final: 0.7319 (p90) REVERT: L 11 ILE cc_start: 0.9582 (mm) cc_final: 0.9186 (mm) REVERT: L 14 GLU cc_start: 0.9009 (pm20) cc_final: 0.8763 (pm20) REVERT: L 22 LEU cc_start: 0.9355 (mt) cc_final: 0.9125 (mt) REVERT: L 44 THR cc_start: 0.9579 (t) cc_final: 0.8961 (p) REVERT: L 47 GLU cc_start: 0.9109 (mt-10) cc_final: 0.8644 (mt-10) REVERT: L 49 GLU cc_start: 0.9021 (tp30) cc_final: 0.8537 (tm-30) REVERT: L 67 ASN cc_start: 0.8765 (m110) cc_final: 0.7765 (m110) REVERT: L 69 TYR cc_start: 0.8024 (p90) cc_final: 0.7576 (p90) REVERT: L 72 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8466 (mm-30) REVERT: L 79 ASP cc_start: 0.9121 (m-30) cc_final: 0.8868 (m-30) REVERT: L 89 LEU cc_start: 0.8966 (mt) cc_final: 0.8640 (mt) REVERT: L 90 GLU cc_start: 0.8870 (mp0) cc_final: 0.8127 (tt0) REVERT: b 5 GLU cc_start: 0.8796 (pt0) cc_final: 0.8378 (pm20) REVERT: b 19 MET cc_start: 0.8694 (mtp) cc_final: 0.8322 (mtp) REVERT: b 43 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7757 (mm-30) REVERT: b 48 MET cc_start: 0.9054 (mmp) cc_final: 0.8786 (mmm) REVERT: b 51 ASN cc_start: 0.8940 (p0) cc_final: 0.8529 (p0) REVERT: b 70 TYR cc_start: 0.9528 (p90) cc_final: 0.9194 (p90) REVERT: b 90 ASN cc_start: 0.9024 (m110) cc_final: 0.8520 (m110) REVERT: b 91 LEU cc_start: 0.9549 (tp) cc_final: 0.9255 (tp) REVERT: b 102 ILE cc_start: 0.9683 (mm) cc_final: 0.9416 (mm) REVERT: b 103 TYR cc_start: 0.8717 (m-10) cc_final: 0.8350 (m-10) REVERT: b 116 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7352 (mp0) REVERT: b 118 PHE cc_start: 0.7134 (m-80) cc_final: 0.5946 (m-80) REVERT: b 135 TYR cc_start: 0.9190 (m-80) cc_final: 0.8919 (m-80) REVERT: b 137 MET cc_start: 0.9105 (mtp) cc_final: 0.8746 (mtp) REVERT: b 164 LEU cc_start: 0.9703 (mt) cc_final: 0.9387 (mp) REVERT: b 168 GLN cc_start: 0.9088 (OUTLIER) cc_final: 0.8796 (mp10) REVERT: b 169 ASN cc_start: 0.8632 (t0) cc_final: 0.7895 (t0) REVERT: b 172 LEU cc_start: 0.9311 (mt) cc_final: 0.8633 (mt) REVERT: b 186 ILE cc_start: 0.9575 (mt) cc_final: 0.9060 (mt) REVERT: b 189 PHE cc_start: 0.9121 (m-10) cc_final: 0.8767 (m-80) REVERT: b 197 GLN cc_start: 0.8464 (mt0) cc_final: 0.8160 (mt0) REVERT: c 435 TYR cc_start: 0.9402 (t80) cc_final: 0.8968 (t80) REVERT: c 439 MET cc_start: 0.9438 (mtt) cc_final: 0.8927 (mtp) REVERT: d 28 LEU cc_start: 0.9346 (mt) cc_final: 0.8859 (mm) REVERT: d 30 GLN cc_start: 0.9101 (tm-30) cc_final: 0.8787 (tm-30) REVERT: d 39 CYS cc_start: 0.7399 (p) cc_final: 0.7016 (p) REVERT: d 44 ASP cc_start: 0.9104 (m-30) cc_final: 0.8795 (m-30) REVERT: d 48 HIS cc_start: 0.8924 (m90) cc_final: 0.8554 (m90) REVERT: d 76 GLU cc_start: 0.9016 (mt-10) cc_final: 0.8711 (mt-10) REVERT: d 81 GLU cc_start: 0.8834 (pp20) cc_final: 0.8546 (pp20) REVERT: d 85 MET cc_start: 0.9522 (ptp) cc_final: 0.8995 (ptp) REVERT: d 105 MET cc_start: 0.8963 (mmm) cc_final: 0.8522 (tpt) REVERT: d 125 LEU cc_start: 0.9075 (mt) cc_final: 0.8788 (mt) REVERT: d 128 LYS cc_start: 0.9421 (mmtt) cc_final: 0.8925 (mmmt) REVERT: d 129 CYS cc_start: 0.8626 (m) cc_final: 0.8008 (m) REVERT: d 176 MET cc_start: 0.8191 (mmm) cc_final: 0.7730 (mmp) REVERT: d 183 ASN cc_start: 0.9326 (t0) cc_final: 0.8750 (t0) REVERT: d 240 LEU cc_start: 0.9166 (mt) cc_final: 0.8901 (mt) REVERT: d 262 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8124 (tm-30) REVERT: d 315 PHE cc_start: 0.9678 (m-80) cc_final: 0.9317 (m-80) REVERT: d 322 LYS cc_start: 0.9623 (mtpp) cc_final: 0.9043 (mtmm) REVERT: d 325 GLU cc_start: 0.9502 (tt0) cc_final: 0.8774 (tm-30) REVERT: d 338 GLN cc_start: 0.9077 (mm-40) cc_final: 0.8807 (mm110) REVERT: d 348 ILE cc_start: 0.9557 (mm) cc_final: 0.9327 (mp) REVERT: g 7 ASN cc_start: 0.8454 (p0) cc_final: 0.7967 (t0) REVERT: g 17 MET cc_start: 0.9420 (ttm) cc_final: 0.8958 (ttp) REVERT: g 28 MET cc_start: 0.9818 (mtm) cc_final: 0.9411 (mtm) REVERT: g 32 TYR cc_start: 0.9005 (t80) cc_final: 0.8275 (t80) REVERT: g 47 MET cc_start: 0.9399 (tmm) cc_final: 0.9140 (ttt) REVERT: g 48 ARG cc_start: 0.8884 (mtp180) cc_final: 0.8256 (mtp180) REVERT: g 51 LEU cc_start: 0.8692 (mm) cc_final: 0.8140 (mm) REVERT: g 53 MET cc_start: 0.8804 (mtm) cc_final: 0.8166 (ttt) REVERT: g 57 ILE cc_start: 0.9458 (mt) cc_final: 0.9046 (mt) REVERT: g 68 TYR cc_start: 0.9590 (m-80) cc_final: 0.9240 (m-80) REVERT: g 90 PHE cc_start: 0.8801 (m-80) cc_final: 0.8544 (m-80) REVERT: g 141 LEU cc_start: 0.9335 (mt) cc_final: 0.8898 (mt) REVERT: g 144 TYR cc_start: 0.8764 (m-80) cc_final: 0.8453 (m-80) REVERT: g 146 LEU cc_start: 0.9764 (tp) cc_final: 0.9522 (tp) REVERT: h 13 PHE cc_start: 0.9253 (t80) cc_final: 0.8488 (t80) REVERT: h 17 MET cc_start: 0.9538 (mtt) cc_final: 0.8973 (mtt) REVERT: h 23 MET cc_start: 0.9518 (mmm) cc_final: 0.9089 (tpp) REVERT: h 24 VAL cc_start: 0.9557 (p) cc_final: 0.9315 (p) REVERT: h 28 MET cc_start: 0.8890 (mtp) cc_final: 0.8022 (tpt) REVERT: h 44 MET cc_start: 0.8114 (tmm) cc_final: 0.7655 (tmm) REVERT: h 48 ARG cc_start: 0.8590 (ttm170) cc_final: 0.7561 (ttm170) REVERT: h 51 LEU cc_start: 0.8511 (mt) cc_final: 0.8028 (mt) REVERT: h 54 LYS cc_start: 0.7130 (mttt) cc_final: 0.6140 (tttp) REVERT: h 57 ILE cc_start: 0.9618 (mt) cc_final: 0.9177 (mt) REVERT: h 60 VAL cc_start: 0.9401 (m) cc_final: 0.9160 (m) REVERT: h 90 PHE cc_start: 0.8918 (m-10) cc_final: 0.8363 (m-80) REVERT: h 112 ILE cc_start: 0.9547 (mm) cc_final: 0.9208 (tp) REVERT: h 127 LEU cc_start: 0.9265 (tt) cc_final: 0.8750 (mp) REVERT: h 128 PHE cc_start: 0.9123 (t80) cc_final: 0.8615 (t80) REVERT: h 137 PHE cc_start: 0.9031 (m-80) cc_final: 0.8581 (m-80) REVERT: h 144 TYR cc_start: 0.9620 (m-10) cc_final: 0.9127 (m-10) REVERT: h 152 LEU cc_start: 0.9621 (mt) cc_final: 0.9394 (mt) REVERT: i 13 PHE cc_start: 0.8651 (t80) cc_final: 0.7731 (t80) REVERT: i 17 MET cc_start: 0.9499 (mmt) cc_final: 0.9094 (mmm) REVERT: i 61 MET cc_start: 0.9447 (mtp) cc_final: 0.9166 (mtp) REVERT: i 64 ILE cc_start: 0.9467 (mt) cc_final: 0.9206 (mt) REVERT: i 76 ILE cc_start: 0.9333 (mt) cc_final: 0.8884 (mt) REVERT: i 90 PHE cc_start: 0.8917 (m-10) cc_final: 0.8158 (m-80) REVERT: i 92 GLN cc_start: 0.9272 (mt0) cc_final: 0.8878 (mt0) REVERT: i 101 LEU cc_start: 0.9433 (mt) cc_final: 0.9180 (mt) REVERT: i 115 ASP cc_start: 0.8680 (t70) cc_final: 0.8054 (t70) REVERT: i 119 ARG cc_start: 0.9250 (mtt90) cc_final: 0.8923 (mtt90) REVERT: i 124 GLN cc_start: 0.8894 (tp-100) cc_final: 0.8510 (tm-30) REVERT: i 126 ARG cc_start: 0.8164 (mmt180) cc_final: 0.7640 (mpt180) REVERT: i 127 LEU cc_start: 0.8767 (tp) cc_final: 0.8069 (tp) REVERT: i 131 MET cc_start: 0.8919 (ttp) cc_final: 0.8366 (ttt) REVERT: i 135 LEU cc_start: 0.9510 (mm) cc_final: 0.9089 (mm) REVERT: i 141 LEU cc_start: 0.9527 (mp) cc_final: 0.9249 (mp) REVERT: i 144 TYR cc_start: 0.8871 (m-10) cc_final: 0.8600 (m-10) REVERT: i 152 LEU cc_start: 0.9615 (mt) cc_final: 0.9375 (mt) REVERT: j 17 MET cc_start: 0.8951 (mtp) cc_final: 0.8565 (mtt) REVERT: j 28 MET cc_start: 0.8902 (mtp) cc_final: 0.8223 (mmm) REVERT: j 47 MET cc_start: 0.8963 (mmm) cc_final: 0.8496 (mmm) REVERT: j 90 PHE cc_start: 0.8552 (m-80) cc_final: 0.7575 (m-10) REVERT: j 108 PHE cc_start: 0.8743 (m-80) cc_final: 0.8341 (m-80) REVERT: j 121 THR cc_start: 0.8766 (m) cc_final: 0.8205 (m) REVERT: j 124 GLN cc_start: 0.8799 (tp-100) cc_final: 0.7921 (tm-30) REVERT: j 127 LEU cc_start: 0.9336 (tp) cc_final: 0.8523 (tp) REVERT: j 131 MET cc_start: 0.8150 (ttp) cc_final: 0.7750 (ttp) REVERT: j 150 LEU cc_start: 0.9725 (mt) cc_final: 0.9514 (mt) REVERT: j 152 LEU cc_start: 0.9408 (tp) cc_final: 0.9151 (tp) REVERT: k 13 PHE cc_start: 0.9133 (t80) cc_final: 0.8653 (t80) REVERT: k 17 MET cc_start: 0.8985 (mtm) cc_final: 0.8609 (mtm) REVERT: k 23 MET cc_start: 0.8959 (mmm) cc_final: 0.8519 (mmm) REVERT: k 32 TYR cc_start: 0.8164 (t80) cc_final: 0.7880 (t80) REVERT: k 44 MET cc_start: 0.9008 (ppp) cc_final: 0.8466 (ppp) REVERT: k 53 MET cc_start: 0.8640 (tmm) cc_final: 0.7933 (mtt) REVERT: k 59 VAL cc_start: 0.9413 (t) cc_final: 0.9096 (t) REVERT: k 65 ILE cc_start: 0.9402 (mt) cc_final: 0.9055 (mt) REVERT: k 68 TYR cc_start: 0.8879 (m-10) cc_final: 0.8351 (m-80) REVERT: k 91 LEU cc_start: 0.9211 (mt) cc_final: 0.8910 (mt) REVERT: k 118 VAL cc_start: 0.9545 (t) cc_final: 0.9316 (t) REVERT: k 131 MET cc_start: 0.8236 (mtt) cc_final: 0.7509 (mtt) REVERT: l 13 PHE cc_start: 0.9174 (t80) cc_final: 0.8568 (t80) REVERT: l 17 MET cc_start: 0.9286 (mmp) cc_final: 0.8848 (mmp) REVERT: l 32 TYR cc_start: 0.8272 (t80) cc_final: 0.7593 (t80) REVERT: l 47 MET cc_start: 0.8148 (mmt) cc_final: 0.7859 (mmt) REVERT: l 48 ARG cc_start: 0.8465 (tmm-80) cc_final: 0.8166 (tmm-80) REVERT: l 90 PHE cc_start: 0.9113 (m-10) cc_final: 0.8412 (m-80) REVERT: l 92 GLN cc_start: 0.8966 (mt0) cc_final: 0.8399 (mt0) REVERT: l 131 MET cc_start: 0.9408 (ttp) cc_final: 0.8963 (ttm) REVERT: m 11 SER cc_start: 0.8683 (p) cc_final: 0.8438 (p) REVERT: m 14 PHE cc_start: 0.9436 (m-80) cc_final: 0.9233 (m-80) REVERT: m 17 MET cc_start: 0.9142 (mtp) cc_final: 0.8897 (mtp) REVERT: m 21 SER cc_start: 0.9210 (m) cc_final: 0.8972 (p) REVERT: m 48 ARG cc_start: 0.8874 (mmm160) cc_final: 0.8503 (mmm160) REVERT: m 51 LEU cc_start: 0.8539 (mt) cc_final: 0.8314 (mt) REVERT: m 53 MET cc_start: 0.8709 (mmm) cc_final: 0.7887 (tmm) REVERT: m 68 TYR cc_start: 0.8638 (m-10) cc_final: 0.8362 (m-10) REVERT: m 86 LEU cc_start: 0.9444 (tp) cc_final: 0.8899 (tp) REVERT: m 90 PHE cc_start: 0.8954 (m-10) cc_final: 0.8537 (m-80) REVERT: m 92 GLN cc_start: 0.9305 (mt0) cc_final: 0.8918 (mt0) REVERT: m 128 PHE cc_start: 0.8358 (t80) cc_final: 0.8043 (t80) REVERT: m 133 LEU cc_start: 0.8740 (tp) cc_final: 0.8290 (tp) REVERT: m 137 PHE cc_start: 0.9118 (m-80) cc_final: 0.8757 (m-80) REVERT: m 144 TYR cc_start: 0.9497 (m-10) cc_final: 0.9057 (m-10) REVERT: n 25 PHE cc_start: 0.9000 (m-80) cc_final: 0.8751 (m-80) REVERT: n 47 MET cc_start: 0.9175 (mmm) cc_final: 0.8717 (mmm) REVERT: n 61 MET cc_start: 0.9267 (mmp) cc_final: 0.8712 (mmm) REVERT: n 68 TYR cc_start: 0.9246 (m-10) cc_final: 0.8873 (m-10) REVERT: n 72 VAL cc_start: 0.9356 (t) cc_final: 0.9110 (p) REVERT: n 86 LEU cc_start: 0.9357 (tp) cc_final: 0.9089 (tp) REVERT: n 90 PHE cc_start: 0.8743 (m-10) cc_final: 0.8100 (m-80) REVERT: n 133 LEU cc_start: 0.9349 (mt) cc_final: 0.9145 (mt) REVERT: n 135 LEU cc_start: 0.9517 (mt) cc_final: 0.9272 (mt) REVERT: n 146 LEU cc_start: 0.8892 (mt) cc_final: 0.8424 (mt) REVERT: o 13 PHE cc_start: 0.8935 (t80) cc_final: 0.8223 (t80) REVERT: o 17 MET cc_start: 0.9165 (mmp) cc_final: 0.8834 (mmt) REVERT: o 20 SER cc_start: 0.8970 (m) cc_final: 0.8763 (m) REVERT: o 23 MET cc_start: 0.9128 (tpp) cc_final: 0.8744 (ttp) REVERT: o 25 PHE cc_start: 0.8404 (m-10) cc_final: 0.8003 (m-10) REVERT: o 57 ILE cc_start: 0.9309 (mt) cc_final: 0.8693 (mm) REVERT: o 64 ILE cc_start: 0.9326 (mt) cc_final: 0.9006 (mt) REVERT: o 65 ILE cc_start: 0.9666 (mp) cc_final: 0.9382 (mp) REVERT: o 68 TYR cc_start: 0.9319 (m-10) cc_final: 0.8844 (m-80) REVERT: o 119 ARG cc_start: 0.9168 (ptp-110) cc_final: 0.8962 (ptp-170) REVERT: o 128 PHE cc_start: 0.8530 (t80) cc_final: 0.8111 (t80) REVERT: o 131 MET cc_start: 0.8832 (ppp) cc_final: 0.8517 (ppp) REVERT: o 144 TYR cc_start: 0.8972 (m-10) cc_final: 0.8637 (m-10) REVERT: o 152 LEU cc_start: 0.9427 (mt) cc_final: 0.9116 (mt) REVERT: o 154 THR cc_start: 0.8156 (t) cc_final: 0.7940 (t) REVERT: p 303 TYR cc_start: 0.8807 (t80) cc_final: 0.8421 (t80) REVERT: p 338 ILE cc_start: 0.7397 (pt) cc_final: 0.7012 (pt) outliers start: 1 outliers final: 0 residues processed: 1030 average time/residue: 0.1118 time to fit residues: 186.8213 Evaluate side-chains 914 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 913 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 274 optimal weight: 10.0000 chunk 201 optimal weight: 6.9990 chunk 22 optimal weight: 20.0000 chunk 162 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 155 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 126 optimal weight: 0.0060 chunk 71 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 196 optimal weight: 5.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 111 HIS L 81 HIS ** b 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 123 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.090878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.071851 restraints weight = 65102.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.074475 restraints weight = 39734.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.076501 restraints weight = 26959.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.077884 restraints weight = 19581.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.078743 restraints weight = 15123.445| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.6300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 19610 Z= 0.159 Angle : 0.716 12.845 26647 Z= 0.372 Chirality : 0.044 0.216 3268 Planarity : 0.004 0.046 3401 Dihedral : 4.125 22.916 2941 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.16), residues: 2771 helix: 1.83 (0.11), residues: 2136 sheet: -2.46 (1.08), residues: 16 loop : -0.57 (0.26), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG h 126 TYR 0.061 0.002 TYR l 68 PHE 0.064 0.002 PHE j 90 TRP 0.038 0.003 TRP b 67 HIS 0.005 0.001 HIS b 128 Details of bonding type rmsd covalent geometry : bond 0.00349 (19610) covalent geometry : angle 0.71578 (26647) hydrogen bonds : bond 0.04867 ( 1741) hydrogen bonds : angle 4.51280 ( 5118) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1025 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1025 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 55 LYS cc_start: 0.9522 (tttp) cc_final: 0.9128 (tptp) REVERT: H 64 GLU cc_start: 0.9285 (tp30) cc_final: 0.8585 (tm-30) REVERT: H 84 ILE cc_start: 0.9463 (mt) cc_final: 0.9222 (mt) REVERT: H 85 GLN cc_start: 0.9066 (mm-40) cc_final: 0.8686 (mm-40) REVERT: H 91 GLN cc_start: 0.7692 (tp-100) cc_final: 0.7168 (tt0) REVERT: H 119 TYR cc_start: 0.7602 (p90) cc_final: 0.7299 (p90) REVERT: L 11 ILE cc_start: 0.9561 (mm) cc_final: 0.9188 (mm) REVERT: L 14 GLU cc_start: 0.9007 (pm20) cc_final: 0.8791 (pm20) REVERT: L 44 THR cc_start: 0.9610 (t) cc_final: 0.8847 (p) REVERT: L 47 GLU cc_start: 0.9088 (mt-10) cc_final: 0.8560 (mt-10) REVERT: L 49 GLU cc_start: 0.8945 (tp30) cc_final: 0.8488 (tm-30) REVERT: L 54 GLN cc_start: 0.8559 (mt0) cc_final: 0.8287 (tp-100) REVERT: L 67 ASN cc_start: 0.8690 (m110) cc_final: 0.7650 (m110) REVERT: L 69 TYR cc_start: 0.8068 (p90) cc_final: 0.7555 (p90) REVERT: L 72 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8457 (mm-30) REVERT: L 73 MET cc_start: 0.8822 (mtm) cc_final: 0.8599 (mtm) REVERT: L 79 ASP cc_start: 0.9127 (m-30) cc_final: 0.8852 (m-30) REVERT: L 90 GLU cc_start: 0.8896 (mp0) cc_final: 0.8128 (tt0) REVERT: b 5 GLU cc_start: 0.8800 (pt0) cc_final: 0.8366 (pm20) REVERT: b 19 MET cc_start: 0.8671 (mtp) cc_final: 0.8293 (mtp) REVERT: b 43 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7697 (mm-30) REVERT: b 48 MET cc_start: 0.9174 (mmp) cc_final: 0.8939 (mmm) REVERT: b 51 ASN cc_start: 0.8824 (p0) cc_final: 0.8494 (p0) REVERT: b 90 ASN cc_start: 0.8931 (m110) cc_final: 0.8681 (m110) REVERT: b 91 LEU cc_start: 0.9560 (tp) cc_final: 0.9250 (tp) REVERT: b 102 ILE cc_start: 0.9671 (mm) cc_final: 0.9403 (mm) REVERT: b 103 TYR cc_start: 0.8748 (m-10) cc_final: 0.8368 (m-10) REVERT: b 111 ILE cc_start: 0.9461 (mm) cc_final: 0.9218 (mm) REVERT: b 116 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7266 (mp0) REVERT: b 118 PHE cc_start: 0.7216 (m-80) cc_final: 0.6229 (m-80) REVERT: b 137 MET cc_start: 0.9129 (mtp) cc_final: 0.8760 (mtp) REVERT: b 164 LEU cc_start: 0.9721 (mt) cc_final: 0.9358 (mp) REVERT: b 168 GLN cc_start: 0.9084 (mp-120) cc_final: 0.8811 (mp10) REVERT: b 169 ASN cc_start: 0.8569 (t0) cc_final: 0.7853 (t0) REVERT: b 172 LEU cc_start: 0.9339 (mt) cc_final: 0.8676 (mt) REVERT: b 186 ILE cc_start: 0.9554 (mt) cc_final: 0.9046 (mt) REVERT: b 189 PHE cc_start: 0.9134 (m-10) cc_final: 0.8783 (m-80) REVERT: b 197 GLN cc_start: 0.8437 (mt0) cc_final: 0.8113 (mt0) REVERT: b 202 LYS cc_start: 0.8931 (tptp) cc_final: 0.8724 (tptp) REVERT: b 203 MET cc_start: 0.8807 (ppp) cc_final: 0.8313 (ppp) REVERT: c 439 MET cc_start: 0.9442 (mtt) cc_final: 0.8963 (mtp) REVERT: d 28 LEU cc_start: 0.9272 (mt) cc_final: 0.8765 (mm) REVERT: d 30 GLN cc_start: 0.9092 (tm-30) cc_final: 0.8786 (tm-30) REVERT: d 39 CYS cc_start: 0.7269 (p) cc_final: 0.6847 (p) REVERT: d 44 ASP cc_start: 0.9101 (m-30) cc_final: 0.8785 (m-30) REVERT: d 48 HIS cc_start: 0.8927 (m90) cc_final: 0.8535 (m90) REVERT: d 76 GLU cc_start: 0.9010 (mt-10) cc_final: 0.8702 (mt-10) REVERT: d 93 LEU cc_start: 0.9709 (tt) cc_final: 0.9485 (tt) REVERT: d 105 MET cc_start: 0.8982 (mmm) cc_final: 0.8529 (tpt) REVERT: d 125 LEU cc_start: 0.9076 (mt) cc_final: 0.8774 (mt) REVERT: d 128 LYS cc_start: 0.9469 (mmtt) cc_final: 0.8926 (mmmt) REVERT: d 129 CYS cc_start: 0.8595 (m) cc_final: 0.7981 (m) REVERT: d 176 MET cc_start: 0.8097 (mmm) cc_final: 0.7733 (mmp) REVERT: d 183 ASN cc_start: 0.9335 (t0) cc_final: 0.8790 (t0) REVERT: d 240 LEU cc_start: 0.9138 (mt) cc_final: 0.8890 (mt) REVERT: d 250 GLU cc_start: 0.8561 (tp30) cc_final: 0.8140 (tp30) REVERT: d 262 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8149 (tm-30) REVERT: d 302 ASN cc_start: 0.9778 (m110) cc_final: 0.9576 (m110) REVERT: d 312 PHE cc_start: 0.8469 (m-80) cc_final: 0.8129 (m-80) REVERT: d 315 PHE cc_start: 0.9686 (m-80) cc_final: 0.9348 (m-80) REVERT: d 322 LYS cc_start: 0.9581 (mtpp) cc_final: 0.9121 (mtmm) REVERT: d 325 GLU cc_start: 0.9554 (tt0) cc_final: 0.8856 (tm-30) REVERT: d 338 GLN cc_start: 0.9066 (mm-40) cc_final: 0.8800 (mm110) REVERT: d 339 ARG cc_start: 0.8809 (mmm160) cc_final: 0.8587 (mmp-170) REVERT: d 348 ILE cc_start: 0.9585 (mm) cc_final: 0.9374 (mp) REVERT: g 7 ASN cc_start: 0.8492 (p0) cc_final: 0.7982 (t0) REVERT: g 28 MET cc_start: 0.9819 (mtm) cc_final: 0.9440 (mtm) REVERT: g 32 TYR cc_start: 0.8984 (t80) cc_final: 0.8271 (t80) REVERT: g 34 THR cc_start: 0.9542 (p) cc_final: 0.9341 (p) REVERT: g 47 MET cc_start: 0.9422 (tmm) cc_final: 0.9115 (ttt) REVERT: g 48 ARG cc_start: 0.8843 (mtp180) cc_final: 0.8248 (mtp180) REVERT: g 51 LEU cc_start: 0.8702 (mm) cc_final: 0.8249 (mm) REVERT: g 53 MET cc_start: 0.8774 (mtm) cc_final: 0.8208 (ttt) REVERT: g 57 ILE cc_start: 0.9466 (mt) cc_final: 0.9026 (mt) REVERT: g 90 PHE cc_start: 0.8913 (m-80) cc_final: 0.8625 (m-80) REVERT: g 141 LEU cc_start: 0.9339 (mt) cc_final: 0.8873 (mt) REVERT: g 144 TYR cc_start: 0.8765 (m-80) cc_final: 0.8448 (m-80) REVERT: h 13 PHE cc_start: 0.9279 (t80) cc_final: 0.8522 (t80) REVERT: h 17 MET cc_start: 0.9560 (mtt) cc_final: 0.8996 (mtt) REVERT: h 23 MET cc_start: 0.9530 (mmm) cc_final: 0.9082 (tpp) REVERT: h 24 VAL cc_start: 0.9546 (p) cc_final: 0.9311 (p) REVERT: h 28 MET cc_start: 0.8844 (mtp) cc_final: 0.7980 (tpt) REVERT: h 44 MET cc_start: 0.8200 (tmm) cc_final: 0.7780 (tmm) REVERT: h 48 ARG cc_start: 0.8606 (ttm170) cc_final: 0.7680 (ttm170) REVERT: h 51 LEU cc_start: 0.8495 (mt) cc_final: 0.8196 (mt) REVERT: h 54 LYS cc_start: 0.7085 (mttt) cc_final: 0.6150 (tttp) REVERT: h 57 ILE cc_start: 0.9608 (mt) cc_final: 0.9149 (mt) REVERT: h 60 VAL cc_start: 0.9414 (m) cc_final: 0.9197 (m) REVERT: h 67 ILE cc_start: 0.9055 (mm) cc_final: 0.8766 (mm) REVERT: h 90 PHE cc_start: 0.8929 (m-10) cc_final: 0.8397 (m-80) REVERT: h 112 ILE cc_start: 0.9513 (mm) cc_final: 0.9213 (tp) REVERT: h 119 ARG cc_start: 0.8700 (mtp180) cc_final: 0.8467 (ttm-80) REVERT: h 127 LEU cc_start: 0.9073 (tt) cc_final: 0.8616 (mp) REVERT: h 128 PHE cc_start: 0.9179 (t80) cc_final: 0.8796 (t80) REVERT: h 137 PHE cc_start: 0.8974 (m-80) cc_final: 0.8557 (m-80) REVERT: h 144 TYR cc_start: 0.9558 (m-10) cc_final: 0.9104 (m-10) REVERT: h 152 LEU cc_start: 0.9604 (mt) cc_final: 0.9381 (mt) REVERT: i 13 PHE cc_start: 0.8602 (t80) cc_final: 0.8332 (t80) REVERT: i 17 MET cc_start: 0.9493 (mmt) cc_final: 0.9134 (mmm) REVERT: i 59 VAL cc_start: 0.9599 (t) cc_final: 0.9369 (t) REVERT: i 61 MET cc_start: 0.9409 (mtp) cc_final: 0.9163 (mtp) REVERT: i 64 ILE cc_start: 0.9457 (mt) cc_final: 0.9206 (mt) REVERT: i 76 ILE cc_start: 0.9351 (mt) cc_final: 0.8891 (mt) REVERT: i 90 PHE cc_start: 0.8882 (m-10) cc_final: 0.8171 (m-80) REVERT: i 92 GLN cc_start: 0.9202 (mt0) cc_final: 0.8835 (mt0) REVERT: i 101 LEU cc_start: 0.9404 (mt) cc_final: 0.9161 (mt) REVERT: i 115 ASP cc_start: 0.8576 (t70) cc_final: 0.7847 (t70) REVERT: i 119 ARG cc_start: 0.9202 (mtt90) cc_final: 0.8784 (mtt90) REVERT: i 124 GLN cc_start: 0.8792 (tp-100) cc_final: 0.8327 (tm-30) REVERT: i 127 LEU cc_start: 0.8773 (tp) cc_final: 0.7994 (tp) REVERT: i 131 MET cc_start: 0.8931 (ttp) cc_final: 0.8403 (ttt) REVERT: i 132 ILE cc_start: 0.8978 (pt) cc_final: 0.8775 (pt) REVERT: i 135 LEU cc_start: 0.9430 (mm) cc_final: 0.9047 (mm) REVERT: i 141 LEU cc_start: 0.9492 (mp) cc_final: 0.9186 (mp) REVERT: i 144 TYR cc_start: 0.8861 (m-10) cc_final: 0.8617 (m-10) REVERT: i 152 LEU cc_start: 0.9610 (mt) cc_final: 0.9377 (mt) REVERT: j 17 MET cc_start: 0.8917 (mtp) cc_final: 0.8493 (mtt) REVERT: j 28 MET cc_start: 0.8976 (mtp) cc_final: 0.8246 (mmm) REVERT: j 47 MET cc_start: 0.8937 (mmm) cc_final: 0.8471 (mmm) REVERT: j 108 PHE cc_start: 0.8756 (m-80) cc_final: 0.8370 (m-80) REVERT: j 121 THR cc_start: 0.8818 (m) cc_final: 0.8420 (p) REVERT: j 124 GLN cc_start: 0.8724 (tp-100) cc_final: 0.7930 (tm-30) REVERT: j 127 LEU cc_start: 0.9308 (tp) cc_final: 0.8565 (tp) REVERT: j 131 MET cc_start: 0.8280 (ttp) cc_final: 0.7908 (ttp) REVERT: j 150 LEU cc_start: 0.9728 (mt) cc_final: 0.9519 (mt) REVERT: j 152 LEU cc_start: 0.9412 (tp) cc_final: 0.9165 (tp) REVERT: k 13 PHE cc_start: 0.9159 (t80) cc_final: 0.8655 (t80) REVERT: k 17 MET cc_start: 0.8946 (mtm) cc_final: 0.8591 (mtm) REVERT: k 23 MET cc_start: 0.8965 (mmm) cc_final: 0.8534 (mmm) REVERT: k 32 TYR cc_start: 0.8145 (t80) cc_final: 0.7789 (t80) REVERT: k 44 MET cc_start: 0.9004 (ppp) cc_final: 0.8432 (ppp) REVERT: k 59 VAL cc_start: 0.9397 (t) cc_final: 0.9062 (t) REVERT: k 65 ILE cc_start: 0.9367 (mt) cc_final: 0.9017 (mt) REVERT: k 68 TYR cc_start: 0.8956 (m-10) cc_final: 0.8482 (m-80) REVERT: k 91 LEU cc_start: 0.9229 (mt) cc_final: 0.8918 (mt) REVERT: k 118 VAL cc_start: 0.9526 (t) cc_final: 0.9291 (t) REVERT: k 123 GLN cc_start: 0.9114 (mm-40) cc_final: 0.8640 (mm-40) REVERT: k 131 MET cc_start: 0.8221 (mtt) cc_final: 0.7463 (mtt) REVERT: k 141 LEU cc_start: 0.9615 (mp) cc_final: 0.9393 (mp) REVERT: l 13 PHE cc_start: 0.9109 (t80) cc_final: 0.8610 (t80) REVERT: l 17 MET cc_start: 0.9276 (mmp) cc_final: 0.8870 (mmp) REVERT: l 28 MET cc_start: 0.8703 (ptm) cc_final: 0.8383 (ptt) REVERT: l 47 MET cc_start: 0.8076 (mmt) cc_final: 0.7775 (mmt) REVERT: l 48 ARG cc_start: 0.8486 (tmm-80) cc_final: 0.8174 (tmm-80) REVERT: l 90 PHE cc_start: 0.9071 (m-10) cc_final: 0.8171 (m-10) REVERT: l 108 PHE cc_start: 0.8393 (t80) cc_final: 0.8085 (t80) REVERT: l 131 MET cc_start: 0.9441 (ttp) cc_final: 0.8964 (ttm) REVERT: m 11 SER cc_start: 0.8743 (p) cc_final: 0.8505 (p) REVERT: m 14 PHE cc_start: 0.9501 (m-80) cc_final: 0.9264 (m-80) REVERT: m 17 MET cc_start: 0.9179 (mtp) cc_final: 0.8971 (mtp) REVERT: m 21 SER cc_start: 0.9151 (m) cc_final: 0.8898 (p) REVERT: m 48 ARG cc_start: 0.8819 (mmm160) cc_final: 0.8476 (mmm160) REVERT: m 53 MET cc_start: 0.8687 (mmm) cc_final: 0.7927 (tmm) REVERT: m 61 MET cc_start: 0.9430 (mmm) cc_final: 0.9155 (mmm) REVERT: m 68 TYR cc_start: 0.8593 (m-10) cc_final: 0.8353 (m-10) REVERT: m 70 LEU cc_start: 0.9381 (mt) cc_final: 0.9179 (mt) REVERT: m 75 LEU cc_start: 0.9342 (mm) cc_final: 0.9001 (mm) REVERT: m 78 ASN cc_start: 0.9229 (t0) cc_final: 0.8557 (p0) REVERT: m 86 LEU cc_start: 0.9421 (tp) cc_final: 0.8882 (tp) REVERT: m 90 PHE cc_start: 0.8928 (m-10) cc_final: 0.8499 (m-80) REVERT: m 92 GLN cc_start: 0.9321 (mt0) cc_final: 0.8938 (mt0) REVERT: m 128 PHE cc_start: 0.8410 (t80) cc_final: 0.8208 (t80) REVERT: m 133 LEU cc_start: 0.8732 (tp) cc_final: 0.8277 (tp) REVERT: m 137 PHE cc_start: 0.9006 (m-80) cc_final: 0.8627 (m-80) REVERT: m 143 LEU cc_start: 0.9234 (tp) cc_final: 0.9008 (tp) REVERT: n 13 PHE cc_start: 0.9029 (t80) cc_final: 0.8071 (t80) REVERT: n 17 MET cc_start: 0.9160 (mmt) cc_final: 0.8773 (mmm) REVERT: n 47 MET cc_start: 0.9206 (mmm) cc_final: 0.8733 (mmm) REVERT: n 61 MET cc_start: 0.9249 (mmp) cc_final: 0.8666 (mmm) REVERT: n 68 TYR cc_start: 0.9252 (m-10) cc_final: 0.8922 (m-10) REVERT: n 72 VAL cc_start: 0.9343 (t) cc_final: 0.9103 (p) REVERT: n 86 LEU cc_start: 0.9386 (tp) cc_final: 0.9102 (tp) REVERT: n 90 PHE cc_start: 0.8681 (m-10) cc_final: 0.8025 (m-80) REVERT: n 135 LEU cc_start: 0.9519 (mt) cc_final: 0.9217 (mt) REVERT: n 146 LEU cc_start: 0.8859 (mt) cc_final: 0.8393 (mt) REVERT: o 13 PHE cc_start: 0.8980 (t80) cc_final: 0.8297 (t80) REVERT: o 17 MET cc_start: 0.9176 (mmp) cc_final: 0.8749 (mmt) REVERT: o 21 SER cc_start: 0.8863 (m) cc_final: 0.7887 (p) REVERT: o 23 MET cc_start: 0.9125 (tpp) cc_final: 0.8725 (ttp) REVERT: o 25 PHE cc_start: 0.8484 (m-10) cc_final: 0.8078 (m-80) REVERT: o 57 ILE cc_start: 0.9305 (mt) cc_final: 0.8680 (mm) REVERT: o 64 ILE cc_start: 0.9275 (mt) cc_final: 0.9006 (mt) REVERT: o 65 ILE cc_start: 0.9658 (mp) cc_final: 0.9334 (mp) REVERT: o 68 TYR cc_start: 0.9297 (m-10) cc_final: 0.8769 (m-80) REVERT: o 90 PHE cc_start: 0.9206 (m-80) cc_final: 0.8797 (m-80) REVERT: o 97 LEU cc_start: 0.9494 (mt) cc_final: 0.9148 (mt) REVERT: o 128 PHE cc_start: 0.8513 (t80) cc_final: 0.8101 (t80) REVERT: o 131 MET cc_start: 0.8799 (ppp) cc_final: 0.8537 (ppp) REVERT: p 303 TYR cc_start: 0.8683 (t80) cc_final: 0.8329 (t80) REVERT: p 308 ASN cc_start: 0.8941 (p0) cc_final: 0.8606 (p0) outliers start: 0 outliers final: 0 residues processed: 1025 average time/residue: 0.1151 time to fit residues: 191.2306 Evaluate side-chains 929 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 929 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 226 optimal weight: 3.9990 chunk 123 optimal weight: 0.9990 chunk 214 optimal weight: 0.0020 chunk 4 optimal weight: 2.9990 chunk 216 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 202 optimal weight: 0.1980 chunk 276 optimal weight: 0.9990 chunk 241 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 overall best weight: 0.8394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 111 HIS L 81 HIS ** b 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 311 HIS ** h 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.090681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.071623 restraints weight = 64740.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.074238 restraints weight = 39681.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.075972 restraints weight = 26991.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.077572 restraints weight = 20015.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.078642 restraints weight = 15494.539| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.6405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 19610 Z= 0.163 Angle : 0.712 11.353 26647 Z= 0.370 Chirality : 0.044 0.272 3268 Planarity : 0.004 0.041 3401 Dihedral : 4.112 24.477 2941 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.16), residues: 2771 helix: 1.97 (0.11), residues: 2072 sheet: -2.48 (1.07), residues: 16 loop : -0.45 (0.24), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG d 327 TYR 0.060 0.002 TYR l 68 PHE 0.061 0.002 PHE j 90 TRP 0.020 0.002 TRP b 67 HIS 0.005 0.001 HIS b 128 Details of bonding type rmsd covalent geometry : bond 0.00365 (19610) covalent geometry : angle 0.71183 (26647) hydrogen bonds : bond 0.04762 ( 1741) hydrogen bonds : angle 4.57482 ( 5118) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3939.17 seconds wall clock time: 69 minutes 35.80 seconds (4175.80 seconds total)