Starting phenix.real_space_refine on Sun Aug 24 15:15:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vqg_21349/08_2025/6vqg_21349.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vqg_21349/08_2025/6vqg_21349.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6vqg_21349/08_2025/6vqg_21349.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vqg_21349/08_2025/6vqg_21349.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vqg_21349/08_2025/6vqg_21349.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vqg_21349/08_2025/6vqg_21349.map" } resolution = 4.2 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= 0.060 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 134 5.16 5 C 13732 2.51 5 N 3383 2.21 5 O 3697 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 119 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20946 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: 3477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3477 Classifications: {'peptide': 441} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 18, 'TRANS': 422} Chain breaks: 2 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PHE:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'GLU:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 56 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: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 71} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "f" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 452 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 3, 'TRANS': 80} Chain breaks: 1 Unresolved non-hydrogen bonds: 210 Unresolved non-hydrogen angles: 271 Unresolved non-hydrogen dihedrals: 168 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'PHE:plan': 4, 'ASN:plan1': 6, 'HIS:plan': 1, 'GLU:plan': 4, 'ASP:plan': 2, 'GLN:plan1': 3, 'TYR:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 107 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: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 432 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 1, 'TRANS': 50} Time building chain proxies: 5.19, per 1000 atoms: 0.25 Number of scatterers: 20946 At special positions: 0 Unit cell: (119.78, 126.14, 160.06, 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 134 16.00 O 3697 8.00 N 3383 7.00 C 13732 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: 2.11 Conformation dependent library (CDL) restraints added in 946.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 120 helices and 3 sheets defined 81.4% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 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: 3.887A 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: 3.742A pdb=" N LEU L 78 " --> pdb=" O VAL L 74 " (cutoff:3.500A) removed outlier: 3.668A 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 371 through 380 Processing helix chain 'a' and resid 391 through 407 removed outlier: 4.914A 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 removed outlier: 3.519A pdb=" N LEU a 452 " --> pdb=" O TYR a 448 " (cutoff:3.500A) Processing helix chain 'a' and resid 481 through 488 Processing helix chain 'a' and resid 492 through 497 removed outlier: 4.390A 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: 4.568A pdb=" N ASN a 534 " --> pdb=" O LEU a 530 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER a 556 " --> pdb=" O GLY a 552 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU a 557 " --> pdb=" O VAL a 553 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N PHE a 558 " --> pdb=" O SER a 554 " (cutoff:3.500A) Processing helix chain 'a' and resid 565 through 571 removed outlier: 3.728A pdb=" N ILE a 569 " --> pdb=" O LYS a 565 " (cutoff:3.500A) Processing helix chain 'a' and resid 572 through 598 removed outlier: 4.305A pdb=" N TYR a 586 " --> pdb=" O SER a 582 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU a 587 " --> pdb=" O LEU a 583 " (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 667 removed outlier: 3.707A pdb=" N VAL a 648 " --> pdb=" O ALA a 644 " (cutoff:3.500A) Proline residue: a 649 - end of helix removed outlier: 5.751A 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 Processing helix chain 'a' and resid 739 through 759 removed outlier: 4.214A 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 removed outlier: 3.518A pdb=" N PHE a 778 " --> pdb=" O LEU a 774 " (cutoff:3.500A) 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: 3.618A pdb=" N SER b 61 " --> pdb=" O ALA b 57 " (cutoff:3.500A) removed outlier: 3.567A 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: 4.221A pdb=" N LYS b 89 " --> pdb=" O ARG b 85 " (cutoff:3.500A) Processing helix chain 'b' and resid 91 through 113 removed outlier: 3.760A pdb=" N GLY b 104 " --> pdb=" O VAL b 100 " (cutoff:3.500A) Processing helix chain 'b' and resid 127 through 169 removed outlier: 3.861A pdb=" N GLN b 168 " --> pdb=" O LEU b 164 " (cutoff:3.500A) Processing helix chain 'b' and resid 172 through 198 removed outlier: 4.093A pdb=" N ILE b 178 " --> pdb=" O VAL b 174 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N VAL b 179 " --> pdb=" O LYS b 175 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLU b 180 " --> pdb=" O ILE b 176 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY b 187 " --> pdb=" O GLY b 183 " (cutoff:3.500A) Processing helix chain 'c' and resid 416 through 442 Processing helix chain 'd' and resid 8 through 25 removed outlier: 4.241A pdb=" N ASP d 12 " --> pdb=" O TYR d 8 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N TYR d 15 " --> pdb=" O VAL d 11 " (cutoff:3.500A) removed outlier: 5.156A 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: 4.715A pdb=" N PHE d 96 " --> pdb=" O PRO d 92 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE d 100 " --> pdb=" O PHE d 96 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N TYR d 104 " --> pdb=" O ILE d 100 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP d 107 " --> pdb=" O SER d 103 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR d 114 " --> pdb=" O ILE d 110 " (cutoff:3.500A) removed outlier: 3.801A 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: 4.209A pdb=" N ALA d 162 " --> pdb=" O PRO d 159 " (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: 3.608A 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: 4.448A 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 339 removed outlier: 3.611A 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 Processing helix chain 'f' and resid 8 through 36 Processing helix chain 'f' and resid 54 through 90 removed outlier: 4.191A pdb=" N ILE f 58 " --> pdb=" O GLY f 54 " (cutoff:3.500A) Processing helix chain 'g' and resid 10 through 46 removed outlier: 3.645A pdb=" N PHE g 14 " --> pdb=" O TYR g 10 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY g 15 " --> pdb=" O SER g 11 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER g 26 " --> pdb=" O ALA g 22 " (cutoff:3.500A) removed outlier: 3.964A 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 removed outlier: 3.543A pdb=" N ARG g 119 " --> pdb=" O ASP g 115 " (cutoff:3.500A) Processing helix chain 'g' and resid 127 through 153 removed outlier: 3.781A pdb=" N SER g 153 " --> pdb=" O ALA g 149 " (cutoff:3.500A) Processing helix chain 'h' and resid 11 through 45 removed outlier: 4.636A pdb=" N GLY h 15 " --> pdb=" O SER h 11 " (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: 4.586A pdb=" N GLY h 130 " --> pdb=" O ARG h 126 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY h 145 " --> pdb=" O LEU h 141 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR h 154 " --> pdb=" O LEU h 150 " (cutoff:3.500A) Processing helix chain 'i' and resid 11 through 48 removed outlier: 4.316A pdb=" N GLY i 15 " --> pdb=" O SER i 11 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET i 23 " --> pdb=" O ALA i 19 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER i 26 " --> pdb=" O ALA i 22 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL i 46 " --> pdb=" O ALA i 42 " (cutoff:3.500A) removed outlier: 3.669A 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: 3.830A pdb=" N GLN i 123 " --> pdb=" O ARG i 119 " (cutoff:3.500A) Processing helix chain 'i' and resid 126 through 154 removed outlier: 4.572A pdb=" N GLY i 130 " --> pdb=" O ARG i 126 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY i 145 " --> pdb=" O LEU i 141 " (cutoff:3.500A) Processing helix chain 'j' and resid 12 through 48 removed outlier: 3.554A pdb=" N MET j 23 " --> pdb=" O ALA j 19 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL j 46 " --> pdb=" O ALA j 42 " (cutoff:3.500A) removed outlier: 4.456A 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: 3.751A pdb=" N ILE j 64 " --> pdb=" O VAL j 60 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE j 65 " --> pdb=" O MET j 61 " (cutoff:3.500A) removed outlier: 4.017A 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: 4.469A pdb=" N GLY j 130 " --> pdb=" O ARG j 126 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY j 145 " --> pdb=" O LEU j 141 " (cutoff:3.500A) Processing helix chain 'k' and resid 10 through 48 removed outlier: 3.953A pdb=" N PHE k 14 " --> pdb=" O TYR k 10 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLY k 15 " --> pdb=" O SER k 11 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET k 23 " --> pdb=" O ALA k 19 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA k 43 " --> pdb=" O THR k 39 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N VAL k 46 " --> pdb=" O ALA k 42 " (cutoff:3.500A) removed outlier: 3.972A 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: 4.420A pdb=" N GLY l 15 " --> pdb=" O SER l 11 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL l 46 " --> pdb=" O ALA l 42 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N MET l 47 " --> pdb=" O ALA l 43 " (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: 3.870A pdb=" N GLN l 123 " --> pdb=" O ARG l 119 " (cutoff:3.500A) Processing helix chain 'l' and resid 126 through 155 removed outlier: 4.339A pdb=" N GLY l 130 " --> pdb=" O ARG l 126 " (cutoff:3.500A) Processing helix chain 'm' and resid 10 through 45 removed outlier: 3.608A 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: 4.677A 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: 3.944A pdb=" N GLN m 123 " --> pdb=" O ARG m 119 " (cutoff:3.500A) Processing helix chain 'm' and resid 126 through 154 removed outlier: 4.523A pdb=" N GLY m 130 " --> pdb=" O ARG m 126 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE m 137 " --> pdb=" O LEU m 133 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR m 154 " --> pdb=" O LEU m 150 " (cutoff:3.500A) Processing helix chain 'n' and resid 10 through 46 removed outlier: 4.389A pdb=" N PHE n 14 " --> pdb=" O TYR n 10 " (cutoff:3.500A) removed outlier: 4.274A 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: 3.992A 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 Processing helix chain 'n' and resid 86 through 123 removed outlier: 3.622A pdb=" N ARG n 119 " --> pdb=" O ASP n 115 " (cutoff:3.500A) Processing helix chain 'n' and resid 126 through 154 removed outlier: 4.652A pdb=" N GLY n 130 " --> pdb=" O ARG n 126 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY n 145 " --> pdb=" O LEU n 141 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR n 154 " --> pdb=" O LEU n 150 " (cutoff:3.500A) Processing helix chain 'o' and resid 11 through 48 removed outlier: 4.410A pdb=" N GLY o 15 " --> pdb=" O SER o 11 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET o 23 " --> pdb=" O ALA o 19 " (cutoff:3.500A) removed outlier: 3.987A 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: 3.510A pdb=" N VAL o 72 " --> pdb=" O TYR o 68 " (cutoff:3.500A) Processing helix chain 'o' and resid 86 through 124 Processing helix chain 'o' and resid 126 through 154 removed outlier: 4.696A pdb=" N GLY o 130 " --> pdb=" O ARG o 126 " (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: 8.521A pdb=" N LEU L 37 " --> pdb=" O ILE L 8 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL L 10 " --> pdb=" O LEU L 37 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA L 9 " --> pdb=" O LEU L 65 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N ASN L 67 " --> pdb=" O ALA L 9 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N ILE L 11 " --> pdb=" O ASN L 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 362 through 363 1744 hydrogen bonds defined for protein. 5124 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: 4.08 Time building geometry restraints manager: 2.67 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: 3287 1.30 - 1.43: 5485 1.43 - 1.56: 12346 1.56 - 1.68: 0 1.68 - 1.81: 248 Bond restraints: 21366 Sorted by residual: bond pdb=" C PRO H 107 " pdb=" O PRO H 107 " ideal model delta sigma weight residual 1.233 1.172 0.061 1.13e-02 7.83e+03 2.93e+01 bond pdb=" N PRO c 417 " pdb=" CD PRO c 417 " ideal model delta sigma weight residual 1.473 1.541 -0.068 1.40e-02 5.10e+03 2.39e+01 bond pdb=" N PRO L 86 " pdb=" CD PRO L 86 " ideal model delta sigma weight residual 1.473 1.538 -0.065 1.40e-02 5.10e+03 2.15e+01 bond pdb=" N GLN h 124 " pdb=" CA GLN h 124 " ideal model delta sigma weight residual 1.462 1.418 0.044 1.06e-02 8.90e+03 1.70e+01 bond pdb=" CA ALA L 109 " pdb=" CB ALA L 109 " ideal model delta sigma weight residual 1.530 1.474 0.056 1.43e-02 4.89e+03 1.53e+01 ... (remaining 21361 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 27387 2.17 - 4.34: 1434 4.34 - 6.52: 117 6.52 - 8.69: 22 8.69 - 10.86: 6 Bond angle restraints: 28966 Sorted by residual: angle pdb=" N GLN d 171 " pdb=" CA GLN d 171 " pdb=" C GLN d 171 " ideal model delta sigma weight residual 111.28 102.51 8.77 1.09e+00 8.42e-01 6.48e+01 angle pdb=" C ILE L 91 " pdb=" N PRO L 92 " pdb=" CA PRO L 92 " ideal model delta sigma weight residual 119.76 127.78 -8.02 1.03e+00 9.43e-01 6.07e+01 angle pdb=" N SER L 104 " pdb=" CA SER L 104 " pdb=" C SER L 104 " ideal model delta sigma weight residual 111.36 103.09 8.27 1.09e+00 8.42e-01 5.76e+01 angle pdb=" C ARG L 108 " pdb=" N ALA L 109 " pdb=" CA ALA L 109 " ideal model delta sigma weight residual 122.72 112.37 10.35 1.38e+00 5.25e-01 5.63e+01 angle pdb=" C ASN m 7 " pdb=" N PRO m 8 " pdb=" CA PRO m 8 " ideal model delta sigma weight residual 119.76 127.21 -7.45 1.03e+00 9.43e-01 5.23e+01 ... (remaining 28961 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 11933 17.95 - 35.89: 352 35.89 - 53.84: 99 53.84 - 71.78: 19 71.78 - 89.73: 28 Dihedral angle restraints: 12431 sinusoidal: 4505 harmonic: 7926 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 -159.85 -20.15 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA MET h 44 " pdb=" C MET h 44 " pdb=" N SER h 45 " pdb=" CA SER h 45 " ideal model delta harmonic sigma weight residual -180.00 -161.92 -18.08 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" N PRO d 5 " pdb=" C PRO d 5 " pdb=" CA PRO d 5 " pdb=" CB PRO d 5 " ideal model delta harmonic sigma weight residual 115.10 106.48 8.62 0 2.50e+00 1.60e-01 1.19e+01 ... (remaining 12428 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2325 0.065 - 0.129: 944 0.129 - 0.194: 75 0.194 - 0.259: 78 0.259 - 0.324: 8 Chirality restraints: 3430 Sorted by residual: chirality pdb=" CA TYR h 68 " pdb=" N TYR h 68 " pdb=" C TYR h 68 " pdb=" CB TYR h 68 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.62e+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 2.82 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CA TYR n 68 " pdb=" N TYR n 68 " pdb=" C TYR n 68 " pdb=" CB TYR n 68 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.23e+00 ... (remaining 3427 not shown) Planarity restraints: 3602 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 2.11e+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 4.34e-02 1.89e+01 pdb=" C ASN k 7 " 0.075 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 3.98e-02 1.58e+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 3599 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3292 2.76 - 3.29: 23730 3.29 - 3.83: 35865 3.83 - 4.36: 43948 4.36 - 4.90: 71613 Nonbonded interactions: 178448 Sorted by model distance: nonbonded pdb=" OG SER a 738 " pdb=" NH1 ARG a 741 " model vdw 2.219 3.120 nonbonded pdb=" NZ LYS H 55 " pdb=" OD2 ASP L 103 " model vdw 2.332 3.120 nonbonded pdb=" NZ LYS H 55 " pdb=" OD2 ASP L 99 " model vdw 2.352 3.120 nonbonded pdb=" OG SER a 738 " pdb=" OE2 GLU a 810 " model vdw 2.355 3.040 nonbonded pdb=" O SER m 11 " pdb=" OG SER m 89 " model vdw 2.356 3.040 ... (remaining 178443 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: 3.810 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: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 20.640 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 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:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 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 0.068 21366 Z= 0.528 Angle : 0.982 10.859 28966 Z= 0.743 Chirality : 0.069 0.324 3430 Planarity : 0.005 0.046 3602 Dihedral : 11.367 89.727 7401 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.56 % Favored : 97.19 % Rotamer: Outliers : 1.36 % Allowed : 0.94 % Favored : 97.70 % 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 aren not related in a simple way. whole: 0.61 (0.15), residues: 2771 helix: 0.83 (0.10), residues: 2145 sheet: -0.53 (1.08), residues: 18 loop : -0.83 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG d 182 TYR 0.011 0.001 TYR d 33 PHE 0.011 0.000 PHE n 137 TRP 0.001 0.000 TRP b 49 HIS 0.000 0.000 HIS d 340 Details of bonding type rmsd covalent geometry : bond 0.00831 (21366) covalent geometry : angle 0.98155 (28966) hydrogen bonds : bond 0.19174 ( 1744) hydrogen bonds : angle 6.88546 ( 5124) *********************** 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 1497 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 1468 time to evaluate : 0.812 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 56 MET cc_start: 0.9149 (tmm) cc_final: 0.8930 (tmm) REVERT: H 61 VAL cc_start: 0.8818 (t) cc_final: 0.8351 (p) REVERT: H 62 MET cc_start: 0.8682 (mmt) cc_final: 0.8347 (mmp) REVERT: H 67 PHE cc_start: 0.8705 (t80) cc_final: 0.8154 (t80) REVERT: H 68 SER cc_start: 0.9256 (m) cc_final: 0.8466 (t) REVERT: H 71 GLU cc_start: 0.9263 (tt0) cc_final: 0.8924 (tt0) REVERT: H 91 GLN cc_start: 0.7634 (tt0) cc_final: 0.7141 (tt0) REVERT: H 93 LYS cc_start: 0.8280 (mttt) cc_final: 0.8017 (mmmt) REVERT: H 112 TYR cc_start: 0.9236 (t80) cc_final: 0.8413 (t80) REVERT: H 140 LYS cc_start: 0.9388 (tttt) cc_final: 0.9085 (ttpt) REVERT: L 11 ILE cc_start: 0.9298 (mt) cc_final: 0.8985 (mt) REVERT: L 28 LEU cc_start: 0.7460 (mt) cc_final: 0.7010 (mp) REVERT: L 35 ASN cc_start: 0.8190 (p0) cc_final: 0.7368 (p0) REVERT: L 38 VAL cc_start: 0.8841 (t) cc_final: 0.8554 (p) REVERT: L 40 GLU cc_start: 0.9270 (mt-10) cc_final: 0.8772 (mp0) REVERT: L 46 ASN cc_start: 0.8613 (m-40) cc_final: 0.8367 (m-40) REVERT: L 49 GLU cc_start: 0.8894 (tt0) cc_final: 0.8644 (pp20) REVERT: L 67 ASN cc_start: 0.9101 (m110) cc_final: 0.8498 (p0) REVERT: L 68 GLN cc_start: 0.7719 (tt0) cc_final: 0.7387 (tp40) REVERT: L 78 LEU cc_start: 0.8494 (mp) cc_final: 0.7978 (tt) REVERT: L 89 LEU cc_start: 0.7837 (mt) cc_final: 0.7528 (mp) REVERT: L 90 GLU cc_start: 0.7929 (mt-10) cc_final: 0.6575 (mt-10) REVERT: L 99 ASP cc_start: 0.6889 (p0) cc_final: 0.6279 (p0) REVERT: L 105 ILE cc_start: 0.8764 (mm) cc_final: 0.8475 (mp) REVERT: a 9 GLU cc_start: 0.6111 (mp0) cc_final: 0.5842 (pp20) REVERT: a 397 ILE cc_start: 0.8826 (mm) cc_final: 0.8624 (tp) REVERT: a 401 PHE cc_start: 0.9148 (t80) cc_final: 0.8648 (t80) REVERT: a 447 ARG cc_start: 0.8471 (ptt-90) cc_final: 0.7623 (ptt-90) REVERT: a 458 ILE cc_start: 0.9235 (mt) cc_final: 0.8973 (mm) REVERT: a 538 MET cc_start: 0.8621 (ttt) cc_final: 0.7976 (tmm) REVERT: a 543 ILE cc_start: 0.9227 (mt) cc_final: 0.9001 (mt) REVERT: a 580 MET cc_start: 0.9557 (ttm) cc_final: 0.9223 (ttm) REVERT: a 634 LYS cc_start: 0.8077 (mttt) cc_final: 0.7492 (tttp) REVERT: a 642 VAL cc_start: 0.9444 (t) cc_final: 0.8840 (p) REVERT: a 717 THR cc_start: 0.9027 (m) cc_final: 0.8776 (p) REVERT: a 721 GLN cc_start: 0.8802 (tp40) cc_final: 0.8164 (tp-100) REVERT: a 729 CYS cc_start: 0.9140 (m) cc_final: 0.8711 (p) REVERT: a 732 CYS cc_start: 0.8826 (m) cc_final: 0.8574 (p) REVERT: a 754 GLU cc_start: 0.9535 (tt0) cc_final: 0.8958 (pt0) REVERT: a 804 LEU cc_start: 0.9391 (tp) cc_final: 0.9152 (tt) REVERT: a 808 TRP cc_start: 0.8935 (m-10) cc_final: 0.8665 (m-10) REVERT: a 809 VAL cc_start: 0.8580 (t) cc_final: 0.8251 (t) REVERT: a 810 GLU cc_start: 0.7526 (mp0) cc_final: 0.7069 (mp0) REVERT: a 814 LYS cc_start: 0.7679 (mmtm) cc_final: 0.7445 (mmtm) REVERT: a 815 PHE cc_start: 0.8255 (p90) cc_final: 0.7979 (p90) REVERT: b 8 TYR cc_start: 0.8963 (m-80) cc_final: 0.8423 (m-80) REVERT: b 19 MET cc_start: 0.8799 (mtp) cc_final: 0.8436 (mtp) REVERT: b 24 ILE cc_start: 0.9418 (tt) cc_final: 0.9214 (tp) REVERT: b 25 CYS cc_start: 0.9120 (m) cc_final: 0.8747 (t) REVERT: b 34 ARG cc_start: 0.8285 (mmm160) cc_final: 0.6383 (tpt170) REVERT: b 44 THR cc_start: 0.8011 (m) cc_final: 0.7671 (m) REVERT: b 48 MET cc_start: 0.9046 (ttt) cc_final: 0.8423 (tmm) REVERT: b 52 LEU cc_start: 0.9601 (mt) cc_final: 0.9181 (mt) REVERT: b 74 SER cc_start: 0.9506 (m) cc_final: 0.9120 (p) REVERT: b 75 SER cc_start: 0.9743 (m) cc_final: 0.9531 (p) REVERT: b 82 LYS cc_start: 0.8886 (mmtt) cc_final: 0.8500 (mmtp) REVERT: b 88 THR cc_start: 0.7359 (m) cc_final: 0.7064 (m) REVERT: b 90 ASN cc_start: 0.8723 (m-40) cc_final: 0.8340 (m-40) REVERT: b 92 VAL cc_start: 0.9026 (p) cc_final: 0.8769 (m) REVERT: b 93 SER cc_start: 0.9503 (p) cc_final: 0.8973 (p) REVERT: b 96 PHE cc_start: 0.8584 (m-80) cc_final: 0.8148 (m-80) REVERT: b 107 MET cc_start: 0.9506 (tpt) cc_final: 0.8901 (tpt) REVERT: b 130 ASN cc_start: 0.9039 (m-40) cc_final: 0.8836 (m-40) REVERT: b 137 MET cc_start: 0.9270 (mtp) cc_final: 0.8952 (ttm) REVERT: b 151 CYS cc_start: 0.9323 (t) cc_final: 0.8987 (t) REVERT: b 154 CYS cc_start: 0.9411 (t) cc_final: 0.9182 (t) REVERT: b 166 ASP cc_start: 0.8857 (t70) cc_final: 0.8638 (t0) REVERT: b 169 ASN cc_start: 0.8966 (t0) cc_final: 0.8648 (t0) REVERT: b 172 LEU cc_start: 0.9089 (mt) cc_final: 0.8258 (mt) REVERT: b 180 GLU cc_start: 0.9709 (mt-10) cc_final: 0.9254 (mt-10) REVERT: b 192 ILE cc_start: 0.9457 (mt) cc_final: 0.9106 (tp) REVERT: c 419 ILE cc_start: 0.8777 (mt) cc_final: 0.8569 (mt) REVERT: c 439 MET cc_start: 0.9498 (mmm) cc_final: 0.9155 (mmm) REVERT: d 50 GLN cc_start: 0.8661 (mt0) cc_final: 0.8304 (tp40) REVERT: d 69 VAL cc_start: 0.9381 (t) cc_final: 0.9159 (p) REVERT: d 81 GLU cc_start: 0.9067 (mt-10) cc_final: 0.8743 (mm-30) REVERT: d 88 HIS cc_start: 0.8699 (m-70) cc_final: 0.8230 (m-70) REVERT: d 91 GLU cc_start: 0.8787 (tt0) cc_final: 0.8382 (tm-30) REVERT: d 98 ASP cc_start: 0.9061 (m-30) cc_final: 0.8394 (t70) REVERT: d 105 MET cc_start: 0.9059 (mtt) cc_final: 0.8539 (mpp) REVERT: d 106 ILE cc_start: 0.9432 (mt) cc_final: 0.9221 (mt) REVERT: d 108 ASN cc_start: 0.9183 (m-40) cc_final: 0.8726 (m-40) REVERT: d 118 HIS cc_start: 0.9065 (m-70) cc_final: 0.8718 (m90) REVERT: d 124 GLU cc_start: 0.8904 (mt-10) cc_final: 0.8634 (mp0) REVERT: d 128 LYS cc_start: 0.9176 (mmtt) cc_final: 0.8599 (mmmm) REVERT: d 191 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8479 (mm-30) REVERT: d 221 PHE cc_start: 0.8406 (m-80) cc_final: 0.7900 (m-80) REVERT: d 236 ASP cc_start: 0.9309 (m-30) cc_final: 0.8983 (t0) REVERT: d 241 PHE cc_start: 0.8192 (m-10) cc_final: 0.7676 (m-10) REVERT: d 244 CYS cc_start: 0.7573 (m) cc_final: 0.7129 (m) REVERT: d 260 ASP cc_start: 0.8196 (t70) cc_final: 0.7950 (t70) REVERT: d 262 GLU cc_start: 0.9068 (tt0) cc_final: 0.8614 (tm-30) REVERT: d 263 GLN cc_start: 0.9292 (mt0) cc_final: 0.8934 (mt0) REVERT: d 266 ASN cc_start: 0.8832 (m-40) cc_final: 0.8509 (m110) REVERT: d 290 LEU cc_start: 0.8433 (tp) cc_final: 0.8176 (tp) REVERT: d 292 ASP cc_start: 0.8971 (m-30) cc_final: 0.8058 (t0) REVERT: d 297 HIS cc_start: 0.8600 (t70) cc_final: 0.8337 (t70) REVERT: d 312 PHE cc_start: 0.8263 (m-10) cc_final: 0.8045 (m-10) REVERT: d 340 HIS cc_start: 0.7331 (m-70) cc_final: 0.6694 (m-70) REVERT: e 13 PHE cc_start: 0.7526 (m-80) cc_final: 0.7070 (m-10) REVERT: e 47 CYS cc_start: 0.7745 (p) cc_final: 0.7440 (p) REVERT: e 54 ILE cc_start: 0.9649 (mt) cc_final: 0.9296 (mt) REVERT: g 25 PHE cc_start: 0.9053 (m-10) cc_final: 0.8747 (m-80) REVERT: g 41 ILE cc_start: 0.9545 (mt) cc_final: 0.9324 (mm) REVERT: g 54 LYS cc_start: 0.8531 (mttt) cc_final: 0.8255 (mmmt) REVERT: g 88 ARG cc_start: 0.8824 (mmm160) cc_final: 0.8294 (tpm170) REVERT: g 91 LEU cc_start: 0.9186 (mt) cc_final: 0.8687 (mt) REVERT: g 144 TYR cc_start: 0.8928 (m-10) cc_final: 0.8609 (m-80) REVERT: g 152 LEU cc_start: 0.8970 (mt) cc_final: 0.8553 (tp) REVERT: h 10 TYR cc_start: 0.9107 (p90) cc_final: 0.8682 (p90) REVERT: h 13 PHE cc_start: 0.9002 (t80) cc_final: 0.8483 (t80) REVERT: h 17 MET cc_start: 0.9175 (mmp) cc_final: 0.8897 (mmm) REVERT: h 41 ILE cc_start: 0.9237 (mt) cc_final: 0.8960 (mt) REVERT: h 85 THR cc_start: 0.9410 (p) cc_final: 0.9179 (p) REVERT: h 91 LEU cc_start: 0.8919 (mt) cc_final: 0.8585 (mt) REVERT: h 108 PHE cc_start: 0.9579 (m-80) cc_final: 0.9352 (m-80) REVERT: h 139 GLU cc_start: 0.8913 (mm-30) cc_final: 0.8100 (mm-30) REVERT: i 23 MET cc_start: 0.9340 (tpt) cc_final: 0.9125 (ttm) REVERT: i 47 MET cc_start: 0.8721 (mmm) cc_final: 0.8450 (mmp) REVERT: i 52 ILE cc_start: 0.9624 (tt) cc_final: 0.9270 (mm) REVERT: i 53 MET cc_start: 0.8728 (mmp) cc_final: 0.8498 (ptt) REVERT: j 44 MET cc_start: 0.7800 (tmm) cc_final: 0.7358 (tmm) REVERT: j 51 LEU cc_start: 0.8815 (mt) cc_final: 0.8502 (mt) REVERT: j 64 ILE cc_start: 0.8621 (mt) cc_final: 0.8044 (mt) REVERT: j 68 TYR cc_start: 0.8744 (m-10) cc_final: 0.8298 (m-80) REVERT: j 72 VAL cc_start: 0.9808 (t) cc_final: 0.9585 (p) REVERT: j 75 LEU cc_start: 0.9367 (tp) cc_final: 0.9036 (tp) REVERT: j 84 ILE cc_start: 0.8355 (mm) cc_final: 0.7767 (mm) REVERT: j 88 ARG cc_start: 0.7946 (ttm-80) cc_final: 0.7533 (mmm160) REVERT: j 91 LEU cc_start: 0.9517 (mt) cc_final: 0.9223 (mp) REVERT: j 121 THR cc_start: 0.8308 (m) cc_final: 0.7854 (p) REVERT: j 127 LEU cc_start: 0.9164 (tp) cc_final: 0.8852 (tt) REVERT: j 140 VAL cc_start: 0.9715 (t) cc_final: 0.9425 (t) REVERT: j 148 VAL cc_start: 0.9450 (t) cc_final: 0.9248 (p) REVERT: k 23 MET cc_start: 0.9072 (tpt) cc_final: 0.8831 (tpt) REVERT: k 54 LYS cc_start: 0.8210 (mttt) cc_final: 0.7770 (mtpp) REVERT: k 55 SER cc_start: 0.8637 (p) cc_final: 0.8220 (p) REVERT: k 76 ILE cc_start: 0.9278 (mt) cc_final: 0.8484 (tt) REVERT: k 85 THR cc_start: 0.9279 (p) cc_final: 0.8924 (p) REVERT: k 119 ARG cc_start: 0.8673 (mtt-85) cc_final: 0.8261 (mtt-85) REVERT: k 121 THR cc_start: 0.9018 (m) cc_final: 0.8674 (p) REVERT: k 127 LEU cc_start: 0.8767 (mp) cc_final: 0.7904 (mp) REVERT: k 131 MET cc_start: 0.9028 (ttp) cc_final: 0.8770 (ptm) REVERT: l 12 SER cc_start: 0.9487 (p) cc_final: 0.9238 (t) REVERT: l 17 MET cc_start: 0.8927 (mmm) cc_final: 0.8629 (mmm) REVERT: l 44 MET cc_start: 0.8591 (tmm) cc_final: 0.8185 (tmm) REVERT: l 52 ILE cc_start: 0.9187 (mt) cc_final: 0.8733 (mt) REVERT: l 53 MET cc_start: 0.8942 (mmp) cc_final: 0.8712 (tmm) REVERT: l 54 LYS cc_start: 0.8796 (mttt) cc_final: 0.8459 (mmtt) REVERT: l 80 LEU cc_start: 0.9309 (tp) cc_final: 0.8730 (tp) REVERT: l 82 ASP cc_start: 0.8950 (p0) cc_final: 0.8724 (t70) REVERT: l 91 LEU cc_start: 0.9387 (mt) cc_final: 0.8996 (mt) REVERT: l 113 VAL cc_start: 0.9474 (t) cc_final: 0.9225 (p) REVERT: l 118 VAL cc_start: 0.9697 (t) cc_final: 0.9326 (m) REVERT: l 119 ARG cc_start: 0.8311 (mtt-85) cc_final: 0.8027 (mtt90) REVERT: l 124 GLN cc_start: 0.8930 (tp-100) cc_final: 0.8478 (tm-30) REVERT: l 131 MET cc_start: 0.9104 (ttp) cc_final: 0.8569 (ttp) REVERT: l 152 LEU cc_start: 0.9338 (mt) cc_final: 0.8790 (tp) REVERT: m 8 PRO cc_start: 0.9113 (Cg_exo) cc_final: 0.8529 (Cg_endo) REVERT: m 17 MET cc_start: 0.9106 (mmm) cc_final: 0.8859 (mmm) REVERT: m 21 SER cc_start: 0.9284 (m) cc_final: 0.8968 (p) REVERT: m 41 ILE cc_start: 0.9560 (mt) cc_final: 0.9320 (mt) REVERT: m 52 ILE cc_start: 0.8108 (mt) cc_final: 0.7806 (mt) REVERT: m 57 ILE cc_start: 0.8737 (mt) cc_final: 0.8441 (mp) REVERT: m 74 VAL cc_start: 0.9575 (t) cc_final: 0.9302 (p) REVERT: m 81 THR cc_start: 0.8642 (t) cc_final: 0.8331 (m) REVERT: m 112 ILE cc_start: 0.8868 (mt) cc_final: 0.8592 (tp) REVERT: m 119 ARG cc_start: 0.8872 (mtt-85) cc_final: 0.8498 (mtt180) REVERT: m 126 ARG cc_start: 0.8927 (mtt90) cc_final: 0.8726 (mtp85) REVERT: m 135 LEU cc_start: 0.9607 (mt) cc_final: 0.9406 (mt) REVERT: m 139 GLU cc_start: 0.9377 (tt0) cc_final: 0.8909 (tt0) REVERT: m 153 SER cc_start: 0.9051 (p) cc_final: 0.8808 (p) REVERT: n 13 PHE cc_start: 0.8891 (t80) cc_final: 0.8444 (t80) REVERT: n 36 LYS cc_start: 0.8605 (mmtt) cc_final: 0.8196 (mttt) REVERT: n 53 MET cc_start: 0.9358 (mmp) cc_final: 0.9105 (mmm) REVERT: n 79 SER cc_start: 0.8634 (m) cc_final: 0.8319 (t) REVERT: n 88 ARG cc_start: 0.8511 (ttm-80) cc_final: 0.8191 (mmm-85) REVERT: n 90 PHE cc_start: 0.9605 (m-80) cc_final: 0.9305 (m-10) REVERT: n 99 VAL cc_start: 0.9803 (p) cc_final: 0.9546 (m) REVERT: n 126 ARG cc_start: 0.8238 (mtt-85) cc_final: 0.7966 (mmm160) REVERT: n 127 LEU cc_start: 0.9345 (tp) cc_final: 0.9134 (tp) REVERT: n 129 VAL cc_start: 0.9014 (t) cc_final: 0.8651 (t) REVERT: n 131 MET cc_start: 0.9299 (ttp) cc_final: 0.8953 (ttt) REVERT: n 144 TYR cc_start: 0.9112 (m-10) cc_final: 0.8780 (m-10) REVERT: o 6 ASN cc_start: 0.9349 (p0) cc_final: 0.9142 (p0) REVERT: o 39 THR cc_start: 0.9294 (m) cc_final: 0.9013 (m) REVERT: o 53 MET cc_start: 0.9199 (mmp) cc_final: 0.8660 (tmm) REVERT: o 61 MET cc_start: 0.7938 (mmp) cc_final: 0.7646 (mmp) REVERT: o 90 PHE cc_start: 0.9499 (m-80) cc_final: 0.9209 (m-80) REVERT: o 124 GLN cc_start: 0.8337 (tp-100) cc_final: 0.8050 (tm-30) REVERT: o 144 TYR cc_start: 0.9238 (m-10) cc_final: 0.8986 (m-10) REVERT: p 313 ILE cc_start: 0.9264 (mt) cc_final: 0.8868 (mt) REVERT: p 330 ASN cc_start: 0.9457 (t0) cc_final: 0.9154 (t0) outliers start: 29 outliers final: 12 residues processed: 1474 average time/residue: 0.1455 time to fit residues: 338.7258 Evaluate side-chains 1010 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 998 time to evaluate : 0.773 ------------------------------------------------------------------------------- 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: 0.8980 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 560 HIS a 601 HIS ** a 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 90 ASN d 88 HIS d 142 ASN d 297 HIS d 328 ASN ** d 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 33 ASN i 78 ASN j 92 GLN ** m 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 92 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.086022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.074133 restraints weight = 71777.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.076879 restraints weight = 39672.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.078729 restraints weight = 25062.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.080083 restraints weight = 17139.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.080996 restraints weight = 12540.539| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 21366 Z= 0.197 Angle : 0.705 11.341 28966 Z= 0.383 Chirality : 0.044 0.192 3430 Planarity : 0.005 0.066 3602 Dihedral : 4.147 19.543 2978 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.28 % Allowed : 1.88 % Favored : 97.84 % 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 aren not related in a simple way. whole: 2.11 (0.15), residues: 2771 helix: 2.01 (0.11), residues: 2088 sheet: -0.42 (1.02), residues: 18 loop : -0.51 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG a 741 TYR 0.033 0.002 TYR j 144 PHE 0.040 0.002 PHE b 189 TRP 0.023 0.002 TRP b 16 HIS 0.009 0.002 HIS d 48 Details of bonding type rmsd covalent geometry : bond 0.00391 (21366) covalent geometry : angle 0.70511 (28966) hydrogen bonds : bond 0.07094 ( 1744) hydrogen bonds : angle 4.95861 ( 5124) *********************** 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 1225 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 1219 time to evaluate : 0.814 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 54 THR cc_start: 0.9079 (m) cc_final: 0.8857 (m) REVERT: H 56 MET cc_start: 0.9197 (tmm) cc_final: 0.8935 (tmm) REVERT: H 58 MET cc_start: 0.9018 (tmm) cc_final: 0.8607 (tmm) REVERT: H 61 VAL cc_start: 0.9027 (t) cc_final: 0.8629 (p) REVERT: H 62 MET cc_start: 0.8819 (mmt) cc_final: 0.8583 (mmp) REVERT: H 64 GLU cc_start: 0.8640 (tp30) cc_final: 0.8315 (tp30) REVERT: H 67 PHE cc_start: 0.8783 (t80) cc_final: 0.8490 (t80) REVERT: H 68 SER cc_start: 0.9348 (m) cc_final: 0.8737 (t) REVERT: H 91 GLN cc_start: 0.8613 (tt0) cc_final: 0.8018 (tt0) REVERT: H 93 LYS cc_start: 0.8873 (mttt) cc_final: 0.8477 (mtpp) REVERT: H 137 ASN cc_start: 0.9038 (m110) cc_final: 0.8618 (m110) REVERT: H 140 LYS cc_start: 0.9453 (tttt) cc_final: 0.9099 (ttpt) REVERT: L 38 VAL cc_start: 0.9326 (t) cc_final: 0.9088 (p) REVERT: L 40 GLU cc_start: 0.8959 (mt-10) cc_final: 0.8627 (mp0) REVERT: L 89 LEU cc_start: 0.8655 (mt) cc_final: 0.8446 (mp) REVERT: L 90 GLU cc_start: 0.7446 (mt-10) cc_final: 0.6606 (mt-10) REVERT: L 95 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7952 (tm-30) REVERT: L 99 ASP cc_start: 0.6910 (p0) cc_final: 0.5847 (t0) REVERT: a 9 GLU cc_start: 0.6577 (mp0) cc_final: 0.6034 (pp20) REVERT: a 388 GLU cc_start: 0.8039 (tp30) cc_final: 0.7516 (tt0) REVERT: a 397 ILE cc_start: 0.9370 (mm) cc_final: 0.9154 (tp) REVERT: a 401 PHE cc_start: 0.8984 (t80) cc_final: 0.8580 (t80) REVERT: a 409 ASP cc_start: 0.7997 (t0) cc_final: 0.7769 (t70) REVERT: a 447 ARG cc_start: 0.8823 (ptt-90) cc_final: 0.7987 (ptt90) REVERT: a 538 MET cc_start: 0.9027 (ttt) cc_final: 0.8384 (tmm) REVERT: a 615 ASN cc_start: 0.8912 (t0) cc_final: 0.8685 (t0) REVERT: a 643 VAL cc_start: 0.8924 (t) cc_final: 0.8420 (p) REVERT: a 646 LEU cc_start: 0.9142 (mp) cc_final: 0.8805 (pp) REVERT: a 647 CYS cc_start: 0.8977 (m) cc_final: 0.8628 (m) REVERT: a 651 MET cc_start: 0.8649 (mmm) cc_final: 0.8063 (mmm) REVERT: a 721 GLN cc_start: 0.8979 (tp40) cc_final: 0.8154 (tp-100) REVERT: a 732 CYS cc_start: 0.8259 (m) cc_final: 0.7545 (m) REVERT: a 794 MET cc_start: 0.9501 (tmm) cc_final: 0.9163 (tmm) REVERT: a 804 LEU cc_start: 0.9491 (tp) cc_final: 0.9235 (tp) REVERT: a 808 TRP cc_start: 0.9104 (m-10) cc_final: 0.8743 (m-10) REVERT: a 810 GLU cc_start: 0.7646 (mp0) cc_final: 0.7078 (mp0) REVERT: b 8 TYR cc_start: 0.9148 (m-80) cc_final: 0.8790 (m-80) REVERT: b 19 MET cc_start: 0.8971 (mtp) cc_final: 0.8436 (mtt) REVERT: b 24 ILE cc_start: 0.9509 (tt) cc_final: 0.9296 (tp) REVERT: b 25 CYS cc_start: 0.9217 (m) cc_final: 0.8868 (t) REVERT: b 34 ARG cc_start: 0.8027 (mmm160) cc_final: 0.6359 (tpt170) REVERT: b 36 ASP cc_start: 0.8187 (t0) cc_final: 0.7981 (t0) REVERT: b 48 MET cc_start: 0.8856 (ttt) cc_final: 0.8500 (tmm) REVERT: b 60 LEU cc_start: 0.9077 (mt) cc_final: 0.8823 (mt) REVERT: b 74 SER cc_start: 0.9505 (m) cc_final: 0.9048 (t) REVERT: b 75 SER cc_start: 0.9660 (m) cc_final: 0.9402 (p) REVERT: b 82 LYS cc_start: 0.8925 (mmtt) cc_final: 0.8502 (mmtp) REVERT: b 90 ASN cc_start: 0.8668 (m110) cc_final: 0.7242 (m110) REVERT: b 98 GLU cc_start: 0.8290 (mt-10) cc_final: 0.8083 (mt-10) REVERT: b 107 MET cc_start: 0.9183 (tpt) cc_final: 0.8500 (tpt) REVERT: b 135 TYR cc_start: 0.9020 (m-80) cc_final: 0.8737 (m-80) REVERT: b 148 ASN cc_start: 0.9778 (m110) cc_final: 0.9553 (m110) REVERT: b 151 CYS cc_start: 0.9213 (t) cc_final: 0.8955 (t) REVERT: b 172 LEU cc_start: 0.8686 (mt) cc_final: 0.8226 (mt) REVERT: c 423 LEU cc_start: 0.9366 (mt) cc_final: 0.9124 (mt) REVERT: c 435 TYR cc_start: 0.8834 (t80) cc_final: 0.8296 (t80) REVERT: c 439 MET cc_start: 0.9478 (mmm) cc_final: 0.9128 (mmm) REVERT: d 50 GLN cc_start: 0.8696 (mt0) cc_final: 0.8394 (tp40) REVERT: d 85 MET cc_start: 0.9233 (mtp) cc_final: 0.8700 (ttp) REVERT: d 98 ASP cc_start: 0.8965 (m-30) cc_final: 0.8544 (t0) REVERT: d 110 ILE cc_start: 0.9458 (mm) cc_final: 0.9210 (mm) REVERT: d 111 LEU cc_start: 0.9489 (tp) cc_final: 0.9246 (tp) REVERT: d 124 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8389 (mp0) REVERT: d 128 LYS cc_start: 0.9197 (mmtt) cc_final: 0.8526 (mttt) REVERT: d 129 CYS cc_start: 0.8725 (m) cc_final: 0.8347 (m) REVERT: d 154 ILE cc_start: 0.9314 (mt) cc_final: 0.8995 (mt) REVERT: d 158 THR cc_start: 0.9300 (m) cc_final: 0.8896 (p) REVERT: d 176 MET cc_start: 0.8202 (mtt) cc_final: 0.7755 (mtt) REVERT: d 191 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8425 (mm-30) REVERT: d 244 CYS cc_start: 0.8222 (m) cc_final: 0.7731 (m) REVERT: d 260 ASP cc_start: 0.8627 (t70) cc_final: 0.8426 (t0) REVERT: d 263 GLN cc_start: 0.9373 (mt0) cc_final: 0.9066 (mt0) REVERT: d 297 HIS cc_start: 0.8957 (t-90) cc_final: 0.8689 (t70) REVERT: d 298 GLU cc_start: 0.9128 (tt0) cc_final: 0.8878 (tm-30) REVERT: d 340 HIS cc_start: 0.8039 (m-70) cc_final: 0.7099 (m-70) REVERT: d 344 ILE cc_start: 0.9151 (tp) cc_final: 0.8636 (mm) REVERT: e 9 PRO cc_start: 0.8212 (Cg_exo) cc_final: 0.7611 (Cg_endo) REVERT: e 13 PHE cc_start: 0.7939 (m-80) cc_final: 0.7334 (m-80) REVERT: e 47 CYS cc_start: 0.8261 (p) cc_final: 0.7767 (p) REVERT: e 54 ILE cc_start: 0.9493 (mt) cc_final: 0.9121 (mt) REVERT: e 68 LEU cc_start: 0.8894 (tp) cc_final: 0.8680 (tp) REVERT: g 10 TYR cc_start: 0.6200 (m-80) cc_final: 0.5711 (m-80) REVERT: g 61 MET cc_start: 0.8123 (mmt) cc_final: 0.7443 (mmm) REVERT: g 84 ILE cc_start: 0.8438 (mm) cc_final: 0.8217 (mm) REVERT: g 86 LEU cc_start: 0.9126 (tp) cc_final: 0.8361 (tp) REVERT: g 88 ARG cc_start: 0.8552 (mmm160) cc_final: 0.7994 (tpm170) REVERT: g 90 PHE cc_start: 0.7796 (m-80) cc_final: 0.6432 (m-80) REVERT: g 135 LEU cc_start: 0.9205 (mt) cc_final: 0.8747 (mt) REVERT: g 139 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7578 (mm-30) REVERT: g 141 LEU cc_start: 0.9490 (mt) cc_final: 0.9127 (mt) REVERT: g 144 TYR cc_start: 0.9091 (m-10) cc_final: 0.8856 (m-80) REVERT: g 151 ILE cc_start: 0.8511 (tp) cc_final: 0.8288 (tp) REVERT: g 152 LEU cc_start: 0.9233 (mt) cc_final: 0.8755 (tp) REVERT: h 10 TYR cc_start: 0.8280 (p90) cc_final: 0.7997 (p90) REVERT: h 13 PHE cc_start: 0.8686 (t80) cc_final: 0.7959 (t80) REVERT: h 17 MET cc_start: 0.8967 (mmp) cc_final: 0.8623 (mmm) REVERT: h 68 TYR cc_start: 0.9016 (m-10) cc_final: 0.8724 (m-10) REVERT: h 75 LEU cc_start: 0.8990 (mt) cc_final: 0.8776 (mt) REVERT: h 97 LEU cc_start: 0.9325 (mm) cc_final: 0.9091 (mm) REVERT: h 127 LEU cc_start: 0.9082 (tp) cc_final: 0.8659 (tp) REVERT: h 131 MET cc_start: 0.9089 (ttt) cc_final: 0.8852 (ttt) REVERT: h 152 LEU cc_start: 0.9419 (tp) cc_final: 0.9162 (tp) REVERT: i 14 PHE cc_start: 0.8805 (m-10) cc_final: 0.8584 (m-10) REVERT: i 110 ILE cc_start: 0.9552 (mt) cc_final: 0.9124 (tt) REVERT: i 119 ARG cc_start: 0.8675 (ttm110) cc_final: 0.8126 (ttm110) REVERT: i 139 GLU cc_start: 0.9195 (tp30) cc_final: 0.8932 (tp30) REVERT: j 61 MET cc_start: 0.9182 (tpp) cc_final: 0.8296 (tpp) REVERT: j 64 ILE cc_start: 0.8982 (mt) cc_final: 0.8593 (mt) REVERT: j 68 TYR cc_start: 0.9022 (m-10) cc_final: 0.8727 (m-80) REVERT: j 70 LEU cc_start: 0.9595 (tp) cc_final: 0.9386 (tp) REVERT: j 108 PHE cc_start: 0.9336 (m-80) cc_final: 0.9073 (m-80) REVERT: j 118 VAL cc_start: 0.9618 (t) cc_final: 0.8428 (p) REVERT: k 32 TYR cc_start: 0.8955 (t80) cc_final: 0.8504 (t80) REVERT: k 48 ARG cc_start: 0.8174 (mmt90) cc_final: 0.7595 (mmt90) REVERT: k 54 LYS cc_start: 0.8381 (mttt) cc_final: 0.7678 (mtpt) REVERT: k 76 ILE cc_start: 0.9296 (mt) cc_final: 0.8281 (tt) REVERT: k 80 LEU cc_start: 0.9174 (mt) cc_final: 0.8953 (mt) REVERT: k 90 PHE cc_start: 0.9041 (m-80) cc_final: 0.8581 (m-80) REVERT: k 92 GLN cc_start: 0.9107 (mt0) cc_final: 0.8454 (mt0) REVERT: k 121 THR cc_start: 0.8976 (m) cc_final: 0.8589 (p) REVERT: k 124 GLN cc_start: 0.9007 (tm-30) cc_final: 0.8426 (tm-30) REVERT: k 137 PHE cc_start: 0.8957 (m-80) cc_final: 0.8333 (m-80) REVERT: k 143 LEU cc_start: 0.9444 (tp) cc_final: 0.9230 (mp) REVERT: k 147 ILE cc_start: 0.9750 (mt) cc_final: 0.9521 (mt) REVERT: k 151 ILE cc_start: 0.9539 (mt) cc_final: 0.9301 (mt) REVERT: l 47 MET cc_start: 0.8076 (tmm) cc_final: 0.7851 (tmm) REVERT: l 48 ARG cc_start: 0.8885 (ptp-110) cc_final: 0.8477 (ptp-110) REVERT: l 52 ILE cc_start: 0.9395 (mt) cc_final: 0.9184 (mt) REVERT: l 54 LYS cc_start: 0.9079 (mttt) cc_final: 0.8494 (mmtt) REVERT: l 55 SER cc_start: 0.9437 (m) cc_final: 0.9078 (p) REVERT: l 61 MET cc_start: 0.8932 (mmm) cc_final: 0.7917 (mmm) REVERT: l 93 LEU cc_start: 0.9389 (tt) cc_final: 0.9185 (pp) REVERT: l 118 VAL cc_start: 0.9775 (t) cc_final: 0.9565 (m) REVERT: l 135 LEU cc_start: 0.9521 (mt) cc_final: 0.9121 (mt) REVERT: l 136 ILE cc_start: 0.9410 (OUTLIER) cc_final: 0.9170 (mp) REVERT: l 152 LEU cc_start: 0.9448 (mt) cc_final: 0.9143 (tp) REVERT: m 8 PRO cc_start: 0.9092 (Cg_exo) cc_final: 0.8862 (Cg_endo) REVERT: m 21 SER cc_start: 0.9421 (m) cc_final: 0.9192 (p) REVERT: m 44 MET cc_start: 0.8956 (ppp) cc_final: 0.8747 (ppp) REVERT: m 52 ILE cc_start: 0.9087 (mt) cc_final: 0.8804 (mt) REVERT: m 92 GLN cc_start: 0.9070 (mt0) cc_final: 0.8857 (mt0) REVERT: m 112 ILE cc_start: 0.9295 (mt) cc_final: 0.9026 (tp) REVERT: m 119 ARG cc_start: 0.8901 (mtt-85) cc_final: 0.8670 (mtt-85) REVERT: m 132 ILE cc_start: 0.9390 (mm) cc_final: 0.9072 (mm) REVERT: n 13 PHE cc_start: 0.8905 (t80) cc_final: 0.8419 (t80) REVERT: n 36 LYS cc_start: 0.8734 (mmtt) cc_final: 0.8216 (mttt) REVERT: n 51 LEU cc_start: 0.8880 (mt) cc_final: 0.8660 (mt) REVERT: n 54 LYS cc_start: 0.8909 (mttt) cc_final: 0.8324 (tttt) REVERT: n 68 TYR cc_start: 0.9455 (m-80) cc_final: 0.9124 (m-80) REVERT: n 75 LEU cc_start: 0.9118 (mt) cc_final: 0.8896 (mt) REVERT: n 80 LEU cc_start: 0.9372 (tp) cc_final: 0.8706 (mt) REVERT: n 88 ARG cc_start: 0.8261 (ttm-80) cc_final: 0.7984 (mmm-85) REVERT: o 32 TYR cc_start: 0.8130 (t80) cc_final: 0.7752 (t80) REVERT: o 44 MET cc_start: 0.8148 (ttp) cc_final: 0.7809 (ttp) REVERT: o 47 MET cc_start: 0.8525 (tpp) cc_final: 0.8211 (tpp) REVERT: o 61 MET cc_start: 0.8496 (mmp) cc_final: 0.8091 (mmp) REVERT: o 74 VAL cc_start: 0.9504 (m) cc_final: 0.9251 (p) REVERT: o 78 ASN cc_start: 0.8720 (p0) cc_final: 0.8374 (p0) REVERT: o 90 PHE cc_start: 0.9312 (m-80) cc_final: 0.8763 (m-80) REVERT: o 110 ILE cc_start: 0.9528 (mt) cc_final: 0.9288 (mt) REVERT: o 139 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8448 (mm-30) REVERT: o 144 TYR cc_start: 0.8832 (m-10) cc_final: 0.8568 (m-10) REVERT: p 305 VAL cc_start: 0.9104 (t) cc_final: 0.8664 (p) REVERT: p 313 ILE cc_start: 0.9414 (mt) cc_final: 0.9192 (mt) REVERT: p 341 ARG cc_start: 0.8754 (ptm-80) cc_final: 0.8312 (ptm-80) outliers start: 6 outliers final: 1 residues processed: 1221 average time/residue: 0.1317 time to fit residues: 257.6926 Evaluate side-chains 968 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 966 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 134 optimal weight: 6.9990 chunk 129 optimal weight: 0.5980 chunk 108 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 259 optimal weight: 6.9990 chunk 252 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 176 optimal weight: 7.9990 chunk 258 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 637 GLN b 90 ASN b 132 HIS d 48 HIS ** d 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 328 ASN ** d 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 33 ASN ** g 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 78 ASN j 124 GLN ** m 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 123 GLN ** o 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 308 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 = 0.3469 r_free = 0.3469 target = 0.085973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.074012 restraints weight = 72435.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.076753 restraints weight = 40097.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.078658 restraints weight = 25349.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.080015 restraints weight = 17309.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.080957 restraints weight = 12602.229| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.4759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 21366 Z= 0.178 Angle : 0.669 10.773 28966 Z= 0.356 Chirality : 0.043 0.394 3430 Planarity : 0.005 0.048 3602 Dihedral : 4.191 26.180 2978 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.38 % Allowed : 1.97 % Favored : 97.65 % 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 aren not related in a simple way. whole: 1.80 (0.15), residues: 2771 helix: 1.80 (0.11), residues: 2092 sheet: -1.03 (1.07), residues: 18 loop : -0.66 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 63 TYR 0.037 0.002 TYR H 138 PHE 0.030 0.002 PHE a 579 TRP 0.026 0.002 TRP b 16 HIS 0.006 0.001 HIS H 111 Details of bonding type rmsd covalent geometry : bond 0.00373 (21366) covalent geometry : angle 0.66903 (28966) hydrogen bonds : bond 0.06307 ( 1744) hydrogen bonds : angle 4.73887 ( 5124) *********************** 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 1186 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 1178 time to evaluate : 0.719 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 56 MET cc_start: 0.9205 (tmm) cc_final: 0.8899 (tmm) REVERT: H 57 LEU cc_start: 0.9447 (tt) cc_final: 0.9178 (tt) REVERT: H 58 MET cc_start: 0.9135 (tmm) cc_final: 0.8622 (tmm) REVERT: H 61 VAL cc_start: 0.9019 (t) cc_final: 0.8655 (p) REVERT: H 63 ARG cc_start: 0.8112 (ttm110) cc_final: 0.7816 (ttm110) REVERT: H 64 GLU cc_start: 0.8599 (tp30) cc_final: 0.8341 (tp30) REVERT: H 68 SER cc_start: 0.9377 (m) cc_final: 0.8711 (t) REVERT: H 91 GLN cc_start: 0.8717 (tt0) cc_final: 0.8002 (tt0) REVERT: H 93 LYS cc_start: 0.8914 (mttt) cc_final: 0.8318 (mtpp) REVERT: H 137 ASN cc_start: 0.9046 (m110) cc_final: 0.8588 (m110) REVERT: H 140 LYS cc_start: 0.9409 (tttt) cc_final: 0.9198 (ttpt) REVERT: L 38 VAL cc_start: 0.9364 (t) cc_final: 0.8872 (p) REVERT: L 40 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8571 (mp0) REVERT: L 58 ARG cc_start: 0.8233 (mtm110) cc_final: 0.7569 (ttm110) REVERT: L 89 LEU cc_start: 0.8524 (mt) cc_final: 0.8178 (mp) REVERT: L 90 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7248 (mt-10) REVERT: L 95 GLU cc_start: 0.8240 (tm-30) cc_final: 0.7888 (tm-30) REVERT: a 388 GLU cc_start: 0.8090 (tp30) cc_final: 0.7407 (tt0) REVERT: a 397 ILE cc_start: 0.9365 (mm) cc_final: 0.9114 (tp) REVERT: a 401 PHE cc_start: 0.9040 (t80) cc_final: 0.8520 (t80) REVERT: a 414 ILE cc_start: 0.9065 (mm) cc_final: 0.8841 (mm) REVERT: a 423 MET cc_start: 0.9341 (mpp) cc_final: 0.8951 (mpp) REVERT: a 467 CYS cc_start: 0.6840 (t) cc_final: 0.6602 (t) REVERT: a 519 ILE cc_start: 0.7927 (mp) cc_final: 0.7718 (mp) REVERT: a 538 MET cc_start: 0.8780 (ttt) cc_final: 0.8110 (tmm) REVERT: a 616 MET cc_start: 0.9351 (ttp) cc_final: 0.9076 (ttp) REVERT: a 621 TYR cc_start: 0.6747 (m-10) cc_final: 0.6515 (m-10) REVERT: a 634 LYS cc_start: 0.8065 (mtpt) cc_final: 0.7524 (tttm) REVERT: a 637 GLN cc_start: 0.8746 (mt0) cc_final: 0.8481 (mt0) REVERT: a 643 VAL cc_start: 0.9099 (t) cc_final: 0.8821 (p) REVERT: a 651 MET cc_start: 0.8619 (mmm) cc_final: 0.8146 (mmm) REVERT: a 721 GLN cc_start: 0.9098 (tp40) cc_final: 0.8353 (tp-100) REVERT: a 725 THR cc_start: 0.9636 (m) cc_final: 0.9379 (m) REVERT: a 759 MET cc_start: 0.8298 (mmm) cc_final: 0.7581 (tmm) REVERT: a 794 MET cc_start: 0.9469 (tmm) cc_final: 0.9266 (tmm) REVERT: a 810 GLU cc_start: 0.7923 (mp0) cc_final: 0.7310 (mp0) REVERT: b 8 TYR cc_start: 0.9166 (m-80) cc_final: 0.8844 (m-80) REVERT: b 19 MET cc_start: 0.8957 (mtp) cc_final: 0.8480 (mtt) REVERT: b 25 CYS cc_start: 0.9266 (m) cc_final: 0.8861 (t) REVERT: b 34 ARG cc_start: 0.8110 (mmm160) cc_final: 0.6324 (tpt170) REVERT: b 40 PHE cc_start: 0.6430 (m-80) cc_final: 0.6224 (m-80) REVERT: b 48 MET cc_start: 0.8944 (ttt) cc_final: 0.8603 (tmm) REVERT: b 71 ILE cc_start: 0.9687 (mm) cc_final: 0.9427 (mm) REVERT: b 74 SER cc_start: 0.9502 (m) cc_final: 0.9051 (t) REVERT: b 75 SER cc_start: 0.9681 (m) cc_final: 0.9380 (p) REVERT: b 82 LYS cc_start: 0.8943 (mmtt) cc_final: 0.8461 (mmtp) REVERT: b 85 ARG cc_start: 0.7430 (tpt170) cc_final: 0.7226 (tpt170) REVERT: b 90 ASN cc_start: 0.8017 (m-40) cc_final: 0.7580 (m-40) REVERT: b 92 VAL cc_start: 0.9178 (m) cc_final: 0.8493 (m) REVERT: b 96 PHE cc_start: 0.9010 (m-80) cc_final: 0.8553 (m-80) REVERT: b 114 MET cc_start: 0.7764 (mtm) cc_final: 0.7553 (mtm) REVERT: b 130 ASN cc_start: 0.9046 (m-40) cc_final: 0.8791 (m-40) REVERT: b 135 TYR cc_start: 0.8908 (m-80) cc_final: 0.8628 (m-80) REVERT: b 137 MET cc_start: 0.9402 (ttt) cc_final: 0.8921 (ttm) REVERT: b 148 ASN cc_start: 0.9753 (m110) cc_final: 0.9491 (m110) REVERT: b 166 ASP cc_start: 0.7987 (p0) cc_final: 0.7591 (p0) REVERT: b 169 ASN cc_start: 0.9108 (t0) cc_final: 0.8687 (t0) REVERT: b 172 LEU cc_start: 0.8588 (mt) cc_final: 0.7829 (mt) REVERT: c 420 TRP cc_start: 0.8104 (t-100) cc_final: 0.7852 (t-100) REVERT: c 423 LEU cc_start: 0.9233 (mt) cc_final: 0.8980 (mt) REVERT: c 432 ILE cc_start: 0.9339 (mt) cc_final: 0.9117 (mt) REVERT: c 439 MET cc_start: 0.9474 (mmm) cc_final: 0.9259 (mmm) REVERT: d 76 GLU cc_start: 0.8711 (tt0) cc_final: 0.8309 (tp30) REVERT: d 81 GLU cc_start: 0.8409 (mm-30) cc_final: 0.8192 (tp30) REVERT: d 85 MET cc_start: 0.9220 (mtp) cc_final: 0.8841 (ttp) REVERT: d 98 ASP cc_start: 0.8911 (m-30) cc_final: 0.8300 (t0) REVERT: d 108 ASN cc_start: 0.8934 (m110) cc_final: 0.8665 (m110) REVERT: d 110 ILE cc_start: 0.9426 (mm) cc_final: 0.9214 (mm) REVERT: d 124 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8477 (mt-10) REVERT: d 128 LYS cc_start: 0.9162 (mmtt) cc_final: 0.8596 (mttt) REVERT: d 129 CYS cc_start: 0.8771 (m) cc_final: 0.8398 (m) REVERT: d 130 HIS cc_start: 0.8366 (t-90) cc_final: 0.8142 (t-90) REVERT: d 138 MET cc_start: 0.7728 (tpp) cc_final: 0.7528 (tpp) REVERT: d 191 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8214 (mm-30) REVERT: d 221 PHE cc_start: 0.8435 (m-10) cc_final: 0.8067 (m-80) REVERT: d 241 PHE cc_start: 0.8509 (m-80) cc_final: 0.8185 (m-80) REVERT: d 244 CYS cc_start: 0.8110 (m) cc_final: 0.7233 (m) REVERT: d 269 ASP cc_start: 0.9183 (m-30) cc_final: 0.8978 (m-30) REVERT: d 297 HIS cc_start: 0.8970 (t-90) cc_final: 0.8636 (t70) REVERT: d 298 GLU cc_start: 0.9130 (tt0) cc_final: 0.8865 (tm-30) REVERT: d 312 PHE cc_start: 0.8271 (m-10) cc_final: 0.8027 (m-10) REVERT: d 344 ILE cc_start: 0.9194 (tp) cc_final: 0.8675 (mm) REVERT: e 9 PRO cc_start: 0.8201 (Cg_exo) cc_final: 0.7668 (Cg_endo) REVERT: e 13 PHE cc_start: 0.7920 (m-80) cc_final: 0.7289 (m-10) REVERT: e 47 CYS cc_start: 0.8336 (p) cc_final: 0.7785 (p) REVERT: e 54 ILE cc_start: 0.9537 (mt) cc_final: 0.9210 (mt) REVERT: e 68 LEU cc_start: 0.8860 (tp) cc_final: 0.8660 (tp) REVERT: g 61 MET cc_start: 0.8075 (mmt) cc_final: 0.7312 (mmm) REVERT: g 84 ILE cc_start: 0.8396 (mm) cc_final: 0.8143 (mm) REVERT: g 87 TYR cc_start: 0.8380 (t80) cc_final: 0.8079 (t80) REVERT: g 88 ARG cc_start: 0.8392 (mmm160) cc_final: 0.7547 (tpm170) REVERT: g 91 LEU cc_start: 0.8988 (mt) cc_final: 0.8287 (mt) REVERT: g 108 PHE cc_start: 0.9115 (m-80) cc_final: 0.8625 (m-80) REVERT: g 131 MET cc_start: 0.9373 (ttt) cc_final: 0.9119 (ttt) REVERT: g 133 LEU cc_start: 0.9291 (mp) cc_final: 0.8867 (mp) REVERT: g 135 LEU cc_start: 0.9106 (mt) cc_final: 0.8601 (mm) REVERT: g 137 PHE cc_start: 0.8978 (m-10) cc_final: 0.8440 (m-80) REVERT: g 139 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7719 (mm-30) REVERT: g 141 LEU cc_start: 0.9448 (mt) cc_final: 0.9058 (mt) REVERT: g 152 LEU cc_start: 0.9401 (mt) cc_final: 0.8746 (tt) REVERT: h 17 MET cc_start: 0.8952 (mmp) cc_final: 0.8570 (mmm) REVERT: h 55 SER cc_start: 0.9485 (p) cc_final: 0.9207 (p) REVERT: h 68 TYR cc_start: 0.9274 (m-10) cc_final: 0.8937 (m-10) REVERT: h 70 LEU cc_start: 0.9032 (tp) cc_final: 0.8800 (tp) REVERT: h 97 LEU cc_start: 0.9382 (mm) cc_final: 0.9135 (mm) REVERT: h 127 LEU cc_start: 0.9099 (tp) cc_final: 0.8564 (tp) REVERT: h 146 LEU cc_start: 0.9586 (tt) cc_final: 0.9353 (tt) REVERT: h 152 LEU cc_start: 0.9355 (tp) cc_final: 0.9124 (tp) REVERT: i 14 PHE cc_start: 0.8867 (m-10) cc_final: 0.8614 (m-10) REVERT: i 51 LEU cc_start: 0.8904 (mt) cc_final: 0.8688 (mt) REVERT: i 110 ILE cc_start: 0.9510 (mt) cc_final: 0.9104 (tt) REVERT: i 119 ARG cc_start: 0.8527 (ttm110) cc_final: 0.8177 (ttm110) REVERT: i 139 GLU cc_start: 0.9167 (tp30) cc_final: 0.8852 (tp30) REVERT: j 45 SER cc_start: 0.8793 (m) cc_final: 0.8592 (t) REVERT: j 48 ARG cc_start: 0.8925 (mpp80) cc_final: 0.8520 (mpp80) REVERT: j 61 MET cc_start: 0.8828 (tpp) cc_final: 0.8600 (tpp) REVERT: j 68 TYR cc_start: 0.9053 (m-10) cc_final: 0.8810 (m-80) REVERT: j 70 LEU cc_start: 0.9656 (tp) cc_final: 0.9280 (tp) REVERT: j 108 PHE cc_start: 0.9321 (m-80) cc_final: 0.9060 (m-80) REVERT: j 127 LEU cc_start: 0.9475 (tp) cc_final: 0.9273 (tt) REVERT: j 136 ILE cc_start: 0.9194 (mm) cc_final: 0.8902 (mm) REVERT: j 143 LEU cc_start: 0.9234 (mt) cc_final: 0.9003 (mt) REVERT: j 146 LEU cc_start: 0.9659 (tp) cc_final: 0.9438 (tp) REVERT: k 32 TYR cc_start: 0.8927 (t80) cc_final: 0.8460 (t80) REVERT: k 48 ARG cc_start: 0.8281 (mmt90) cc_final: 0.7904 (mmt90) REVERT: k 54 LYS cc_start: 0.8387 (mttt) cc_final: 0.7078 (mtpp) REVERT: k 76 ILE cc_start: 0.9331 (mt) cc_final: 0.8296 (tt) REVERT: k 80 LEU cc_start: 0.9160 (mt) cc_final: 0.8893 (mt) REVERT: k 92 GLN cc_start: 0.9126 (mt0) cc_final: 0.8516 (mt0) REVERT: k 123 GLN cc_start: 0.8748 (tp40) cc_final: 0.7698 (tm-30) REVERT: k 124 GLN cc_start: 0.9027 (tm-30) cc_final: 0.8384 (tm-30) REVERT: k 137 PHE cc_start: 0.8880 (m-80) cc_final: 0.8284 (m-80) REVERT: k 147 ILE cc_start: 0.9713 (mt) cc_final: 0.9409 (tp) REVERT: l 48 ARG cc_start: 0.8599 (ptp-110) cc_final: 0.7882 (ptp-110) REVERT: l 54 LYS cc_start: 0.9089 (mttt) cc_final: 0.8423 (mmtt) REVERT: l 55 SER cc_start: 0.9451 (m) cc_final: 0.9171 (p) REVERT: l 118 VAL cc_start: 0.9755 (t) cc_final: 0.9485 (m) REVERT: l 123 GLN cc_start: 0.8903 (mp10) cc_final: 0.8615 (mp10) REVERT: l 152 LEU cc_start: 0.9509 (mt) cc_final: 0.9082 (tp) REVERT: m 8 PRO cc_start: 0.9132 (Cg_exo) cc_final: 0.8860 (Cg_endo) REVERT: m 21 SER cc_start: 0.9397 (m) cc_final: 0.9150 (p) REVERT: m 44 MET cc_start: 0.9078 (ppp) cc_final: 0.8867 (ppp) REVERT: m 52 ILE cc_start: 0.9207 (mt) cc_final: 0.8844 (mt) REVERT: m 53 MET cc_start: 0.8944 (tpp) cc_final: 0.8725 (tpp) REVERT: m 61 MET cc_start: 0.9536 (mmm) cc_final: 0.9128 (mmm) REVERT: m 86 LEU cc_start: 0.9122 (tp) cc_final: 0.8638 (tp) REVERT: m 90 PHE cc_start: 0.9290 (m-80) cc_final: 0.8526 (m-80) REVERT: m 92 GLN cc_start: 0.9065 (mt0) cc_final: 0.8808 (mt0) REVERT: m 112 ILE cc_start: 0.9295 (mt) cc_final: 0.9084 (tp) REVERT: m 132 ILE cc_start: 0.9427 (mm) cc_final: 0.9077 (mm) REVERT: n 13 PHE cc_start: 0.8831 (t80) cc_final: 0.8504 (t80) REVERT: n 36 LYS cc_start: 0.8684 (mmtt) cc_final: 0.8136 (mttt) REVERT: n 51 LEU cc_start: 0.8992 (mt) cc_final: 0.8668 (mt) REVERT: n 54 LYS cc_start: 0.8850 (mttt) cc_final: 0.8194 (tttt) REVERT: n 68 TYR cc_start: 0.9637 (m-80) cc_final: 0.9168 (m-80) REVERT: n 80 LEU cc_start: 0.9277 (tp) cc_final: 0.8855 (mt) REVERT: n 81 THR cc_start: 0.9406 (p) cc_final: 0.9204 (t) REVERT: n 88 ARG cc_start: 0.8251 (ttm-80) cc_final: 0.7728 (mmm-85) REVERT: n 119 ARG cc_start: 0.8092 (ttm110) cc_final: 0.7877 (mtm-85) REVERT: n 127 LEU cc_start: 0.9459 (tp) cc_final: 0.9241 (tp) REVERT: n 129 VAL cc_start: 0.8640 (t) cc_final: 0.8382 (t) REVERT: n 140 VAL cc_start: 0.9627 (t) cc_final: 0.9320 (t) REVERT: n 141 LEU cc_start: 0.9578 (mt) cc_final: 0.9341 (mt) REVERT: n 144 TYR cc_start: 0.9149 (m-10) cc_final: 0.8656 (m-10) REVERT: o 13 PHE cc_start: 0.8803 (t80) cc_final: 0.8471 (t80) REVERT: o 32 TYR cc_start: 0.8293 (t80) cc_final: 0.7793 (t80) REVERT: o 44 MET cc_start: 0.8177 (ttp) cc_final: 0.7825 (ttp) REVERT: o 61 MET cc_start: 0.8462 (mmp) cc_final: 0.8169 (mmp) REVERT: o 80 LEU cc_start: 0.9296 (mm) cc_final: 0.9056 (mm) REVERT: o 90 PHE cc_start: 0.9300 (m-80) cc_final: 0.8620 (m-10) REVERT: o 110 ILE cc_start: 0.9590 (mt) cc_final: 0.9227 (mt) REVERT: o 147 ILE cc_start: 0.9372 (mt) cc_final: 0.9069 (tp) REVERT: p 305 VAL cc_start: 0.9078 (t) cc_final: 0.8657 (p) REVERT: p 313 ILE cc_start: 0.9549 (mt) cc_final: 0.9217 (mt) outliers start: 8 outliers final: 0 residues processed: 1179 average time/residue: 0.1323 time to fit residues: 250.5629 Evaluate side-chains 954 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 954 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 97 optimal weight: 5.9990 chunk 237 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 chunk 145 optimal weight: 0.9990 chunk 156 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 201 optimal weight: 0.7980 chunk 219 optimal weight: 0.9980 chunk 250 optimal weight: 0.9990 chunk 168 optimal weight: 0.9980 chunk 259 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 48 HIS ** d 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 328 ASN e 33 ASN ** j 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.085697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.073655 restraints weight = 72600.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.076385 restraints weight = 40256.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.078288 restraints weight = 25548.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.079607 restraints weight = 17657.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.080556 restraints weight = 12908.324| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.5230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 21366 Z= 0.175 Angle : 0.667 10.102 28966 Z= 0.350 Chirality : 0.042 0.342 3430 Planarity : 0.005 0.046 3602 Dihedral : 4.180 22.845 2978 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.60 % Favored : 97.37 % Rotamer: Outliers : 0.23 % Allowed : 1.92 % Favored : 97.84 % 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 aren not related in a simple way. whole: 1.80 (0.15), residues: 2771 helix: 1.81 (0.11), residues: 2075 sheet: -0.93 (1.14), residues: 18 loop : -0.63 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG j 48 TYR 0.039 0.002 TYR H 138 PHE 0.033 0.002 PHE n 90 TRP 0.027 0.002 TRP b 16 HIS 0.005 0.001 HIS a 749 Details of bonding type rmsd covalent geometry : bond 0.00369 (21366) covalent geometry : angle 0.66676 (28966) hydrogen bonds : bond 0.05812 ( 1744) hydrogen bonds : angle 4.65665 ( 5124) *********************** 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 1166 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 1161 time to evaluate : 0.737 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 56 MET cc_start: 0.9105 (tmm) cc_final: 0.8761 (tmm) REVERT: H 57 LEU cc_start: 0.9465 (tt) cc_final: 0.9206 (tt) REVERT: H 58 MET cc_start: 0.9228 (tmm) cc_final: 0.8816 (tmm) REVERT: H 64 GLU cc_start: 0.8575 (tp30) cc_final: 0.8207 (tp30) REVERT: H 68 SER cc_start: 0.9411 (m) cc_final: 0.8903 (t) REVERT: H 91 GLN cc_start: 0.8892 (tt0) cc_final: 0.8199 (tt0) REVERT: H 93 LYS cc_start: 0.8791 (mttt) cc_final: 0.8397 (mtpp) REVERT: H 111 HIS cc_start: 0.7673 (t-90) cc_final: 0.7429 (t-90) REVERT: H 134 LEU cc_start: 0.9394 (tp) cc_final: 0.9153 (tp) REVERT: H 137 ASN cc_start: 0.9080 (m110) cc_final: 0.8555 (m110) REVERT: H 140 LYS cc_start: 0.9362 (tttt) cc_final: 0.9011 (ttpt) REVERT: L 22 LEU cc_start: 0.9515 (mt) cc_final: 0.9274 (mt) REVERT: L 38 VAL cc_start: 0.9474 (t) cc_final: 0.8895 (p) REVERT: L 40 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8570 (mp0) REVERT: L 46 ASN cc_start: 0.8455 (m-40) cc_final: 0.8198 (p0) REVERT: L 58 ARG cc_start: 0.8332 (mtm110) cc_final: 0.7840 (ttm110) REVERT: L 73 MET cc_start: 0.8470 (mtp) cc_final: 0.8099 (ptp) REVERT: L 89 LEU cc_start: 0.8522 (mt) cc_final: 0.8210 (mp) REVERT: L 90 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7128 (mt-10) REVERT: L 95 GLU cc_start: 0.8268 (tm-30) cc_final: 0.7961 (tm-30) REVERT: L 99 ASP cc_start: 0.5992 (p0) cc_final: 0.5753 (t0) REVERT: a 8 GLU cc_start: 0.8317 (mm-30) cc_final: 0.8027 (mm-30) REVERT: a 9 GLU cc_start: 0.6875 (mp0) cc_final: 0.6228 (pp20) REVERT: a 388 GLU cc_start: 0.8025 (tp30) cc_final: 0.7308 (tt0) REVERT: a 401 PHE cc_start: 0.9054 (t80) cc_final: 0.8548 (t80) REVERT: a 414 ILE cc_start: 0.9033 (mm) cc_final: 0.8808 (mm) REVERT: a 423 MET cc_start: 0.9293 (mpp) cc_final: 0.8867 (mpp) REVERT: a 449 ILE cc_start: 0.9571 (mt) cc_final: 0.9171 (mt) REVERT: a 453 MET cc_start: 0.8812 (mtp) cc_final: 0.8210 (mtp) REVERT: a 467 CYS cc_start: 0.6599 (t) cc_final: 0.6378 (t) REVERT: a 519 ILE cc_start: 0.7980 (mp) cc_final: 0.7726 (mp) REVERT: a 533 LEU cc_start: 0.8731 (tp) cc_final: 0.8508 (tp) REVERT: a 538 MET cc_start: 0.8406 (ttt) cc_final: 0.7872 (tmm) REVERT: a 580 MET cc_start: 0.8739 (mmm) cc_final: 0.8509 (mmm) REVERT: a 616 MET cc_start: 0.9309 (ttp) cc_final: 0.8844 (ttp) REVERT: a 621 TYR cc_start: 0.6831 (m-10) cc_final: 0.6483 (m-10) REVERT: a 634 LYS cc_start: 0.7960 (mtpt) cc_final: 0.7324 (tttp) REVERT: a 637 GLN cc_start: 0.8767 (mt0) cc_final: 0.8113 (mt0) REVERT: a 643 VAL cc_start: 0.9135 (t) cc_final: 0.8895 (p) REVERT: a 651 MET cc_start: 0.8778 (mmm) cc_final: 0.8186 (mmm) REVERT: a 721 GLN cc_start: 0.9166 (tp40) cc_final: 0.8326 (tp-100) REVERT: a 725 THR cc_start: 0.9625 (m) cc_final: 0.9297 (m) REVERT: a 759 MET cc_start: 0.8135 (mmm) cc_final: 0.7475 (tmm) REVERT: a 804 LEU cc_start: 0.9520 (tp) cc_final: 0.9318 (tt) REVERT: a 810 GLU cc_start: 0.7694 (mp0) cc_final: 0.7298 (mp0) REVERT: a 814 LYS cc_start: 0.8400 (mmmt) cc_final: 0.8175 (mmtm) REVERT: b 4 LEU cc_start: 0.9310 (mt) cc_final: 0.9056 (mt) REVERT: b 8 TYR cc_start: 0.9176 (m-80) cc_final: 0.8712 (m-80) REVERT: b 19 MET cc_start: 0.8927 (mtp) cc_final: 0.8423 (mtt) REVERT: b 25 CYS cc_start: 0.9247 (m) cc_final: 0.8853 (t) REVERT: b 34 ARG cc_start: 0.8257 (mmm160) cc_final: 0.6411 (tpt170) REVERT: b 36 ASP cc_start: 0.8244 (t70) cc_final: 0.7670 (t0) REVERT: b 40 PHE cc_start: 0.6565 (m-80) cc_final: 0.6193 (m-80) REVERT: b 48 MET cc_start: 0.8840 (ttt) cc_final: 0.8320 (tmm) REVERT: b 52 LEU cc_start: 0.9477 (mt) cc_final: 0.9220 (mt) REVERT: b 71 ILE cc_start: 0.9682 (mm) cc_final: 0.9425 (mm) REVERT: b 74 SER cc_start: 0.9519 (m) cc_final: 0.9118 (t) REVERT: b 75 SER cc_start: 0.9675 (m) cc_final: 0.9389 (p) REVERT: b 82 LYS cc_start: 0.8946 (mmtt) cc_final: 0.8456 (mmtp) REVERT: b 96 PHE cc_start: 0.9204 (m-80) cc_final: 0.8572 (m-80) REVERT: b 129 ARG cc_start: 0.8881 (mpp80) cc_final: 0.8532 (mmm-85) REVERT: b 130 ASN cc_start: 0.9053 (m-40) cc_final: 0.8769 (m-40) REVERT: b 135 TYR cc_start: 0.8838 (m-80) cc_final: 0.8411 (m-80) REVERT: b 137 MET cc_start: 0.9404 (ttt) cc_final: 0.8928 (ttm) REVERT: b 148 ASN cc_start: 0.9704 (m110) cc_final: 0.9375 (m110) REVERT: b 164 LEU cc_start: 0.9326 (mp) cc_final: 0.8619 (mp) REVERT: b 169 ASN cc_start: 0.9161 (t0) cc_final: 0.8694 (t0) REVERT: b 172 LEU cc_start: 0.8642 (mt) cc_final: 0.8099 (mt) REVERT: b 188 LEU cc_start: 0.9366 (tt) cc_final: 0.9090 (tp) REVERT: c 420 TRP cc_start: 0.8295 (t-100) cc_final: 0.7803 (t-100) REVERT: c 423 LEU cc_start: 0.9221 (mt) cc_final: 0.8984 (mt) REVERT: c 439 MET cc_start: 0.9458 (mmm) cc_final: 0.9185 (mmm) REVERT: d 23 LEU cc_start: 0.9158 (mm) cc_final: 0.8892 (mm) REVERT: d 76 GLU cc_start: 0.8635 (tt0) cc_final: 0.8175 (tp30) REVERT: d 85 MET cc_start: 0.9144 (mtp) cc_final: 0.8921 (ttp) REVERT: d 98 ASP cc_start: 0.8877 (m-30) cc_final: 0.8266 (t0) REVERT: d 101 THR cc_start: 0.9483 (p) cc_final: 0.9247 (p) REVERT: d 108 ASN cc_start: 0.8911 (m110) cc_final: 0.8639 (m110) REVERT: d 110 ILE cc_start: 0.9450 (mm) cc_final: 0.9241 (mm) REVERT: d 124 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8441 (mt-10) REVERT: d 128 LYS cc_start: 0.9240 (mmtt) cc_final: 0.8426 (mttt) REVERT: d 129 CYS cc_start: 0.8705 (m) cc_final: 0.8403 (m) REVERT: d 130 HIS cc_start: 0.8263 (t-90) cc_final: 0.8003 (t-90) REVERT: d 154 ILE cc_start: 0.9195 (mt) cc_final: 0.8933 (mt) REVERT: d 176 MET cc_start: 0.8253 (mtt) cc_final: 0.7903 (mtt) REVERT: d 191 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8236 (mm-30) REVERT: d 241 PHE cc_start: 0.8526 (m-80) cc_final: 0.8189 (m-80) REVERT: d 244 CYS cc_start: 0.8079 (m) cc_final: 0.7295 (m) REVERT: d 269 ASP cc_start: 0.9186 (m-30) cc_final: 0.8940 (m-30) REVERT: d 297 HIS cc_start: 0.9039 (t-90) cc_final: 0.8435 (t-90) REVERT: d 298 GLU cc_start: 0.9195 (tt0) cc_final: 0.8907 (tm-30) REVERT: d 344 ILE cc_start: 0.9191 (tp) cc_final: 0.8654 (mm) REVERT: e 9 PRO cc_start: 0.8205 (Cg_exo) cc_final: 0.7843 (Cg_endo) REVERT: e 13 PHE cc_start: 0.7795 (m-80) cc_final: 0.7253 (m-80) REVERT: e 47 CYS cc_start: 0.8300 (p) cc_final: 0.7592 (p) REVERT: e 52 TRP cc_start: 0.9442 (t60) cc_final: 0.9175 (t60) REVERT: e 68 LEU cc_start: 0.8806 (tp) cc_final: 0.8590 (tp) REVERT: g 25 PHE cc_start: 0.9002 (m-80) cc_final: 0.8696 (m-80) REVERT: g 44 MET cc_start: 0.9496 (ppp) cc_final: 0.8906 (ppp) REVERT: g 61 MET cc_start: 0.7977 (mmt) cc_final: 0.7570 (mmm) REVERT: g 84 ILE cc_start: 0.8516 (mm) cc_final: 0.8231 (mm) REVERT: g 88 ARG cc_start: 0.8402 (mmm160) cc_final: 0.7953 (mmt180) REVERT: g 108 PHE cc_start: 0.9187 (m-80) cc_final: 0.8517 (m-80) REVERT: g 133 LEU cc_start: 0.9249 (mp) cc_final: 0.8873 (mp) REVERT: g 137 PHE cc_start: 0.8807 (m-10) cc_final: 0.8527 (m-80) REVERT: g 144 TYR cc_start: 0.9049 (m-80) cc_final: 0.8740 (m-80) REVERT: g 152 LEU cc_start: 0.9461 (mt) cc_final: 0.9124 (tp) REVERT: h 13 PHE cc_start: 0.8694 (t80) cc_final: 0.8107 (t80) REVERT: h 17 MET cc_start: 0.8961 (mmp) cc_final: 0.8728 (mmm) REVERT: h 55 SER cc_start: 0.9520 (p) cc_final: 0.9250 (p) REVERT: h 68 TYR cc_start: 0.9388 (m-10) cc_final: 0.9017 (m-10) REVERT: h 127 LEU cc_start: 0.9168 (tp) cc_final: 0.8686 (tp) REVERT: h 146 LEU cc_start: 0.9536 (tt) cc_final: 0.9270 (tt) REVERT: h 152 LEU cc_start: 0.9388 (tp) cc_final: 0.9073 (tp) REVERT: i 44 MET cc_start: 0.8004 (ppp) cc_final: 0.7751 (ppp) REVERT: i 61 MET cc_start: 0.9178 (mtm) cc_final: 0.8578 (ptm) REVERT: i 110 ILE cc_start: 0.9492 (mt) cc_final: 0.9080 (tt) REVERT: i 135 LEU cc_start: 0.9334 (mm) cc_final: 0.9119 (mm) REVERT: i 139 GLU cc_start: 0.9269 (tp30) cc_final: 0.8968 (tp30) REVERT: i 144 TYR cc_start: 0.8704 (m-80) cc_final: 0.8461 (m-80) REVERT: j 41 ILE cc_start: 0.9225 (pt) cc_final: 0.9003 (pt) REVERT: j 45 SER cc_start: 0.8985 (m) cc_final: 0.8346 (t) REVERT: j 61 MET cc_start: 0.8906 (tpp) cc_final: 0.8654 (tpp) REVERT: j 64 ILE cc_start: 0.9103 (mp) cc_final: 0.8769 (mp) REVERT: j 70 LEU cc_start: 0.9662 (tp) cc_final: 0.9336 (tp) REVERT: j 136 ILE cc_start: 0.9193 (mm) cc_final: 0.8909 (mm) REVERT: j 146 LEU cc_start: 0.9670 (tp) cc_final: 0.9435 (tp) REVERT: k 32 TYR cc_start: 0.8925 (t80) cc_final: 0.8517 (t80) REVERT: k 48 ARG cc_start: 0.8205 (mmt90) cc_final: 0.7883 (mmt90) REVERT: k 54 LYS cc_start: 0.8412 (mttt) cc_final: 0.7255 (mtpt) REVERT: k 67 ILE cc_start: 0.9596 (mt) cc_final: 0.9395 (mm) REVERT: k 76 ILE cc_start: 0.9365 (mt) cc_final: 0.8583 (tt) REVERT: k 90 PHE cc_start: 0.8873 (m-80) cc_final: 0.8434 (m-80) REVERT: k 92 GLN cc_start: 0.9111 (mt0) cc_final: 0.8847 (mt0) REVERT: k 123 GLN cc_start: 0.8790 (tp40) cc_final: 0.8220 (tp-100) REVERT: k 124 GLN cc_start: 0.9021 (tm-30) cc_final: 0.8296 (tm-30) REVERT: k 137 PHE cc_start: 0.8969 (m-80) cc_final: 0.8364 (m-80) REVERT: k 147 ILE cc_start: 0.9703 (mt) cc_final: 0.9466 (tp) REVERT: k 150 LEU cc_start: 0.8936 (tt) cc_final: 0.8677 (mp) REVERT: l 47 MET cc_start: 0.7990 (tmm) cc_final: 0.7506 (tmm) REVERT: l 54 LYS cc_start: 0.9041 (mttt) cc_final: 0.8334 (mmtt) REVERT: l 68 TYR cc_start: 0.9349 (m-80) cc_final: 0.9148 (m-80) REVERT: l 90 PHE cc_start: 0.8945 (m-10) cc_final: 0.8099 (m-80) REVERT: l 91 LEU cc_start: 0.9476 (mt) cc_final: 0.9250 (mm) REVERT: l 101 LEU cc_start: 0.9384 (mt) cc_final: 0.9136 (mt) REVERT: l 118 VAL cc_start: 0.9769 (t) cc_final: 0.9561 (m) REVERT: l 123 GLN cc_start: 0.8841 (mp10) cc_final: 0.8561 (mp10) REVERT: l 152 LEU cc_start: 0.9480 (mt) cc_final: 0.9183 (tp) REVERT: m 8 PRO cc_start: 0.9159 (Cg_exo) cc_final: 0.8932 (Cg_endo) REVERT: m 13 PHE cc_start: 0.9455 (t80) cc_final: 0.9168 (t80) REVERT: m 21 SER cc_start: 0.9404 (m) cc_final: 0.9124 (p) REVERT: m 47 MET cc_start: 0.8200 (tpp) cc_final: 0.7910 (tpp) REVERT: m 48 ARG cc_start: 0.8766 (mmm-85) cc_final: 0.8367 (mmm-85) REVERT: m 52 ILE cc_start: 0.9281 (mt) cc_final: 0.8956 (mt) REVERT: m 61 MET cc_start: 0.9431 (mmm) cc_final: 0.8914 (mmm) REVERT: m 86 LEU cc_start: 0.9084 (tp) cc_final: 0.8610 (tp) REVERT: m 90 PHE cc_start: 0.9295 (m-80) cc_final: 0.8493 (m-80) REVERT: m 92 GLN cc_start: 0.9057 (mt0) cc_final: 0.8805 (mt0) REVERT: m 112 ILE cc_start: 0.9262 (mt) cc_final: 0.9039 (tp) REVERT: m 132 ILE cc_start: 0.9421 (mm) cc_final: 0.9122 (mm) REVERT: n 13 PHE cc_start: 0.8793 (t80) cc_final: 0.8173 (t80) REVERT: n 36 LYS cc_start: 0.8622 (mmtt) cc_final: 0.8120 (mttt) REVERT: n 51 LEU cc_start: 0.8989 (mt) cc_final: 0.8696 (mt) REVERT: n 57 ILE cc_start: 0.9429 (mm) cc_final: 0.9196 (mm) REVERT: n 68 TYR cc_start: 0.9643 (m-80) cc_final: 0.9157 (m-80) REVERT: n 80 LEU cc_start: 0.9176 (tp) cc_final: 0.8775 (mt) REVERT: n 88 ARG cc_start: 0.8174 (ttm-80) cc_final: 0.7808 (mmm-85) REVERT: n 90 PHE cc_start: 0.9473 (m-80) cc_final: 0.8995 (m-80) REVERT: n 127 LEU cc_start: 0.9481 (tp) cc_final: 0.9265 (tp) REVERT: n 140 VAL cc_start: 0.9603 (t) cc_final: 0.9212 (t) REVERT: n 141 LEU cc_start: 0.9544 (mt) cc_final: 0.9256 (mt) REVERT: n 144 TYR cc_start: 0.9159 (m-10) cc_final: 0.8566 (m-10) REVERT: o 13 PHE cc_start: 0.8783 (t80) cc_final: 0.8318 (t80) REVERT: o 32 TYR cc_start: 0.8229 (t80) cc_final: 0.7803 (t80) REVERT: o 44 MET cc_start: 0.8204 (ttp) cc_final: 0.7853 (ttp) REVERT: o 90 PHE cc_start: 0.9350 (m-80) cc_final: 0.9048 (m-80) REVERT: p 305 VAL cc_start: 0.9145 (t) cc_final: 0.8729 (p) REVERT: p 341 ARG cc_start: 0.8809 (ptm-80) cc_final: 0.8322 (ptm160) outliers start: 5 outliers final: 0 residues processed: 1161 average time/residue: 0.1258 time to fit residues: 236.4142 Evaluate side-chains 977 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 977 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 157 optimal weight: 3.9990 chunk 175 optimal weight: 0.9990 chunk 21 optimal weight: 0.0000 chunk 264 optimal weight: 0.7980 chunk 278 optimal weight: 2.9990 chunk 188 optimal weight: 0.9990 chunk 272 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 95 optimal weight: 0.0770 overall best weight: 0.5142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 751 GLN ** a 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 90 ASN ** d 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 33 ASN ** j 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 7 ASN ** o 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.086832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.074617 restraints weight = 72876.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.077414 restraints weight = 40384.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.079369 restraints weight = 25541.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.080702 restraints weight = 17479.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.081665 restraints weight = 12719.910| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.5583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 21366 Z= 0.160 Angle : 0.670 10.879 28966 Z= 0.348 Chirality : 0.043 0.414 3430 Planarity : 0.004 0.050 3602 Dihedral : 4.164 21.722 2978 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.38 % Allowed : 1.55 % Favored : 98.08 % 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 aren not related in a simple way. whole: 1.65 (0.16), residues: 2771 helix: 1.72 (0.11), residues: 2076 sheet: -0.75 (1.23), residues: 18 loop : -0.76 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG a 741 TYR 0.056 0.002 TYR m 144 PHE 0.026 0.002 PHE b 189 TRP 0.028 0.002 TRP b 16 HIS 0.006 0.001 HIS H 111 Details of bonding type rmsd covalent geometry : bond 0.00328 (21366) covalent geometry : angle 0.67029 (28966) hydrogen bonds : bond 0.05549 ( 1744) hydrogen bonds : angle 4.59382 ( 5124) *********************** 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 1161 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 1153 time to evaluate : 0.785 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 56 MET cc_start: 0.9050 (tmm) cc_final: 0.8683 (tmm) REVERT: H 57 LEU cc_start: 0.9520 (tt) cc_final: 0.9175 (tt) REVERT: H 58 MET cc_start: 0.9295 (tmm) cc_final: 0.8906 (tmm) REVERT: H 64 GLU cc_start: 0.8508 (tp30) cc_final: 0.8195 (tp30) REVERT: H 67 PHE cc_start: 0.8632 (t80) cc_final: 0.8318 (t80) REVERT: H 68 SER cc_start: 0.9391 (m) cc_final: 0.8900 (t) REVERT: H 91 GLN cc_start: 0.8862 (tt0) cc_final: 0.8012 (tt0) REVERT: H 134 LEU cc_start: 0.9346 (tp) cc_final: 0.9071 (tp) REVERT: H 137 ASN cc_start: 0.9119 (m110) cc_final: 0.8510 (m110) REVERT: H 140 LYS cc_start: 0.9309 (tttt) cc_final: 0.9026 (ttpt) REVERT: L 38 VAL cc_start: 0.9519 (t) cc_final: 0.8905 (p) REVERT: L 40 GLU cc_start: 0.8925 (mt-10) cc_final: 0.8662 (mp0) REVERT: L 49 GLU cc_start: 0.8871 (pt0) cc_final: 0.7949 (pp20) REVERT: L 58 ARG cc_start: 0.8308 (mtm110) cc_final: 0.7804 (ttm110) REVERT: L 69 TYR cc_start: 0.7534 (p90) cc_final: 0.7299 (p90) REVERT: L 73 MET cc_start: 0.8568 (mtm) cc_final: 0.8273 (ptp) REVERT: L 89 LEU cc_start: 0.8456 (mt) cc_final: 0.8150 (mp) REVERT: L 90 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7117 (mt-10) REVERT: L 95 GLU cc_start: 0.8308 (tm-30) cc_final: 0.7999 (tm-30) REVERT: L 99 ASP cc_start: 0.6079 (p0) cc_final: 0.5818 (t0) REVERT: a 8 GLU cc_start: 0.8284 (mm-30) cc_final: 0.8002 (mm-30) REVERT: a 9 GLU cc_start: 0.6863 (mp0) cc_final: 0.6149 (pp20) REVERT: a 388 GLU cc_start: 0.8155 (tp30) cc_final: 0.7528 (tt0) REVERT: a 397 ILE cc_start: 0.9281 (mm) cc_final: 0.8986 (tp) REVERT: a 401 PHE cc_start: 0.9137 (t80) cc_final: 0.8611 (t80) REVERT: a 414 ILE cc_start: 0.8952 (mm) cc_final: 0.8720 (mm) REVERT: a 449 ILE cc_start: 0.9527 (mt) cc_final: 0.9083 (mt) REVERT: a 453 MET cc_start: 0.8853 (mtp) cc_final: 0.8415 (mtp) REVERT: a 467 CYS cc_start: 0.6599 (t) cc_final: 0.6350 (t) REVERT: a 533 LEU cc_start: 0.8880 (tp) cc_final: 0.8652 (tp) REVERT: a 538 MET cc_start: 0.8423 (ttt) cc_final: 0.8028 (ttt) REVERT: a 540 MET cc_start: 0.9108 (mmm) cc_final: 0.8667 (mmm) REVERT: a 580 MET cc_start: 0.8896 (mmm) cc_final: 0.8598 (mmm) REVERT: a 616 MET cc_start: 0.9300 (ttp) cc_final: 0.8869 (ttp) REVERT: a 621 TYR cc_start: 0.6749 (m-10) cc_final: 0.6488 (m-10) REVERT: a 634 LYS cc_start: 0.7940 (mtpt) cc_final: 0.7267 (tttp) REVERT: a 637 GLN cc_start: 0.8872 (mt0) cc_final: 0.8219 (mt0) REVERT: a 643 VAL cc_start: 0.9091 (t) cc_final: 0.8889 (p) REVERT: a 651 MET cc_start: 0.9035 (mmm) cc_final: 0.8225 (mmm) REVERT: a 721 GLN cc_start: 0.9186 (tp40) cc_final: 0.8409 (tp-100) REVERT: a 725 THR cc_start: 0.9622 (m) cc_final: 0.9345 (m) REVERT: a 759 MET cc_start: 0.8096 (mmm) cc_final: 0.7481 (tmm) REVERT: a 801 LEU cc_start: 0.9499 (tt) cc_final: 0.9291 (tt) REVERT: a 804 LEU cc_start: 0.9548 (tp) cc_final: 0.9311 (tt) REVERT: a 810 GLU cc_start: 0.7591 (mp0) cc_final: 0.7272 (mp0) REVERT: b 19 MET cc_start: 0.8950 (mtp) cc_final: 0.8476 (mtp) REVERT: b 25 CYS cc_start: 0.9251 (m) cc_final: 0.8852 (t) REVERT: b 30 ASP cc_start: 0.8706 (t70) cc_final: 0.8443 (t0) REVERT: b 34 ARG cc_start: 0.8284 (mmm160) cc_final: 0.6374 (tpt170) REVERT: b 36 ASP cc_start: 0.8201 (t70) cc_final: 0.7666 (t0) REVERT: b 48 MET cc_start: 0.8741 (ttt) cc_final: 0.8179 (tmm) REVERT: b 52 LEU cc_start: 0.9482 (mt) cc_final: 0.9174 (mt) REVERT: b 71 ILE cc_start: 0.9607 (mm) cc_final: 0.9315 (mm) REVERT: b 74 SER cc_start: 0.9492 (m) cc_final: 0.9069 (t) REVERT: b 75 SER cc_start: 0.9614 (m) cc_final: 0.9364 (p) REVERT: b 82 LYS cc_start: 0.8961 (mmtt) cc_final: 0.8638 (mtpp) REVERT: b 86 ILE cc_start: 0.8960 (mt) cc_final: 0.8618 (mt) REVERT: b 96 PHE cc_start: 0.9193 (m-80) cc_final: 0.8519 (m-80) REVERT: b 114 MET cc_start: 0.7451 (mtm) cc_final: 0.7081 (mtm) REVERT: b 130 ASN cc_start: 0.9062 (m-40) cc_final: 0.8858 (m-40) REVERT: b 135 TYR cc_start: 0.8846 (m-80) cc_final: 0.8564 (m-10) REVERT: b 137 MET cc_start: 0.9362 (ttt) cc_final: 0.8877 (tpp) REVERT: b 148 ASN cc_start: 0.9606 (m110) cc_final: 0.9294 (m110) REVERT: b 164 LEU cc_start: 0.9293 (mp) cc_final: 0.8745 (mm) REVERT: b 169 ASN cc_start: 0.9183 (t0) cc_final: 0.8599 (t0) REVERT: b 172 LEU cc_start: 0.8649 (mt) cc_final: 0.7995 (mt) REVERT: c 439 MET cc_start: 0.9423 (mmm) cc_final: 0.9124 (mmm) REVERT: d 40 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7566 (mm-30) REVERT: d 76 GLU cc_start: 0.8648 (tt0) cc_final: 0.8207 (tp30) REVERT: d 85 MET cc_start: 0.9198 (mtp) cc_final: 0.8832 (ttp) REVERT: d 98 ASP cc_start: 0.8811 (m-30) cc_final: 0.8218 (t0) REVERT: d 108 ASN cc_start: 0.8861 (m110) cc_final: 0.8573 (m110) REVERT: d 111 LEU cc_start: 0.9422 (tp) cc_final: 0.9185 (tt) REVERT: d 124 GLU cc_start: 0.8795 (mt-10) cc_final: 0.8424 (mt-10) REVERT: d 128 LYS cc_start: 0.9159 (mmtt) cc_final: 0.8398 (mttt) REVERT: d 129 CYS cc_start: 0.8657 (m) cc_final: 0.8355 (m) REVERT: d 130 HIS cc_start: 0.8298 (t-90) cc_final: 0.8047 (t-90) REVERT: d 176 MET cc_start: 0.8224 (mtt) cc_final: 0.7918 (mtt) REVERT: d 191 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8259 (mm-30) REVERT: d 221 PHE cc_start: 0.8402 (m-10) cc_final: 0.8053 (m-80) REVERT: d 241 PHE cc_start: 0.8569 (m-80) cc_final: 0.8241 (m-80) REVERT: d 244 CYS cc_start: 0.8106 (m) cc_final: 0.7378 (m) REVERT: d 257 ARG cc_start: 0.9563 (mmm-85) cc_final: 0.9096 (mtp180) REVERT: d 269 ASP cc_start: 0.9214 (m-30) cc_final: 0.8971 (m-30) REVERT: d 297 HIS cc_start: 0.8980 (t-90) cc_final: 0.8624 (t70) REVERT: d 298 GLU cc_start: 0.9175 (tt0) cc_final: 0.8899 (tm-30) REVERT: e 9 PRO cc_start: 0.8216 (Cg_exo) cc_final: 0.7889 (Cg_endo) REVERT: e 13 PHE cc_start: 0.7798 (m-80) cc_final: 0.7290 (m-80) REVERT: e 47 CYS cc_start: 0.8242 (p) cc_final: 0.7674 (p) REVERT: e 49 TYR cc_start: 0.8604 (t80) cc_final: 0.8177 (t80) REVERT: e 52 TRP cc_start: 0.9394 (t60) cc_final: 0.9139 (t60) REVERT: e 68 LEU cc_start: 0.8756 (tp) cc_final: 0.8531 (tp) REVERT: f 67 TYR cc_start: 0.8513 (m-80) cc_final: 0.8259 (m-80) REVERT: g 25 PHE cc_start: 0.9027 (m-80) cc_final: 0.8738 (m-80) REVERT: g 41 ILE cc_start: 0.9586 (mp) cc_final: 0.9373 (mm) REVERT: g 44 MET cc_start: 0.9549 (ppp) cc_final: 0.8956 (ppp) REVERT: g 61 MET cc_start: 0.7882 (mmt) cc_final: 0.7174 (mmm) REVERT: g 84 ILE cc_start: 0.8576 (mm) cc_final: 0.8276 (mm) REVERT: g 87 TYR cc_start: 0.8417 (t80) cc_final: 0.8082 (t80) REVERT: g 88 ARG cc_start: 0.8422 (mmm160) cc_final: 0.7985 (mmt180) REVERT: g 91 LEU cc_start: 0.8951 (mt) cc_final: 0.8744 (mt) REVERT: g 108 PHE cc_start: 0.9035 (m-80) cc_final: 0.8579 (m-10) REVERT: g 141 LEU cc_start: 0.9438 (mt) cc_final: 0.9039 (mt) REVERT: g 144 TYR cc_start: 0.9097 (m-80) cc_final: 0.8612 (m-80) REVERT: g 152 LEU cc_start: 0.9467 (mt) cc_final: 0.9117 (tp) REVERT: h 13 PHE cc_start: 0.8618 (t80) cc_final: 0.8015 (t80) REVERT: h 17 MET cc_start: 0.8927 (mmp) cc_final: 0.8680 (mmm) REVERT: h 55 SER cc_start: 0.9531 (p) cc_final: 0.9281 (p) REVERT: h 68 TYR cc_start: 0.9392 (m-10) cc_final: 0.9101 (m-10) REVERT: h 75 LEU cc_start: 0.8856 (mt) cc_final: 0.8651 (mt) REVERT: h 92 GLN cc_start: 0.8949 (mt0) cc_final: 0.8301 (mt0) REVERT: h 127 LEU cc_start: 0.9193 (tp) cc_final: 0.8756 (tp) REVERT: i 44 MET cc_start: 0.8047 (ppp) cc_final: 0.7663 (ppp) REVERT: i 61 MET cc_start: 0.9238 (mtm) cc_final: 0.8657 (ptm) REVERT: i 65 ILE cc_start: 0.9406 (mm) cc_final: 0.9180 (mm) REVERT: i 110 ILE cc_start: 0.9504 (mt) cc_final: 0.9114 (tt) REVERT: j 17 MET cc_start: 0.8864 (tpt) cc_final: 0.8632 (tpt) REVERT: j 48 ARG cc_start: 0.8972 (mpp80) cc_final: 0.8545 (mpp80) REVERT: j 61 MET cc_start: 0.8925 (tpp) cc_final: 0.8682 (tpp) REVERT: j 70 LEU cc_start: 0.9658 (tp) cc_final: 0.9349 (tp) REVERT: j 127 LEU cc_start: 0.9076 (tt) cc_final: 0.8754 (tt) REVERT: j 131 MET cc_start: 0.8836 (ttt) cc_final: 0.8582 (ttt) REVERT: j 136 ILE cc_start: 0.9185 (mm) cc_final: 0.8885 (mm) REVERT: k 32 TYR cc_start: 0.8900 (t80) cc_final: 0.8515 (t80) REVERT: k 48 ARG cc_start: 0.8056 (mmt90) cc_final: 0.7725 (mmt90) REVERT: k 54 LYS cc_start: 0.8395 (mttt) cc_final: 0.7159 (mtpt) REVERT: k 65 ILE cc_start: 0.9512 (mt) cc_final: 0.9285 (tp) REVERT: k 76 ILE cc_start: 0.9358 (mt) cc_final: 0.8392 (tt) REVERT: k 90 PHE cc_start: 0.8927 (m-80) cc_final: 0.8562 (m-80) REVERT: k 92 GLN cc_start: 0.9126 (mt0) cc_final: 0.8806 (mt0) REVERT: k 123 GLN cc_start: 0.8829 (tp40) cc_final: 0.7772 (tm-30) REVERT: k 124 GLN cc_start: 0.9055 (tm-30) cc_final: 0.8113 (tm-30) REVERT: k 143 LEU cc_start: 0.9491 (tp) cc_final: 0.9197 (mm) REVERT: k 147 ILE cc_start: 0.9689 (mt) cc_final: 0.9417 (tp) REVERT: k 150 LEU cc_start: 0.8945 (tt) cc_final: 0.8675 (mp) REVERT: l 47 MET cc_start: 0.8007 (tmm) cc_final: 0.7505 (tmm) REVERT: l 54 LYS cc_start: 0.9028 (mttt) cc_final: 0.8292 (mmtt) REVERT: l 90 PHE cc_start: 0.8363 (m-10) cc_final: 0.7660 (m-80) REVERT: l 93 LEU cc_start: 0.9337 (tt) cc_final: 0.9123 (pp) REVERT: l 101 LEU cc_start: 0.9371 (mt) cc_final: 0.9112 (mt) REVERT: l 118 VAL cc_start: 0.9760 (t) cc_final: 0.9395 (m) REVERT: l 123 GLN cc_start: 0.8767 (mp10) cc_final: 0.8509 (mp10) REVERT: l 131 MET cc_start: 0.8923 (ttp) cc_final: 0.8675 (ttp) REVERT: l 152 LEU cc_start: 0.9502 (mt) cc_final: 0.9139 (tp) REVERT: m 13 PHE cc_start: 0.9414 (t80) cc_final: 0.9167 (t80) REVERT: m 21 SER cc_start: 0.9375 (m) cc_final: 0.9068 (p) REVERT: m 25 PHE cc_start: 0.8730 (m-80) cc_final: 0.8466 (m-80) REVERT: m 47 MET cc_start: 0.8245 (tpp) cc_final: 0.7915 (tpp) REVERT: m 48 ARG cc_start: 0.8760 (mmm-85) cc_final: 0.8263 (mmm-85) REVERT: m 52 ILE cc_start: 0.9291 (mt) cc_final: 0.8965 (mt) REVERT: m 61 MET cc_start: 0.9403 (mmm) cc_final: 0.8971 (mmm) REVERT: m 80 LEU cc_start: 0.9463 (mt) cc_final: 0.9255 (mt) REVERT: m 86 LEU cc_start: 0.9094 (tp) cc_final: 0.8650 (tp) REVERT: m 90 PHE cc_start: 0.9358 (m-10) cc_final: 0.8603 (m-80) REVERT: m 92 GLN cc_start: 0.9015 (mt0) cc_final: 0.8800 (mt0) REVERT: n 13 PHE cc_start: 0.8659 (t80) cc_final: 0.8414 (t80) REVERT: n 36 LYS cc_start: 0.8560 (mmtt) cc_final: 0.8078 (mmtt) REVERT: n 45 SER cc_start: 0.9071 (m) cc_final: 0.8808 (p) REVERT: n 51 LEU cc_start: 0.8935 (mt) cc_final: 0.8708 (mt) REVERT: n 57 ILE cc_start: 0.9408 (mm) cc_final: 0.9162 (mm) REVERT: n 68 TYR cc_start: 0.9635 (m-80) cc_final: 0.9051 (m-80) REVERT: n 75 LEU cc_start: 0.9027 (mt) cc_final: 0.8788 (mt) REVERT: n 80 LEU cc_start: 0.9136 (tp) cc_final: 0.8775 (mt) REVERT: n 88 ARG cc_start: 0.8197 (ttm-80) cc_final: 0.7384 (mmm-85) REVERT: n 90 PHE cc_start: 0.9460 (m-80) cc_final: 0.8850 (m-80) REVERT: n 127 LEU cc_start: 0.9472 (tp) cc_final: 0.9261 (tp) REVERT: n 129 VAL cc_start: 0.8660 (t) cc_final: 0.8316 (t) REVERT: n 140 VAL cc_start: 0.9600 (t) cc_final: 0.9165 (t) REVERT: n 141 LEU cc_start: 0.9521 (mt) cc_final: 0.9244 (mt) REVERT: n 144 TYR cc_start: 0.9056 (m-10) cc_final: 0.8515 (m-10) REVERT: o 23 MET cc_start: 0.9304 (tpp) cc_final: 0.9013 (tpp) REVERT: o 44 MET cc_start: 0.8191 (ttp) cc_final: 0.7829 (ttp) REVERT: o 90 PHE cc_start: 0.9344 (m-10) cc_final: 0.8565 (m-80) REVERT: o 110 ILE cc_start: 0.9601 (mt) cc_final: 0.9388 (mt) REVERT: o 144 TYR cc_start: 0.8408 (m-10) cc_final: 0.8142 (m-10) REVERT: p 305 VAL cc_start: 0.9125 (t) cc_final: 0.8923 (p) REVERT: p 326 TYR cc_start: 0.8531 (t80) cc_final: 0.8319 (t80) REVERT: p 330 ASN cc_start: 0.8924 (m-40) cc_final: 0.8603 (m-40) REVERT: p 339 ILE cc_start: 0.7970 (mm) cc_final: 0.7055 (mt) outliers start: 8 outliers final: 0 residues processed: 1153 average time/residue: 0.1347 time to fit residues: 250.1343 Evaluate side-chains 946 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 946 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 166 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 226 optimal weight: 0.9990 chunk 177 optimal weight: 5.9990 chunk 227 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 chunk 135 optimal weight: 9.9990 chunk 179 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 ASN ** a 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 751 GLN ** d 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 33 ASN ** j 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 7 ASN ** o 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.086455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.074092 restraints weight = 75521.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.076722 restraints weight = 43352.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.078570 restraints weight = 28174.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.079881 restraints weight = 19882.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.080870 restraints weight = 14727.599| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.5877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 21366 Z= 0.175 Angle : 0.667 9.367 28966 Z= 0.351 Chirality : 0.042 0.216 3430 Planarity : 0.004 0.055 3602 Dihedral : 4.133 21.256 2978 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.78 % Favored : 97.19 % Rotamer: Outliers : 0.09 % Allowed : 1.55 % Favored : 98.36 % 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 aren not related in a simple way. whole: 1.69 (0.16), residues: 2771 helix: 1.77 (0.11), residues: 2074 sheet: -0.88 (1.28), residues: 18 loop : -0.80 (0.24), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 75 TYR 0.055 0.002 TYR m 144 PHE 0.025 0.002 PHE e 51 TRP 0.041 0.002 TRP a 595 HIS 0.005 0.001 HIS a 412 Details of bonding type rmsd covalent geometry : bond 0.00370 (21366) covalent geometry : angle 0.66710 (28966) hydrogen bonds : bond 0.05336 ( 1744) hydrogen bonds : angle 4.61066 ( 5124) *********************** 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 1092 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1090 time to evaluate : 0.929 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: H 56 MET cc_start: 0.9031 (tmm) cc_final: 0.8666 (tmm) REVERT: H 57 LEU cc_start: 0.9487 (tt) cc_final: 0.9150 (tt) REVERT: H 58 MET cc_start: 0.9385 (tmm) cc_final: 0.8946 (tmm) REVERT: H 64 GLU cc_start: 0.8503 (tp30) cc_final: 0.8110 (tp30) REVERT: H 68 SER cc_start: 0.9419 (m) cc_final: 0.8967 (t) REVERT: H 91 GLN cc_start: 0.8944 (tt0) cc_final: 0.8168 (tt0) REVERT: H 111 HIS cc_start: 0.7831 (t-90) cc_final: 0.7506 (t-170) REVERT: H 137 ASN cc_start: 0.9068 (m-40) cc_final: 0.8519 (m110) REVERT: H 140 LYS cc_start: 0.9359 (tttt) cc_final: 0.8982 (ttpt) REVERT: L 22 LEU cc_start: 0.9494 (mt) cc_final: 0.9268 (mt) REVERT: L 38 VAL cc_start: 0.9555 (t) cc_final: 0.8955 (p) REVERT: L 49 GLU cc_start: 0.8885 (pt0) cc_final: 0.7966 (pp20) REVERT: L 58 ARG cc_start: 0.8373 (mtm110) cc_final: 0.7719 (ttm110) REVERT: L 69 TYR cc_start: 0.7492 (p90) cc_final: 0.7291 (p90) REVERT: L 73 MET cc_start: 0.8602 (mtm) cc_final: 0.8279 (ptp) REVERT: L 89 LEU cc_start: 0.8543 (mt) cc_final: 0.8260 (mp) REVERT: L 95 GLU cc_start: 0.8365 (tm-30) cc_final: 0.8031 (tm-30) REVERT: L 99 ASP cc_start: 0.6204 (p0) cc_final: 0.6001 (t0) REVERT: a 8 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8022 (mm-30) REVERT: a 9 GLU cc_start: 0.7012 (mp0) cc_final: 0.6235 (pp20) REVERT: a 388 GLU cc_start: 0.8301 (tp30) cc_final: 0.7476 (tt0) REVERT: a 397 ILE cc_start: 0.9324 (mm) cc_final: 0.9033 (tp) REVERT: a 401 PHE cc_start: 0.9182 (t80) cc_final: 0.8576 (t80) REVERT: a 414 ILE cc_start: 0.8874 (mm) cc_final: 0.8583 (mm) REVERT: a 449 ILE cc_start: 0.9484 (mt) cc_final: 0.9043 (mt) REVERT: a 453 MET cc_start: 0.8983 (mtp) cc_final: 0.8583 (mtp) REVERT: a 467 CYS cc_start: 0.6522 (t) cc_final: 0.6139 (t) REVERT: a 519 ILE cc_start: 0.7898 (mp) cc_final: 0.7677 (mp) REVERT: a 538 MET cc_start: 0.8512 (ttt) cc_final: 0.8139 (ppp) REVERT: a 580 MET cc_start: 0.8937 (mmm) cc_final: 0.8624 (mmm) REVERT: a 616 MET cc_start: 0.9308 (ttp) cc_final: 0.8895 (ttp) REVERT: a 634 LYS cc_start: 0.7914 (mtpt) cc_final: 0.7661 (mtpt) REVERT: a 636 ILE cc_start: 0.9320 (mm) cc_final: 0.9016 (tp) REVERT: a 637 GLN cc_start: 0.8898 (mt0) cc_final: 0.8112 (mt0) REVERT: a 651 MET cc_start: 0.9049 (mmm) cc_final: 0.8243 (mmm) REVERT: a 721 GLN cc_start: 0.9220 (tp40) cc_final: 0.8440 (tp-100) REVERT: a 725 THR cc_start: 0.9640 (m) cc_final: 0.9404 (m) REVERT: a 759 MET cc_start: 0.8120 (mmm) cc_final: 0.7463 (tmm) REVERT: a 801 LEU cc_start: 0.9519 (tt) cc_final: 0.9306 (tt) REVERT: a 804 LEU cc_start: 0.9536 (tp) cc_final: 0.9322 (tt) REVERT: b 19 MET cc_start: 0.8933 (mtp) cc_final: 0.8415 (mtt) REVERT: b 25 CYS cc_start: 0.9235 (m) cc_final: 0.8871 (t) REVERT: b 30 ASP cc_start: 0.8780 (t70) cc_final: 0.8544 (t0) REVERT: b 34 ARG cc_start: 0.8378 (mmm160) cc_final: 0.6416 (tpt170) REVERT: b 36 ASP cc_start: 0.8275 (t70) cc_final: 0.7628 (t0) REVERT: b 48 MET cc_start: 0.8749 (ttt) cc_final: 0.8286 (tmm) REVERT: b 52 LEU cc_start: 0.9494 (mt) cc_final: 0.9125 (mt) REVERT: b 70 TYR cc_start: 0.9015 (p90) cc_final: 0.8665 (p90) REVERT: b 71 ILE cc_start: 0.9636 (mm) cc_final: 0.9223 (mm) REVERT: b 74 SER cc_start: 0.9510 (m) cc_final: 0.9140 (t) REVERT: b 75 SER cc_start: 0.9617 (m) cc_final: 0.9367 (p) REVERT: b 82 LYS cc_start: 0.9033 (mmtt) cc_final: 0.8546 (mmtp) REVERT: b 88 THR cc_start: 0.8874 (t) cc_final: 0.8672 (t) REVERT: b 98 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8463 (mm-30) REVERT: b 129 ARG cc_start: 0.8946 (mpp80) cc_final: 0.8706 (mmm-85) REVERT: b 130 ASN cc_start: 0.9028 (m-40) cc_final: 0.8789 (m-40) REVERT: b 135 TYR cc_start: 0.8947 (m-80) cc_final: 0.8499 (m-10) REVERT: b 137 MET cc_start: 0.9342 (ttt) cc_final: 0.8862 (tpp) REVERT: b 148 ASN cc_start: 0.9617 (m110) cc_final: 0.9300 (m-40) REVERT: b 150 PHE cc_start: 0.9082 (m-80) cc_final: 0.8848 (m-10) REVERT: b 164 LEU cc_start: 0.9325 (mp) cc_final: 0.8726 (mm) REVERT: b 168 GLN cc_start: 0.8910 (mp10) cc_final: 0.8636 (mp10) REVERT: b 169 ASN cc_start: 0.9169 (t0) cc_final: 0.8440 (t0) REVERT: b 172 LEU cc_start: 0.8633 (mt) cc_final: 0.7921 (mt) REVERT: c 423 LEU cc_start: 0.9200 (mt) cc_final: 0.8938 (mt) REVERT: c 439 MET cc_start: 0.9340 (mmm) cc_final: 0.9129 (mmm) REVERT: d 23 LEU cc_start: 0.9225 (mm) cc_final: 0.8937 (mm) REVERT: d 40 GLU cc_start: 0.8316 (mt-10) cc_final: 0.7714 (mm-30) REVERT: d 76 GLU cc_start: 0.8620 (tt0) cc_final: 0.8189 (tp30) REVERT: d 85 MET cc_start: 0.9254 (mtp) cc_final: 0.8896 (ttp) REVERT: d 98 ASP cc_start: 0.8825 (m-30) cc_final: 0.8200 (t0) REVERT: d 108 ASN cc_start: 0.8808 (m110) cc_final: 0.8524 (m110) REVERT: d 110 ILE cc_start: 0.9455 (mm) cc_final: 0.9230 (mm) REVERT: d 111 LEU cc_start: 0.9445 (tp) cc_final: 0.9240 (tt) REVERT: d 124 GLU cc_start: 0.8782 (mt-10) cc_final: 0.8468 (mt-10) REVERT: d 128 LYS cc_start: 0.9163 (mmtt) cc_final: 0.8477 (mttt) REVERT: d 129 CYS cc_start: 0.8701 (m) cc_final: 0.8416 (m) REVERT: d 130 HIS cc_start: 0.8354 (t-90) cc_final: 0.8114 (t-90) REVERT: d 176 MET cc_start: 0.8290 (mtt) cc_final: 0.7963 (mtt) REVERT: d 191 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8188 (mm-30) REVERT: d 241 PHE cc_start: 0.8644 (m-80) cc_final: 0.8345 (m-80) REVERT: d 244 CYS cc_start: 0.8071 (m) cc_final: 0.7211 (m) REVERT: d 257 ARG cc_start: 0.9564 (mmm-85) cc_final: 0.9106 (mtp180) REVERT: d 297 HIS cc_start: 0.9018 (t-90) cc_final: 0.8404 (t-90) REVERT: d 298 GLU cc_start: 0.9212 (tt0) cc_final: 0.8902 (tm-30) REVERT: d 328 ASN cc_start: 0.9482 (m-40) cc_final: 0.9162 (m-40) REVERT: d 335 CYS cc_start: 0.8669 (m) cc_final: 0.8060 (t) REVERT: e 9 PRO cc_start: 0.8253 (Cg_exo) cc_final: 0.7948 (Cg_endo) REVERT: e 13 PHE cc_start: 0.7852 (m-80) cc_final: 0.7331 (m-80) REVERT: e 47 CYS cc_start: 0.8287 (p) cc_final: 0.7450 (p) REVERT: e 52 TRP cc_start: 0.9485 (t60) cc_final: 0.9226 (t60) REVERT: e 68 LEU cc_start: 0.8808 (tp) cc_final: 0.8535 (tp) REVERT: f 67 TYR cc_start: 0.8588 (m-80) cc_final: 0.8226 (m-80) REVERT: g 25 PHE cc_start: 0.9092 (m-80) cc_final: 0.8772 (m-80) REVERT: g 32 TYR cc_start: 0.9154 (t80) cc_final: 0.8937 (t80) REVERT: g 45 SER cc_start: 0.9690 (p) cc_final: 0.9358 (p) REVERT: g 61 MET cc_start: 0.7938 (mmt) cc_final: 0.7521 (mmt) REVERT: g 88 ARG cc_start: 0.8462 (mmm160) cc_final: 0.8022 (mmt180) REVERT: g 108 PHE cc_start: 0.9010 (m-80) cc_final: 0.8345 (m-80) REVERT: g 131 MET cc_start: 0.9388 (ttt) cc_final: 0.9039 (ttt) REVERT: g 137 PHE cc_start: 0.8899 (m-10) cc_final: 0.8621 (m-80) REVERT: g 141 LEU cc_start: 0.9299 (mt) cc_final: 0.9052 (mt) REVERT: g 144 TYR cc_start: 0.9133 (m-80) cc_final: 0.8428 (m-80) REVERT: h 55 SER cc_start: 0.9553 (p) cc_final: 0.9306 (p) REVERT: h 68 TYR cc_start: 0.9404 (m-10) cc_final: 0.9107 (m-10) REVERT: h 127 LEU cc_start: 0.9232 (tp) cc_final: 0.8846 (tp) REVERT: i 44 MET cc_start: 0.8092 (ppp) cc_final: 0.7589 (ppp) REVERT: i 61 MET cc_start: 0.9255 (mtm) cc_final: 0.8631 (ptp) REVERT: i 64 ILE cc_start: 0.9047 (mt) cc_final: 0.8825 (mt) REVERT: i 65 ILE cc_start: 0.9384 (mm) cc_final: 0.8879 (mm) REVERT: i 68 TYR cc_start: 0.9189 (m-10) cc_final: 0.8896 (m-80) REVERT: i 110 ILE cc_start: 0.9505 (mt) cc_final: 0.9125 (tt) REVERT: i 139 GLU cc_start: 0.9199 (tp30) cc_final: 0.8683 (tp30) REVERT: j 17 MET cc_start: 0.8743 (tpt) cc_final: 0.8539 (tpt) REVERT: j 48 ARG cc_start: 0.9030 (mpp80) cc_final: 0.8642 (mpp80) REVERT: j 61 MET cc_start: 0.8911 (tpp) cc_final: 0.8636 (tpp) REVERT: j 70 LEU cc_start: 0.9672 (tp) cc_final: 0.9362 (tp) REVERT: j 118 VAL cc_start: 0.9680 (t) cc_final: 0.9421 (p) REVERT: j 127 LEU cc_start: 0.9155 (tt) cc_final: 0.8650 (tt) REVERT: j 131 MET cc_start: 0.8905 (ttt) cc_final: 0.8502 (ttt) REVERT: j 136 ILE cc_start: 0.9213 (mm) cc_final: 0.8910 (mm) REVERT: j 143 LEU cc_start: 0.9207 (mt) cc_final: 0.8943 (mt) REVERT: k 32 TYR cc_start: 0.8888 (t80) cc_final: 0.8477 (t80) REVERT: k 48 ARG cc_start: 0.8155 (mmt90) cc_final: 0.7935 (mmt90) REVERT: k 54 LYS cc_start: 0.8335 (mttt) cc_final: 0.7389 (tttt) REVERT: k 65 ILE cc_start: 0.9580 (mt) cc_final: 0.9354 (tp) REVERT: k 76 ILE cc_start: 0.9383 (mt) cc_final: 0.8221 (tt) REVERT: k 80 LEU cc_start: 0.9196 (mt) cc_final: 0.8957 (mt) REVERT: k 92 GLN cc_start: 0.9159 (mt0) cc_final: 0.8607 (mt0) REVERT: k 123 GLN cc_start: 0.8878 (tp40) cc_final: 0.7830 (tm-30) REVERT: k 124 GLN cc_start: 0.9028 (tm-30) cc_final: 0.8245 (tm-30) REVERT: k 133 LEU cc_start: 0.9240 (mt) cc_final: 0.8860 (mt) REVERT: k 137 PHE cc_start: 0.9052 (m-80) cc_final: 0.8375 (m-80) REVERT: k 147 ILE cc_start: 0.9684 (mt) cc_final: 0.9418 (tp) REVERT: k 150 LEU cc_start: 0.9015 (tt) cc_final: 0.8728 (mt) REVERT: l 32 TYR cc_start: 0.9191 (t80) cc_final: 0.8965 (t80) REVERT: l 47 MET cc_start: 0.7903 (tmm) cc_final: 0.7606 (tmm) REVERT: l 48 ARG cc_start: 0.8880 (ptp-110) cc_final: 0.8589 (ptp-110) REVERT: l 54 LYS cc_start: 0.9009 (mttt) cc_final: 0.8243 (mmtt) REVERT: l 61 MET cc_start: 0.9127 (mmm) cc_final: 0.8486 (mpp) REVERT: l 118 VAL cc_start: 0.9767 (t) cc_final: 0.9412 (m) REVERT: l 123 GLN cc_start: 0.8768 (mp10) cc_final: 0.8515 (mp10) REVERT: l 131 MET cc_start: 0.8921 (ttp) cc_final: 0.8686 (ttp) REVERT: l 147 ILE cc_start: 0.9185 (mt) cc_final: 0.8962 (mm) REVERT: m 13 PHE cc_start: 0.9452 (t80) cc_final: 0.9184 (t80) REVERT: m 17 MET cc_start: 0.9261 (mtm) cc_final: 0.9013 (mtm) REVERT: m 21 SER cc_start: 0.9388 (m) cc_final: 0.9059 (p) REVERT: m 25 PHE cc_start: 0.8874 (m-80) cc_final: 0.8603 (m-80) REVERT: m 47 MET cc_start: 0.8311 (tpp) cc_final: 0.7951 (tpp) REVERT: m 48 ARG cc_start: 0.8769 (mmm-85) cc_final: 0.8356 (mmm-85) REVERT: m 52 ILE cc_start: 0.9364 (mt) cc_final: 0.8983 (mt) REVERT: m 61 MET cc_start: 0.9490 (mmm) cc_final: 0.9167 (mmm) REVERT: m 80 LEU cc_start: 0.9421 (mt) cc_final: 0.9185 (mt) REVERT: m 86 LEU cc_start: 0.9083 (tp) cc_final: 0.8613 (tp) REVERT: m 90 PHE cc_start: 0.9366 (m-10) cc_final: 0.8633 (m-80) REVERT: m 92 GLN cc_start: 0.9000 (mt0) cc_final: 0.8788 (mt0) REVERT: n 13 PHE cc_start: 0.8774 (t80) cc_final: 0.8194 (t80) REVERT: n 17 MET cc_start: 0.9067 (mmt) cc_final: 0.8721 (mmt) REVERT: n 36 LYS cc_start: 0.8577 (mmtt) cc_final: 0.8074 (mmtt) REVERT: n 45 SER cc_start: 0.9096 (m) cc_final: 0.8849 (p) REVERT: n 57 ILE cc_start: 0.9420 (mm) cc_final: 0.9148 (mm) REVERT: n 61 MET cc_start: 0.8921 (mmp) cc_final: 0.8674 (mmm) REVERT: n 68 TYR cc_start: 0.9630 (m-80) cc_final: 0.9046 (m-80) REVERT: n 75 LEU cc_start: 0.9033 (mt) cc_final: 0.8804 (mt) REVERT: n 80 LEU cc_start: 0.9158 (tp) cc_final: 0.8702 (mt) REVERT: n 88 ARG cc_start: 0.8197 (ttm-80) cc_final: 0.7951 (mmm160) REVERT: n 90 PHE cc_start: 0.9601 (m-80) cc_final: 0.9346 (m-80) REVERT: n 124 GLN cc_start: 0.9008 (tp-100) cc_final: 0.8091 (tm-30) REVERT: n 127 LEU cc_start: 0.9494 (tp) cc_final: 0.9279 (tp) REVERT: n 128 PHE cc_start: 0.9026 (t80) cc_final: 0.8812 (t80) REVERT: n 129 VAL cc_start: 0.8788 (t) cc_final: 0.8370 (t) REVERT: n 140 VAL cc_start: 0.9553 (t) cc_final: 0.9099 (t) REVERT: n 141 LEU cc_start: 0.9525 (mt) cc_final: 0.9247 (mt) REVERT: n 144 TYR cc_start: 0.9130 (m-10) cc_final: 0.8557 (m-10) REVERT: o 28 MET cc_start: 0.8839 (ttt) cc_final: 0.8612 (ttt) REVERT: o 44 MET cc_start: 0.8087 (ttp) cc_final: 0.7730 (ttp) REVERT: o 90 PHE cc_start: 0.9253 (m-10) cc_final: 0.8495 (m-80) REVERT: o 108 PHE cc_start: 0.9247 (m-80) cc_final: 0.7951 (m-80) REVERT: o 110 ILE cc_start: 0.9620 (mt) cc_final: 0.9397 (mt) REVERT: p 326 TYR cc_start: 0.8567 (t80) cc_final: 0.8350 (t80) REVERT: p 330 ASN cc_start: 0.8997 (m-40) cc_final: 0.8677 (m-40) REVERT: p 339 ILE cc_start: 0.7426 (mm) cc_final: 0.6943 (mt) outliers start: 2 outliers final: 0 residues processed: 1090 average time/residue: 0.1371 time to fit residues: 241.7173 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 : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 85 optimal weight: 0.0040 chunk 99 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 143 optimal weight: 0.6980 chunk 227 optimal weight: 2.9990 chunk 243 optimal weight: 3.9990 chunk 253 optimal weight: 2.9990 chunk 223 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 overall best weight: 1.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 751 GLN ** d 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 7 ASN n 92 GLN o 7 ASN ** o 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.084930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.072835 restraints weight = 73375.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.075504 restraints weight = 41077.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.077394 restraints weight = 26167.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.078720 restraints weight = 18081.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.079679 restraints weight = 13323.596| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.6179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 21366 Z= 0.174 Angle : 0.687 10.863 28966 Z= 0.357 Chirality : 0.043 0.412 3430 Planarity : 0.004 0.059 3602 Dihedral : 4.166 20.114 2978 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.85 % Favored : 97.11 % Rotamer: Outliers : 0.09 % Allowed : 1.83 % Favored : 98.08 % 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 aren not related in a simple way. whole: 1.63 (0.16), residues: 2771 helix: 1.72 (0.11), residues: 2068 sheet: -1.19 (1.19), residues: 18 loop : -0.78 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 75 TYR 0.045 0.002 TYR i 144 PHE 0.054 0.002 PHE o 108 TRP 0.031 0.002 TRP b 16 HIS 0.004 0.001 HIS H 111 Details of bonding type rmsd covalent geometry : bond 0.00370 (21366) covalent geometry : angle 0.68715 (28966) hydrogen bonds : bond 0.05231 ( 1744) hydrogen bonds : angle 4.61281 ( 5124) *********************** 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 1064 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1062 time to evaluate : 0.803 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: H 56 MET cc_start: 0.9053 (tmm) cc_final: 0.8669 (tmm) REVERT: H 57 LEU cc_start: 0.9458 (tt) cc_final: 0.9151 (tt) REVERT: H 58 MET cc_start: 0.9422 (tmm) cc_final: 0.9034 (tmm) REVERT: H 62 MET cc_start: 0.8892 (mmm) cc_final: 0.8670 (mmm) REVERT: H 64 GLU cc_start: 0.8517 (tp30) cc_final: 0.8108 (tp30) REVERT: H 68 SER cc_start: 0.9445 (m) cc_final: 0.9079 (t) REVERT: H 91 GLN cc_start: 0.9115 (tt0) cc_final: 0.8616 (tt0) REVERT: H 137 ASN cc_start: 0.9087 (m-40) cc_final: 0.8590 (m110) REVERT: H 140 LYS cc_start: 0.9382 (tttt) cc_final: 0.9023 (ttpt) REVERT: H 147 GLU cc_start: 0.9148 (tt0) cc_final: 0.8590 (tp30) REVERT: H 151 LEU cc_start: 0.9173 (mm) cc_final: 0.8964 (mm) REVERT: L 11 ILE cc_start: 0.8993 (mm) cc_final: 0.8745 (tp) REVERT: L 22 LEU cc_start: 0.9491 (mt) cc_final: 0.9257 (mt) REVERT: L 49 GLU cc_start: 0.8848 (pt0) cc_final: 0.8023 (pp20) REVERT: L 58 ARG cc_start: 0.8430 (mtm110) cc_final: 0.7621 (ttm110) REVERT: L 73 MET cc_start: 0.8610 (mtm) cc_final: 0.8245 (ptp) REVERT: L 89 LEU cc_start: 0.8507 (mt) cc_final: 0.8243 (mp) REVERT: L 95 GLU cc_start: 0.8415 (tm-30) cc_final: 0.8084 (tm-30) REVERT: L 99 ASP cc_start: 0.6223 (p0) cc_final: 0.6007 (t0) REVERT: a 388 GLU cc_start: 0.8270 (tp30) cc_final: 0.7332 (tt0) REVERT: a 397 ILE cc_start: 0.9330 (mm) cc_final: 0.8958 (tp) REVERT: a 401 PHE cc_start: 0.9187 (t80) cc_final: 0.8566 (t80) REVERT: a 414 ILE cc_start: 0.8897 (mm) cc_final: 0.8644 (mm) REVERT: a 423 MET cc_start: 0.9293 (mpp) cc_final: 0.8952 (mpp) REVERT: a 449 ILE cc_start: 0.9461 (mt) cc_final: 0.9044 (mt) REVERT: a 453 MET cc_start: 0.9005 (mtp) cc_final: 0.8600 (mtp) REVERT: a 467 CYS cc_start: 0.6445 (t) cc_final: 0.6171 (t) REVERT: a 538 MET cc_start: 0.8562 (ttt) cc_final: 0.8175 (ppp) REVERT: a 580 MET cc_start: 0.8958 (mmm) cc_final: 0.8633 (mmm) REVERT: a 616 MET cc_start: 0.9272 (ttp) cc_final: 0.8799 (tmm) REVERT: a 636 ILE cc_start: 0.9313 (mm) cc_final: 0.9038 (tp) REVERT: a 637 GLN cc_start: 0.8661 (mt0) cc_final: 0.8438 (mt0) REVERT: a 651 MET cc_start: 0.9005 (mmm) cc_final: 0.8182 (mmm) REVERT: a 721 GLN cc_start: 0.9271 (tp40) cc_final: 0.8610 (tp-100) REVERT: a 725 THR cc_start: 0.9649 (m) cc_final: 0.9445 (m) REVERT: a 759 MET cc_start: 0.8097 (mmm) cc_final: 0.7439 (tmm) REVERT: a 801 LEU cc_start: 0.9488 (tt) cc_final: 0.9254 (tt) REVERT: a 804 LEU cc_start: 0.9488 (tp) cc_final: 0.9201 (tt) REVERT: a 810 GLU cc_start: 0.7825 (mp0) cc_final: 0.6987 (mp0) REVERT: b 19 MET cc_start: 0.8923 (mtp) cc_final: 0.8420 (mtt) REVERT: b 25 CYS cc_start: 0.9219 (m) cc_final: 0.8844 (t) REVERT: b 30 ASP cc_start: 0.8745 (t70) cc_final: 0.8510 (t0) REVERT: b 34 ARG cc_start: 0.8328 (mmm160) cc_final: 0.6554 (tpt170) REVERT: b 36 ASP cc_start: 0.8363 (t70) cc_final: 0.7749 (t0) REVERT: b 48 MET cc_start: 0.8758 (ttt) cc_final: 0.8351 (tmm) REVERT: b 52 LEU cc_start: 0.9496 (mt) cc_final: 0.9121 (mt) REVERT: b 70 TYR cc_start: 0.9019 (p90) cc_final: 0.8596 (p90) REVERT: b 71 ILE cc_start: 0.9613 (mm) cc_final: 0.9187 (mm) REVERT: b 74 SER cc_start: 0.9512 (m) cc_final: 0.9158 (t) REVERT: b 75 SER cc_start: 0.9631 (m) cc_final: 0.9361 (p) REVERT: b 82 LYS cc_start: 0.9097 (mmtt) cc_final: 0.8617 (mmtp) REVERT: b 98 GLU cc_start: 0.8779 (mm-30) cc_final: 0.8443 (mm-30) REVERT: b 130 ASN cc_start: 0.9090 (m-40) cc_final: 0.8860 (m-40) REVERT: b 135 TYR cc_start: 0.8938 (m-80) cc_final: 0.8507 (m-10) REVERT: b 137 MET cc_start: 0.9367 (ttt) cc_final: 0.8883 (tpp) REVERT: b 148 ASN cc_start: 0.9615 (m110) cc_final: 0.9285 (m110) REVERT: b 169 ASN cc_start: 0.9155 (t0) cc_final: 0.8378 (t0) REVERT: b 172 LEU cc_start: 0.8648 (mt) cc_final: 0.7931 (mt) REVERT: b 186 ILE cc_start: 0.9187 (mt) cc_final: 0.8984 (mt) REVERT: c 423 LEU cc_start: 0.9153 (mt) cc_final: 0.8927 (mt) REVERT: c 439 MET cc_start: 0.9318 (mmm) cc_final: 0.8827 (mmm) REVERT: d 3 PHE cc_start: 0.7750 (m-80) cc_final: 0.7059 (m-10) REVERT: d 23 LEU cc_start: 0.9208 (mm) cc_final: 0.8965 (mm) REVERT: d 40 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7732 (mp0) REVERT: d 76 GLU cc_start: 0.8589 (tt0) cc_final: 0.8007 (tp30) REVERT: d 85 MET cc_start: 0.9243 (mtp) cc_final: 0.8913 (ttp) REVERT: d 98 ASP cc_start: 0.8873 (m-30) cc_final: 0.8166 (t0) REVERT: d 105 MET cc_start: 0.8882 (ttm) cc_final: 0.8543 (ttm) REVERT: d 108 ASN cc_start: 0.8795 (m110) cc_final: 0.8206 (m110) REVERT: d 110 ILE cc_start: 0.9441 (mm) cc_final: 0.9221 (mm) REVERT: d 111 LEU cc_start: 0.9422 (tp) cc_final: 0.9195 (tt) REVERT: d 124 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8447 (mt-10) REVERT: d 128 LYS cc_start: 0.9140 (mmtt) cc_final: 0.8441 (mttt) REVERT: d 130 HIS cc_start: 0.8287 (t-90) cc_final: 0.7842 (t-90) REVERT: d 176 MET cc_start: 0.8203 (mtt) cc_final: 0.7883 (mtt) REVERT: d 191 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8221 (mm-30) REVERT: d 214 PHE cc_start: 0.9250 (t80) cc_final: 0.8818 (t80) REVERT: d 241 PHE cc_start: 0.8698 (m-80) cc_final: 0.8342 (m-80) REVERT: d 244 CYS cc_start: 0.8126 (m) cc_final: 0.7355 (m) REVERT: d 257 ARG cc_start: 0.9579 (mmm-85) cc_final: 0.9077 (mtp-110) REVERT: d 297 HIS cc_start: 0.9060 (t-90) cc_final: 0.8450 (t-90) REVERT: d 298 GLU cc_start: 0.9213 (tt0) cc_final: 0.8918 (tm-30) REVERT: d 335 CYS cc_start: 0.8631 (m) cc_final: 0.8041 (t) REVERT: e 9 PRO cc_start: 0.8277 (Cg_exo) cc_final: 0.7961 (Cg_endo) REVERT: e 13 PHE cc_start: 0.7941 (m-80) cc_final: 0.7428 (m-80) REVERT: e 47 CYS cc_start: 0.8332 (p) cc_final: 0.7463 (p) REVERT: e 52 TRP cc_start: 0.9488 (t60) cc_final: 0.9223 (t60) REVERT: e 68 LEU cc_start: 0.8725 (tp) cc_final: 0.8410 (tp) REVERT: f 67 TYR cc_start: 0.8631 (m-80) cc_final: 0.8234 (m-80) REVERT: g 25 PHE cc_start: 0.9102 (m-80) cc_final: 0.8822 (m-80) REVERT: g 44 MET cc_start: 0.9551 (ppp) cc_final: 0.8885 (ppp) REVERT: g 45 SER cc_start: 0.9675 (p) cc_final: 0.9187 (p) REVERT: g 61 MET cc_start: 0.8113 (mmt) cc_final: 0.7678 (mmt) REVERT: g 88 ARG cc_start: 0.8422 (mmm160) cc_final: 0.8011 (mmt180) REVERT: g 108 PHE cc_start: 0.9126 (m-80) cc_final: 0.8352 (m-80) REVERT: g 131 MET cc_start: 0.9419 (ttt) cc_final: 0.9061 (ttt) REVERT: g 137 PHE cc_start: 0.8863 (m-10) cc_final: 0.8630 (m-80) REVERT: g 141 LEU cc_start: 0.9277 (mt) cc_final: 0.9021 (mt) REVERT: g 144 TYR cc_start: 0.9107 (m-80) cc_final: 0.8410 (m-80) REVERT: h 55 SER cc_start: 0.9572 (p) cc_final: 0.9371 (p) REVERT: h 146 LEU cc_start: 0.9541 (tt) cc_final: 0.9222 (tt) REVERT: i 44 MET cc_start: 0.8118 (ppp) cc_final: 0.7605 (ppp) REVERT: i 47 MET cc_start: 0.8908 (mmp) cc_final: 0.8382 (mmt) REVERT: i 61 MET cc_start: 0.9250 (mtm) cc_final: 0.8705 (ptp) REVERT: i 64 ILE cc_start: 0.8945 (mt) cc_final: 0.8675 (mt) REVERT: i 65 ILE cc_start: 0.9253 (mm) cc_final: 0.8899 (mm) REVERT: i 68 TYR cc_start: 0.9149 (m-10) cc_final: 0.8782 (m-80) REVERT: i 90 PHE cc_start: 0.7960 (m-10) cc_final: 0.7343 (m-80) REVERT: i 110 ILE cc_start: 0.9549 (mt) cc_final: 0.9228 (tt) REVERT: i 139 GLU cc_start: 0.9142 (tp30) cc_final: 0.8299 (tp30) REVERT: j 17 MET cc_start: 0.8782 (tpt) cc_final: 0.8355 (tpt) REVERT: j 48 ARG cc_start: 0.9063 (mpp80) cc_final: 0.8651 (mpp80) REVERT: j 61 MET cc_start: 0.8909 (tpp) cc_final: 0.8659 (tpp) REVERT: j 70 LEU cc_start: 0.9676 (tp) cc_final: 0.9426 (tp) REVERT: j 118 VAL cc_start: 0.9673 (t) cc_final: 0.9400 (p) REVERT: j 127 LEU cc_start: 0.9135 (tt) cc_final: 0.8610 (tt) REVERT: j 131 MET cc_start: 0.8940 (ttt) cc_final: 0.8608 (ttt) REVERT: j 136 ILE cc_start: 0.9178 (mm) cc_final: 0.8861 (mm) REVERT: j 143 LEU cc_start: 0.9288 (mt) cc_final: 0.9023 (mt) REVERT: k 32 TYR cc_start: 0.8840 (t80) cc_final: 0.8367 (t80) REVERT: k 47 MET cc_start: 0.8645 (mpp) cc_final: 0.8359 (mpp) REVERT: k 48 ARG cc_start: 0.8138 (mmt90) cc_final: 0.7920 (mmt90) REVERT: k 54 LYS cc_start: 0.8338 (mttt) cc_final: 0.7386 (tttt) REVERT: k 61 MET cc_start: 0.9139 (mtm) cc_final: 0.8853 (mpp) REVERT: k 76 ILE cc_start: 0.9432 (mt) cc_final: 0.8325 (tt) REVERT: k 80 LEU cc_start: 0.9175 (mt) cc_final: 0.8910 (mt) REVERT: k 90 PHE cc_start: 0.8860 (m-80) cc_final: 0.8482 (m-80) REVERT: k 92 GLN cc_start: 0.9156 (mt0) cc_final: 0.8668 (mt0) REVERT: k 123 GLN cc_start: 0.8902 (tp40) cc_final: 0.7810 (tm-30) REVERT: k 124 GLN cc_start: 0.9022 (tm-30) cc_final: 0.8246 (tm-30) REVERT: k 128 PHE cc_start: 0.7438 (t80) cc_final: 0.7231 (t80) REVERT: k 133 LEU cc_start: 0.9262 (mt) cc_final: 0.8853 (mt) REVERT: k 137 PHE cc_start: 0.9113 (m-80) cc_final: 0.8397 (m-80) REVERT: k 150 LEU cc_start: 0.9003 (tt) cc_final: 0.8712 (mt) REVERT: l 54 LYS cc_start: 0.8957 (mttt) cc_final: 0.8160 (mmtt) REVERT: l 61 MET cc_start: 0.9089 (mmm) cc_final: 0.8215 (mmm) REVERT: l 90 PHE cc_start: 0.8525 (m-10) cc_final: 0.8110 (m-80) REVERT: l 101 LEU cc_start: 0.9403 (mt) cc_final: 0.9114 (mt) REVERT: l 118 VAL cc_start: 0.9759 (t) cc_final: 0.9404 (m) REVERT: l 123 GLN cc_start: 0.8772 (mp10) cc_final: 0.8524 (mp10) REVERT: l 131 MET cc_start: 0.8927 (ttp) cc_final: 0.8665 (ttp) REVERT: m 13 PHE cc_start: 0.9450 (t80) cc_final: 0.9139 (t80) REVERT: m 17 MET cc_start: 0.9271 (mtm) cc_final: 0.9015 (mtm) REVERT: m 21 SER cc_start: 0.9360 (m) cc_final: 0.8994 (p) REVERT: m 25 PHE cc_start: 0.8930 (m-80) cc_final: 0.8594 (m-80) REVERT: m 47 MET cc_start: 0.8347 (tpp) cc_final: 0.7755 (tpp) REVERT: m 48 ARG cc_start: 0.8769 (mmm-85) cc_final: 0.8098 (mmm-85) REVERT: m 52 ILE cc_start: 0.9367 (mt) cc_final: 0.9035 (mt) REVERT: m 53 MET cc_start: 0.9042 (tpp) cc_final: 0.8836 (tpp) REVERT: m 61 MET cc_start: 0.9520 (mmm) cc_final: 0.9197 (mmm) REVERT: m 80 LEU cc_start: 0.9395 (mt) cc_final: 0.9152 (mt) REVERT: m 86 LEU cc_start: 0.9111 (tp) cc_final: 0.8680 (tp) REVERT: m 90 PHE cc_start: 0.9407 (m-10) cc_final: 0.8760 (m-80) REVERT: m 92 GLN cc_start: 0.9068 (mt0) cc_final: 0.8756 (mt0) REVERT: n 13 PHE cc_start: 0.8771 (t80) cc_final: 0.8110 (t80) REVERT: n 17 MET cc_start: 0.9085 (mmt) cc_final: 0.8682 (mmt) REVERT: n 36 LYS cc_start: 0.8659 (mmtt) cc_final: 0.8200 (mmtp) REVERT: n 45 SER cc_start: 0.9087 (m) cc_final: 0.8820 (p) REVERT: n 57 ILE cc_start: 0.9417 (mm) cc_final: 0.9151 (mm) REVERT: n 61 MET cc_start: 0.9003 (mmp) cc_final: 0.8757 (mmm) REVERT: n 68 TYR cc_start: 0.9649 (m-80) cc_final: 0.9044 (m-80) REVERT: n 75 LEU cc_start: 0.9047 (mt) cc_final: 0.8809 (mt) REVERT: n 88 ARG cc_start: 0.8230 (ttm-80) cc_final: 0.7896 (mmm160) REVERT: n 90 PHE cc_start: 0.9617 (m-80) cc_final: 0.9317 (m-80) REVERT: n 124 GLN cc_start: 0.8996 (tp-100) cc_final: 0.8118 (tm-30) REVERT: n 127 LEU cc_start: 0.9537 (tp) cc_final: 0.9312 (tp) REVERT: n 128 PHE cc_start: 0.8918 (t80) cc_final: 0.8677 (t80) REVERT: n 129 VAL cc_start: 0.8743 (t) cc_final: 0.8193 (t) REVERT: o 32 TYR cc_start: 0.8394 (t80) cc_final: 0.7993 (t80) REVERT: o 44 MET cc_start: 0.8157 (ttp) cc_final: 0.7812 (ttp) REVERT: o 90 PHE cc_start: 0.9261 (m-10) cc_final: 0.8637 (m-80) REVERT: o 110 ILE cc_start: 0.9640 (mt) cc_final: 0.9413 (mt) REVERT: o 151 ILE cc_start: 0.9657 (mm) cc_final: 0.9450 (tp) REVERT: p 330 ASN cc_start: 0.8947 (m-40) cc_final: 0.8656 (m110) REVERT: p 338 ILE cc_start: 0.8889 (pt) cc_final: 0.8687 (pt) REVERT: p 339 ILE cc_start: 0.7569 (mm) cc_final: 0.7033 (mt) outliers start: 2 outliers final: 0 residues processed: 1063 average time/residue: 0.1378 time to fit residues: 236.5474 Evaluate side-chains 919 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 919 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 209 optimal weight: 0.7980 chunk 238 optimal weight: 0.9980 chunk 253 optimal weight: 0.9980 chunk 166 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 255 optimal weight: 2.9990 chunk 180 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 191 optimal weight: 5.9990 chunk 268 optimal weight: 0.7980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 81 HIS a 724 HIS ** a 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 33 ASN ** e 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 7 ASN o 7 ASN ** p 308 ASN ** 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 = 0.3467 r_free = 0.3467 target = 0.086368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.073973 restraints weight = 72483.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.076693 restraints weight = 40669.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.078619 restraints weight = 26071.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.079949 restraints weight = 18131.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.080926 restraints weight = 13389.811| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.6365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 21366 Z= 0.166 Angle : 0.708 11.135 28966 Z= 0.365 Chirality : 0.043 0.197 3430 Planarity : 0.004 0.052 3602 Dihedral : 4.190 20.018 2978 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.96 % Favored : 97.00 % Rotamer: Outliers : 0.09 % Allowed : 1.08 % Favored : 98.83 % 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 aren not related in a simple way. whole: 1.62 (0.16), residues: 2771 helix: 1.72 (0.11), residues: 2065 sheet: -0.98 (1.21), residues: 18 loop : -0.79 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG H 126 TYR 0.037 0.002 TYR h 144 PHE 0.027 0.002 PHE b 189 TRP 0.036 0.002 TRP b 16 HIS 0.005 0.001 HIS H 111 Details of bonding type rmsd covalent geometry : bond 0.00360 (21366) covalent geometry : angle 0.70800 (28966) hydrogen bonds : bond 0.05224 ( 1744) hydrogen bonds : angle 4.62139 ( 5124) *********************** 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 1085 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1083 time to evaluate : 0.797 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: H 56 MET cc_start: 0.9040 (tmm) cc_final: 0.8654 (tmm) REVERT: H 57 LEU cc_start: 0.9437 (tt) cc_final: 0.9136 (tt) REVERT: H 58 MET cc_start: 0.9443 (tmm) cc_final: 0.9060 (tmm) REVERT: H 62 MET cc_start: 0.8843 (mmm) cc_final: 0.8607 (mmm) REVERT: H 64 GLU cc_start: 0.8506 (tp30) cc_final: 0.8090 (tp30) REVERT: H 68 SER cc_start: 0.9415 (m) cc_final: 0.8974 (t) REVERT: H 91 GLN cc_start: 0.9093 (tt0) cc_final: 0.8622 (tt0) REVERT: H 137 ASN cc_start: 0.9037 (m-40) cc_final: 0.8538 (m110) REVERT: H 140 LYS cc_start: 0.9376 (tttt) cc_final: 0.9017 (ttpt) REVERT: H 151 LEU cc_start: 0.9194 (mm) cc_final: 0.8919 (mm) REVERT: L 7 LEU cc_start: 0.8468 (mt) cc_final: 0.8082 (pp) REVERT: L 22 LEU cc_start: 0.9450 (mt) cc_final: 0.9195 (mt) REVERT: L 49 GLU cc_start: 0.8855 (pt0) cc_final: 0.7983 (pp20) REVERT: L 58 ARG cc_start: 0.8437 (mtm110) cc_final: 0.7563 (ttm110) REVERT: L 73 MET cc_start: 0.8590 (mtm) cc_final: 0.8224 (ptp) REVERT: L 95 GLU cc_start: 0.8420 (tm-30) cc_final: 0.8079 (tm-30) REVERT: L 99 ASP cc_start: 0.6157 (p0) cc_final: 0.5930 (t0) REVERT: a 388 GLU cc_start: 0.8212 (tp30) cc_final: 0.7318 (tt0) REVERT: a 397 ILE cc_start: 0.9309 (mm) cc_final: 0.8943 (tp) REVERT: a 401 PHE cc_start: 0.9160 (t80) cc_final: 0.8562 (t80) REVERT: a 414 ILE cc_start: 0.8845 (mm) cc_final: 0.8617 (mm) REVERT: a 423 MET cc_start: 0.9281 (mpp) cc_final: 0.8964 (mpp) REVERT: a 449 ILE cc_start: 0.9442 (mt) cc_final: 0.9003 (mt) REVERT: a 453 MET cc_start: 0.8988 (mtp) cc_final: 0.8499 (mtp) REVERT: a 467 CYS cc_start: 0.6419 (t) cc_final: 0.6125 (t) REVERT: a 519 ILE cc_start: 0.7880 (mp) cc_final: 0.7610 (mp) REVERT: a 536 PHE cc_start: 0.9363 (t80) cc_final: 0.9144 (t80) REVERT: a 540 MET cc_start: 0.9236 (mmm) cc_final: 0.8790 (mmm) REVERT: a 549 MET cc_start: 0.9420 (mmm) cc_final: 0.9088 (mmm) REVERT: a 580 MET cc_start: 0.8980 (mmm) cc_final: 0.8641 (mmm) REVERT: a 616 MET cc_start: 0.9239 (ttp) cc_final: 0.8811 (tmm) REVERT: a 636 ILE cc_start: 0.9310 (mm) cc_final: 0.9021 (tp) REVERT: a 651 MET cc_start: 0.8619 (mmm) cc_final: 0.8074 (mmm) REVERT: a 721 GLN cc_start: 0.9204 (tp40) cc_final: 0.8526 (tp-100) REVERT: a 725 THR cc_start: 0.9641 (m) cc_final: 0.9381 (m) REVERT: a 759 MET cc_start: 0.8094 (mmm) cc_final: 0.7423 (tmm) REVERT: a 801 LEU cc_start: 0.9499 (tt) cc_final: 0.9286 (tt) REVERT: a 810 GLU cc_start: 0.7743 (mp0) cc_final: 0.7043 (mp0) REVERT: b 19 MET cc_start: 0.8919 (mtp) cc_final: 0.8407 (mtt) REVERT: b 25 CYS cc_start: 0.9197 (m) cc_final: 0.8831 (t) REVERT: b 30 ASP cc_start: 0.8751 (t70) cc_final: 0.8516 (t0) REVERT: b 34 ARG cc_start: 0.8285 (mmm160) cc_final: 0.6452 (tpt170) REVERT: b 36 ASP cc_start: 0.7731 (t70) cc_final: 0.7151 (t0) REVERT: b 48 MET cc_start: 0.8794 (ttt) cc_final: 0.8279 (tmm) REVERT: b 52 LEU cc_start: 0.9500 (mt) cc_final: 0.9104 (mt) REVERT: b 70 TYR cc_start: 0.8983 (p90) cc_final: 0.8534 (p90) REVERT: b 71 ILE cc_start: 0.9601 (mm) cc_final: 0.9172 (mm) REVERT: b 74 SER cc_start: 0.9517 (m) cc_final: 0.9163 (t) REVERT: b 75 SER cc_start: 0.9622 (m) cc_final: 0.9331 (p) REVERT: b 82 LYS cc_start: 0.9051 (mmtt) cc_final: 0.8594 (mmtp) REVERT: b 90 ASN cc_start: 0.8402 (m110) cc_final: 0.8131 (m110) REVERT: b 96 PHE cc_start: 0.9308 (m-80) cc_final: 0.8650 (m-80) REVERT: b 98 GLU cc_start: 0.8783 (mm-30) cc_final: 0.8444 (mm-30) REVERT: b 114 MET cc_start: 0.7644 (mtm) cc_final: 0.7247 (mtm) REVERT: b 130 ASN cc_start: 0.9084 (m-40) cc_final: 0.8836 (m-40) REVERT: b 135 TYR cc_start: 0.8919 (m-80) cc_final: 0.8476 (m-10) REVERT: b 137 MET cc_start: 0.9374 (ttt) cc_final: 0.8900 (tpp) REVERT: b 148 ASN cc_start: 0.9605 (m110) cc_final: 0.9258 (m110) REVERT: b 169 ASN cc_start: 0.9135 (t0) cc_final: 0.8347 (t0) REVERT: b 172 LEU cc_start: 0.8609 (mt) cc_final: 0.7890 (mt) REVERT: b 203 MET cc_start: 0.8585 (mpp) cc_final: 0.8063 (mtp) REVERT: c 423 LEU cc_start: 0.9154 (mt) cc_final: 0.8903 (mt) REVERT: c 439 MET cc_start: 0.9296 (mmm) cc_final: 0.8796 (mmm) REVERT: c 442 SER cc_start: 0.8540 (t) cc_final: 0.8242 (t) REVERT: d 3 PHE cc_start: 0.7848 (m-80) cc_final: 0.7121 (m-10) REVERT: d 40 GLU cc_start: 0.8326 (mt-10) cc_final: 0.7767 (mp0) REVERT: d 76 GLU cc_start: 0.8576 (tt0) cc_final: 0.8129 (tp30) REVERT: d 85 MET cc_start: 0.9280 (mtp) cc_final: 0.8964 (ttp) REVERT: d 98 ASP cc_start: 0.8859 (m-30) cc_final: 0.8185 (t0) REVERT: d 105 MET cc_start: 0.8903 (ttm) cc_final: 0.8469 (ttm) REVERT: d 110 ILE cc_start: 0.9402 (mm) cc_final: 0.9195 (mm) REVERT: d 124 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8458 (mt-10) REVERT: d 128 LYS cc_start: 0.9192 (mmtt) cc_final: 0.8552 (mttt) REVERT: d 176 MET cc_start: 0.8162 (mtt) cc_final: 0.7869 (mtt) REVERT: d 191 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8228 (mm-30) REVERT: d 211 ILE cc_start: 0.9519 (mt) cc_final: 0.9279 (tp) REVERT: d 221 PHE cc_start: 0.8415 (m-10) cc_final: 0.8141 (m-80) REVERT: d 241 PHE cc_start: 0.8715 (m-80) cc_final: 0.8436 (m-80) REVERT: d 244 CYS cc_start: 0.8141 (m) cc_final: 0.7388 (m) REVERT: d 257 ARG cc_start: 0.9584 (mmm-85) cc_final: 0.9071 (mtp-110) REVERT: d 297 HIS cc_start: 0.8992 (t-90) cc_final: 0.8336 (t-90) REVERT: d 298 GLU cc_start: 0.9200 (tt0) cc_final: 0.8923 (tm-30) REVERT: d 335 CYS cc_start: 0.8616 (m) cc_final: 0.8038 (t) REVERT: e 9 PRO cc_start: 0.8224 (Cg_exo) cc_final: 0.7900 (Cg_endo) REVERT: e 13 PHE cc_start: 0.7963 (m-80) cc_final: 0.7453 (m-80) REVERT: e 47 CYS cc_start: 0.8347 (p) cc_final: 0.7503 (p) REVERT: e 49 TYR cc_start: 0.8725 (t80) cc_final: 0.8485 (t80) REVERT: e 52 TRP cc_start: 0.9477 (t60) cc_final: 0.9134 (t60) REVERT: e 68 LEU cc_start: 0.8718 (tp) cc_final: 0.8254 (tp) REVERT: f 67 TYR cc_start: 0.8640 (m-80) cc_final: 0.8219 (m-80) REVERT: g 25 PHE cc_start: 0.9036 (m-80) cc_final: 0.8778 (m-80) REVERT: g 41 ILE cc_start: 0.9584 (mp) cc_final: 0.9314 (mm) REVERT: g 45 SER cc_start: 0.9658 (p) cc_final: 0.9258 (p) REVERT: g 61 MET cc_start: 0.8070 (mmt) cc_final: 0.7666 (mmt) REVERT: g 88 ARG cc_start: 0.8390 (mmm160) cc_final: 0.7985 (mmt180) REVERT: g 108 PHE cc_start: 0.9091 (m-80) cc_final: 0.8352 (m-80) REVERT: g 131 MET cc_start: 0.9408 (ttt) cc_final: 0.9030 (ttt) REVERT: g 137 PHE cc_start: 0.8810 (m-10) cc_final: 0.8549 (m-80) REVERT: g 141 LEU cc_start: 0.9247 (mt) cc_final: 0.9003 (mt) REVERT: g 144 TYR cc_start: 0.9125 (m-80) cc_final: 0.8473 (m-80) REVERT: g 152 LEU cc_start: 0.9491 (mt) cc_final: 0.9291 (mt) REVERT: h 17 MET cc_start: 0.8658 (mmm) cc_final: 0.8320 (mmm) REVERT: h 84 ILE cc_start: 0.8247 (mt) cc_final: 0.7989 (pt) REVERT: h 97 LEU cc_start: 0.9376 (mm) cc_final: 0.9175 (mm) REVERT: h 150 LEU cc_start: 0.9244 (mt) cc_final: 0.9009 (mt) REVERT: i 14 PHE cc_start: 0.8986 (m-10) cc_final: 0.8515 (m-10) REVERT: i 44 MET cc_start: 0.8137 (ppp) cc_final: 0.7599 (ppp) REVERT: i 47 MET cc_start: 0.8954 (mmp) cc_final: 0.8409 (mmt) REVERT: i 61 MET cc_start: 0.9255 (mtm) cc_final: 0.8702 (ptp) REVERT: i 64 ILE cc_start: 0.8924 (mt) cc_final: 0.8647 (mt) REVERT: i 65 ILE cc_start: 0.9273 (mm) cc_final: 0.8925 (mm) REVERT: i 68 TYR cc_start: 0.9142 (m-10) cc_final: 0.8642 (m-80) REVERT: i 75 LEU cc_start: 0.8841 (mt) cc_final: 0.8637 (mt) REVERT: i 86 LEU cc_start: 0.9367 (tt) cc_final: 0.8749 (tp) REVERT: i 90 PHE cc_start: 0.7766 (m-10) cc_final: 0.7329 (m-80) REVERT: i 110 ILE cc_start: 0.9536 (mt) cc_final: 0.9219 (tt) REVERT: i 139 GLU cc_start: 0.9183 (tp30) cc_final: 0.8279 (tp30) REVERT: j 17 MET cc_start: 0.8697 (tpt) cc_final: 0.8277 (tpt) REVERT: j 48 ARG cc_start: 0.9037 (mpp80) cc_final: 0.8696 (mpp80) REVERT: j 61 MET cc_start: 0.8930 (tpp) cc_final: 0.8662 (tpp) REVERT: j 68 TYR cc_start: 0.9028 (m-80) cc_final: 0.8753 (m-80) REVERT: j 70 LEU cc_start: 0.9650 (tp) cc_final: 0.9321 (tp) REVERT: j 118 VAL cc_start: 0.9658 (t) cc_final: 0.9368 (p) REVERT: j 127 LEU cc_start: 0.9136 (tt) cc_final: 0.8230 (tt) REVERT: j 136 ILE cc_start: 0.9168 (mm) cc_final: 0.8850 (mm) REVERT: k 32 TYR cc_start: 0.8856 (t80) cc_final: 0.8355 (t80) REVERT: k 47 MET cc_start: 0.8667 (mpp) cc_final: 0.8385 (mpp) REVERT: k 48 ARG cc_start: 0.8063 (mmt90) cc_final: 0.7819 (mmt90) REVERT: k 54 LYS cc_start: 0.8375 (mttt) cc_final: 0.7423 (tttt) REVERT: k 61 MET cc_start: 0.9216 (mtm) cc_final: 0.8927 (mpp) REVERT: k 76 ILE cc_start: 0.9441 (mt) cc_final: 0.8553 (tt) REVERT: k 80 LEU cc_start: 0.9173 (mt) cc_final: 0.8878 (mt) REVERT: k 92 GLN cc_start: 0.9138 (mt0) cc_final: 0.8879 (mt0) REVERT: k 123 GLN cc_start: 0.8907 (tp40) cc_final: 0.8296 (tp40) REVERT: k 124 GLN cc_start: 0.9001 (tm-30) cc_final: 0.8607 (tm-30) REVERT: k 133 LEU cc_start: 0.9258 (mt) cc_final: 0.8862 (mt) REVERT: k 137 PHE cc_start: 0.9071 (m-80) cc_final: 0.8465 (m-80) REVERT: k 147 ILE cc_start: 0.9636 (mt) cc_final: 0.9355 (tp) REVERT: k 150 LEU cc_start: 0.9000 (tt) cc_final: 0.8702 (mt) REVERT: l 32 TYR cc_start: 0.9238 (t80) cc_final: 0.8772 (t80) REVERT: l 54 LYS cc_start: 0.8939 (mttt) cc_final: 0.8151 (mmtt) REVERT: l 61 MET cc_start: 0.9122 (mmm) cc_final: 0.8235 (mmm) REVERT: l 68 TYR cc_start: 0.9022 (m-80) cc_final: 0.8568 (m-80) REVERT: l 90 PHE cc_start: 0.8578 (m-10) cc_final: 0.8122 (m-80) REVERT: l 101 LEU cc_start: 0.9387 (mt) cc_final: 0.9167 (mt) REVERT: l 118 VAL cc_start: 0.9758 (t) cc_final: 0.9409 (m) REVERT: l 123 GLN cc_start: 0.8777 (mp10) cc_final: 0.8552 (mp10) REVERT: l 131 MET cc_start: 0.8935 (ttp) cc_final: 0.8667 (ttp) REVERT: l 152 LEU cc_start: 0.9533 (mp) cc_final: 0.8961 (tp) REVERT: m 13 PHE cc_start: 0.9421 (t80) cc_final: 0.9098 (t80) REVERT: m 17 MET cc_start: 0.9283 (mtm) cc_final: 0.9009 (mtm) REVERT: m 21 SER cc_start: 0.9345 (m) cc_final: 0.8908 (p) REVERT: m 25 PHE cc_start: 0.8925 (m-80) cc_final: 0.8528 (m-80) REVERT: m 47 MET cc_start: 0.8324 (tpp) cc_final: 0.7671 (tpp) REVERT: m 48 ARG cc_start: 0.8714 (mmm-85) cc_final: 0.8094 (mmm-85) REVERT: m 52 ILE cc_start: 0.9378 (mt) cc_final: 0.9146 (mt) REVERT: m 61 MET cc_start: 0.9523 (mmm) cc_final: 0.9199 (mmm) REVERT: m 80 LEU cc_start: 0.9359 (mt) cc_final: 0.9125 (mt) REVERT: m 86 LEU cc_start: 0.9087 (tp) cc_final: 0.8715 (tp) REVERT: m 90 PHE cc_start: 0.9352 (m-10) cc_final: 0.8735 (m-80) REVERT: m 92 GLN cc_start: 0.9074 (mt0) cc_final: 0.8775 (mt0) REVERT: n 13 PHE cc_start: 0.8689 (t80) cc_final: 0.8018 (t80) REVERT: n 17 MET cc_start: 0.9030 (mmt) cc_final: 0.8618 (mmt) REVERT: n 36 LYS cc_start: 0.8648 (mmtt) cc_final: 0.8210 (mmtp) REVERT: n 45 SER cc_start: 0.9108 (m) cc_final: 0.8864 (p) REVERT: n 57 ILE cc_start: 0.9366 (mm) cc_final: 0.9110 (mm) REVERT: n 61 MET cc_start: 0.9013 (mmp) cc_final: 0.8780 (mmm) REVERT: n 68 TYR cc_start: 0.9640 (m-80) cc_final: 0.9081 (m-80) REVERT: n 75 LEU cc_start: 0.9032 (mt) cc_final: 0.8789 (mt) REVERT: n 88 ARG cc_start: 0.8266 (ttm-80) cc_final: 0.7944 (mmm160) REVERT: n 90 PHE cc_start: 0.9617 (m-80) cc_final: 0.9357 (m-80) REVERT: n 124 GLN cc_start: 0.8971 (tp-100) cc_final: 0.8092 (tm-30) REVERT: n 127 LEU cc_start: 0.9516 (tp) cc_final: 0.9300 (tp) REVERT: n 128 PHE cc_start: 0.8861 (t80) cc_final: 0.8634 (t80) REVERT: n 133 LEU cc_start: 0.9685 (mm) cc_final: 0.9471 (mm) REVERT: n 140 VAL cc_start: 0.9517 (t) cc_final: 0.9165 (t) REVERT: n 141 LEU cc_start: 0.9575 (mt) cc_final: 0.9287 (mt) REVERT: n 144 TYR cc_start: 0.9101 (m-10) cc_final: 0.8566 (m-10) REVERT: o 44 MET cc_start: 0.8144 (ttp) cc_final: 0.7781 (ttp) REVERT: o 48 ARG cc_start: 0.8689 (ptp-110) cc_final: 0.8430 (ptp-110) REVERT: o 68 TYR cc_start: 0.8520 (m-10) cc_final: 0.7949 (m-80) REVERT: o 90 PHE cc_start: 0.9083 (m-10) cc_final: 0.8619 (m-10) REVERT: o 143 LEU cc_start: 0.9217 (tp) cc_final: 0.8777 (mt) REVERT: p 313 ILE cc_start: 0.9484 (mt) cc_final: 0.9052 (mt) REVERT: p 339 ILE cc_start: 0.7671 (mm) cc_final: 0.7170 (mt) outliers start: 2 outliers final: 0 residues processed: 1084 average time/residue: 0.1388 time to fit residues: 243.3763 Evaluate side-chains 922 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 922 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 218 optimal weight: 0.0030 chunk 194 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 73 optimal weight: 7.9990 chunk 217 optimal weight: 6.9990 chunk 263 optimal weight: 2.9990 chunk 138 optimal weight: 10.0000 chunk 78 optimal weight: 7.9990 chunk 133 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 276 optimal weight: 0.7980 overall best weight: 1.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 81 HIS ** a 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 751 GLN ** d 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 130 HIS ** d 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 92 GLN j 124 GLN m 7 ASN o 7 ASN ** p 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.085537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.073417 restraints weight = 73023.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.076084 restraints weight = 40667.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.077949 restraints weight = 25929.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.079258 restraints weight = 18061.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.080206 restraints weight = 13290.661| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.6525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 21366 Z= 0.182 Angle : 0.723 12.785 28966 Z= 0.378 Chirality : 0.044 0.340 3430 Planarity : 0.005 0.057 3602 Dihedral : 4.224 20.387 2978 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.25 % Favored : 96.72 % Rotamer: Outliers : 0.09 % Allowed : 0.80 % Favored : 99.11 % 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 aren not related in a simple way. whole: 1.55 (0.16), residues: 2771 helix: 1.66 (0.11), residues: 2075 sheet: -1.03 (1.21), residues: 18 loop : -0.83 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG m 119 TYR 0.032 0.002 TYR H 138 PHE 0.039 0.002 PHE b 33 TRP 0.036 0.002 TRP b 16 HIS 0.005 0.001 HIS a 412 Details of bonding type rmsd covalent geometry : bond 0.00400 (21366) covalent geometry : angle 0.72338 (28966) hydrogen bonds : bond 0.05219 ( 1744) hydrogen bonds : angle 4.65609 ( 5124) *********************** 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 1052 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1050 time to evaluate : 0.767 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 56 MET cc_start: 0.9029 (tmm) cc_final: 0.8622 (tmm) REVERT: H 57 LEU cc_start: 0.9437 (tt) cc_final: 0.9117 (tt) REVERT: H 58 MET cc_start: 0.9442 (tmm) cc_final: 0.9125 (tmm) REVERT: H 62 MET cc_start: 0.8852 (mmm) cc_final: 0.8637 (mmm) REVERT: H 64 GLU cc_start: 0.8507 (tp30) cc_final: 0.8110 (tp30) REVERT: H 68 SER cc_start: 0.9447 (m) cc_final: 0.9073 (t) REVERT: H 91 GLN cc_start: 0.9142 (tt0) cc_final: 0.8662 (tt0) REVERT: H 137 ASN cc_start: 0.9007 (m-40) cc_final: 0.8493 (m110) REVERT: H 140 LYS cc_start: 0.9387 (tttt) cc_final: 0.9026 (ttpt) REVERT: H 147 GLU cc_start: 0.9126 (tp30) cc_final: 0.8876 (tp30) REVERT: L 22 LEU cc_start: 0.9442 (mt) cc_final: 0.9200 (mt) REVERT: L 49 GLU cc_start: 0.8903 (pt0) cc_final: 0.7992 (pp20) REVERT: L 58 ARG cc_start: 0.8532 (mtm110) cc_final: 0.7761 (ttm110) REVERT: L 73 MET cc_start: 0.8579 (mtm) cc_final: 0.8220 (ptp) REVERT: L 95 GLU cc_start: 0.8453 (tm-30) cc_final: 0.8152 (tm-30) REVERT: L 99 ASP cc_start: 0.6294 (p0) cc_final: 0.6038 (t0) REVERT: a 388 GLU cc_start: 0.8244 (tp30) cc_final: 0.7509 (tt0) REVERT: a 397 ILE cc_start: 0.9320 (mm) cc_final: 0.8955 (tp) REVERT: a 401 PHE cc_start: 0.9167 (t80) cc_final: 0.8572 (t80) REVERT: a 403 PHE cc_start: 0.9054 (t80) cc_final: 0.8781 (t80) REVERT: a 414 ILE cc_start: 0.8858 (mm) cc_final: 0.8581 (mm) REVERT: a 423 MET cc_start: 0.9270 (mpp) cc_final: 0.8949 (mpp) REVERT: a 449 ILE cc_start: 0.9445 (mt) cc_final: 0.9029 (mt) REVERT: a 453 MET cc_start: 0.9012 (mtp) cc_final: 0.8532 (mtp) REVERT: a 467 CYS cc_start: 0.6322 (t) cc_final: 0.6010 (t) REVERT: a 540 MET cc_start: 0.9231 (mmm) cc_final: 0.8834 (mmm) REVERT: a 549 MET cc_start: 0.9451 (mmm) cc_final: 0.9112 (mmm) REVERT: a 576 GLU cc_start: 0.9004 (pm20) cc_final: 0.8555 (pm20) REVERT: a 580 MET cc_start: 0.8888 (mmm) cc_final: 0.8521 (mmm) REVERT: a 616 MET cc_start: 0.9211 (ttp) cc_final: 0.8786 (tmm) REVERT: a 636 ILE cc_start: 0.9331 (mm) cc_final: 0.9059 (tp) REVERT: a 651 MET cc_start: 0.8847 (mmm) cc_final: 0.8427 (mmt) REVERT: a 721 GLN cc_start: 0.9231 (tp40) cc_final: 0.8774 (tp-100) REVERT: a 759 MET cc_start: 0.8048 (mmm) cc_final: 0.7516 (tmm) REVERT: a 801 LEU cc_start: 0.9504 (tt) cc_final: 0.9271 (tt) REVERT: a 810 GLU cc_start: 0.7723 (mp0) cc_final: 0.6961 (mp0) REVERT: b 19 MET cc_start: 0.8926 (mtp) cc_final: 0.8418 (mtt) REVERT: b 25 CYS cc_start: 0.9192 (m) cc_final: 0.8831 (t) REVERT: b 30 ASP cc_start: 0.8741 (t70) cc_final: 0.8512 (t0) REVERT: b 34 ARG cc_start: 0.8405 (mmm160) cc_final: 0.6666 (tpt170) REVERT: b 36 ASP cc_start: 0.7948 (t70) cc_final: 0.7432 (t0) REVERT: b 48 MET cc_start: 0.8746 (ttt) cc_final: 0.8305 (tmm) REVERT: b 52 LEU cc_start: 0.9510 (mt) cc_final: 0.9024 (mt) REVERT: b 70 TYR cc_start: 0.8973 (p90) cc_final: 0.8498 (p90) REVERT: b 71 ILE cc_start: 0.9598 (mm) cc_final: 0.9160 (mm) REVERT: b 74 SER cc_start: 0.9542 (m) cc_final: 0.9216 (t) REVERT: b 75 SER cc_start: 0.9612 (m) cc_final: 0.9345 (p) REVERT: b 82 LYS cc_start: 0.9082 (mmtt) cc_final: 0.8641 (mmtp) REVERT: b 86 ILE cc_start: 0.8946 (mt) cc_final: 0.8542 (mt) REVERT: b 90 ASN cc_start: 0.8399 (m110) cc_final: 0.7873 (m110) REVERT: b 98 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8432 (mm-30) REVERT: b 130 ASN cc_start: 0.9118 (m-40) cc_final: 0.8888 (m-40) REVERT: b 135 TYR cc_start: 0.8948 (m-80) cc_final: 0.8508 (m-10) REVERT: b 137 MET cc_start: 0.9371 (ttt) cc_final: 0.8938 (tpp) REVERT: b 148 ASN cc_start: 0.9609 (m110) cc_final: 0.9247 (m110) REVERT: b 169 ASN cc_start: 0.9131 (t0) cc_final: 0.8253 (t0) REVERT: b 172 LEU cc_start: 0.8578 (mt) cc_final: 0.7853 (mt) REVERT: b 203 MET cc_start: 0.8609 (mpp) cc_final: 0.8017 (mtp) REVERT: c 439 MET cc_start: 0.9241 (mmm) cc_final: 0.8755 (mmm) REVERT: c 442 SER cc_start: 0.8538 (t) cc_final: 0.8321 (t) REVERT: d 3 PHE cc_start: 0.8003 (m-80) cc_final: 0.7507 (m-10) REVERT: d 40 GLU cc_start: 0.8308 (mt-10) cc_final: 0.7782 (mp0) REVERT: d 76 GLU cc_start: 0.8657 (tt0) cc_final: 0.8087 (tp30) REVERT: d 85 MET cc_start: 0.9264 (mtp) cc_final: 0.8936 (ttp) REVERT: d 98 ASP cc_start: 0.8872 (m-30) cc_final: 0.8154 (t0) REVERT: d 110 ILE cc_start: 0.9404 (mm) cc_final: 0.9201 (mm) REVERT: d 124 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8477 (mt-10) REVERT: d 128 LYS cc_start: 0.9258 (mmtt) cc_final: 0.8592 (mttt) REVERT: d 176 MET cc_start: 0.8166 (mtt) cc_final: 0.7924 (mtp) REVERT: d 191 GLU cc_start: 0.8854 (mm-30) cc_final: 0.8244 (mm-30) REVERT: d 211 ILE cc_start: 0.9499 (mt) cc_final: 0.9268 (tp) REVERT: d 214 PHE cc_start: 0.9193 (t80) cc_final: 0.8765 (t80) REVERT: d 221 PHE cc_start: 0.8439 (m-10) cc_final: 0.8100 (m-80) REVERT: d 241 PHE cc_start: 0.8766 (m-80) cc_final: 0.8456 (m-80) REVERT: d 244 CYS cc_start: 0.8087 (m) cc_final: 0.7225 (m) REVERT: d 257 ARG cc_start: 0.9579 (mmm-85) cc_final: 0.9071 (mtp-110) REVERT: d 297 HIS cc_start: 0.9010 (t-90) cc_final: 0.8394 (t-90) REVERT: d 298 GLU cc_start: 0.9222 (tt0) cc_final: 0.8905 (tm-30) REVERT: d 335 CYS cc_start: 0.8636 (m) cc_final: 0.8045 (t) REVERT: e 9 PRO cc_start: 0.8218 (Cg_exo) cc_final: 0.7840 (Cg_endo) REVERT: e 13 PHE cc_start: 0.8071 (m-80) cc_final: 0.7494 (m-80) REVERT: e 47 CYS cc_start: 0.8398 (p) cc_final: 0.7567 (p) REVERT: e 49 TYR cc_start: 0.8750 (t80) cc_final: 0.8544 (t80) REVERT: e 68 LEU cc_start: 0.8903 (tp) cc_final: 0.8613 (tp) REVERT: f 67 TYR cc_start: 0.8683 (m-80) cc_final: 0.8269 (m-80) REVERT: g 25 PHE cc_start: 0.9027 (m-80) cc_final: 0.8777 (m-80) REVERT: g 45 SER cc_start: 0.9570 (p) cc_final: 0.9307 (p) REVERT: g 51 LEU cc_start: 0.9098 (mt) cc_final: 0.8839 (mt) REVERT: g 61 MET cc_start: 0.8203 (mmt) cc_final: 0.7778 (mmt) REVERT: g 88 ARG cc_start: 0.8574 (mmm160) cc_final: 0.7974 (mmt180) REVERT: g 108 PHE cc_start: 0.9079 (m-80) cc_final: 0.8363 (m-80) REVERT: g 137 PHE cc_start: 0.8832 (m-10) cc_final: 0.8572 (m-80) REVERT: g 141 LEU cc_start: 0.9228 (mt) cc_final: 0.8997 (mt) REVERT: g 144 TYR cc_start: 0.9092 (m-80) cc_final: 0.8463 (m-80) REVERT: g 152 LEU cc_start: 0.9518 (mt) cc_final: 0.9313 (mt) REVERT: h 17 MET cc_start: 0.8708 (mmm) cc_final: 0.8355 (mmm) REVERT: h 54 LYS cc_start: 0.8836 (mmmt) cc_final: 0.8433 (mmmt) REVERT: h 84 ILE cc_start: 0.8195 (mt) cc_final: 0.7901 (pt) REVERT: h 97 LEU cc_start: 0.9349 (mm) cc_final: 0.9142 (mm) REVERT: h 146 LEU cc_start: 0.9574 (tp) cc_final: 0.9372 (tp) REVERT: h 150 LEU cc_start: 0.9242 (mt) cc_final: 0.8994 (mt) REVERT: i 14 PHE cc_start: 0.9016 (m-10) cc_final: 0.8603 (m-10) REVERT: i 61 MET cc_start: 0.9265 (mtm) cc_final: 0.8697 (ptp) REVERT: i 64 ILE cc_start: 0.8937 (mt) cc_final: 0.8517 (mt) REVERT: i 65 ILE cc_start: 0.9246 (mm) cc_final: 0.8851 (mm) REVERT: i 68 TYR cc_start: 0.9133 (m-10) cc_final: 0.8655 (m-80) REVERT: i 75 LEU cc_start: 0.8828 (mt) cc_final: 0.8625 (mt) REVERT: i 86 LEU cc_start: 0.9376 (tt) cc_final: 0.8729 (tp) REVERT: i 90 PHE cc_start: 0.7866 (m-10) cc_final: 0.7433 (m-80) REVERT: i 110 ILE cc_start: 0.9525 (mt) cc_final: 0.9224 (tt) REVERT: i 139 GLU cc_start: 0.9130 (tp30) cc_final: 0.8096 (tp30) REVERT: j 17 MET cc_start: 0.8670 (tpt) cc_final: 0.8257 (tpt) REVERT: j 48 ARG cc_start: 0.9077 (mpp80) cc_final: 0.8703 (mpp80) REVERT: j 61 MET cc_start: 0.8903 (tpp) cc_final: 0.8605 (tpp) REVERT: j 68 TYR cc_start: 0.9017 (m-80) cc_final: 0.8803 (m-80) REVERT: j 70 LEU cc_start: 0.9661 (tp) cc_final: 0.9340 (tp) REVERT: j 134 ILE cc_start: 0.8789 (pt) cc_final: 0.8579 (pt) REVERT: j 136 ILE cc_start: 0.9192 (mm) cc_final: 0.8900 (mm) REVERT: j 143 LEU cc_start: 0.9186 (mt) cc_final: 0.8980 (mt) REVERT: k 32 TYR cc_start: 0.8846 (t80) cc_final: 0.8349 (t80) REVERT: k 47 MET cc_start: 0.8718 (mpp) cc_final: 0.8436 (mpp) REVERT: k 48 ARG cc_start: 0.8153 (mmt90) cc_final: 0.7844 (mmt90) REVERT: k 54 LYS cc_start: 0.8380 (mttt) cc_final: 0.7245 (ttmm) REVERT: k 76 ILE cc_start: 0.9454 (mt) cc_final: 0.8312 (tt) REVERT: k 80 LEU cc_start: 0.9156 (mt) cc_final: 0.8845 (mt) REVERT: k 92 GLN cc_start: 0.9163 (mt0) cc_final: 0.8784 (mt0) REVERT: k 123 GLN cc_start: 0.8929 (tp40) cc_final: 0.8301 (tp40) REVERT: k 124 GLN cc_start: 0.9016 (tm-30) cc_final: 0.8658 (tm-30) REVERT: k 133 LEU cc_start: 0.9263 (mt) cc_final: 0.8875 (mt) REVERT: k 137 PHE cc_start: 0.9093 (m-80) cc_final: 0.8475 (m-80) REVERT: k 147 ILE cc_start: 0.9627 (mt) cc_final: 0.9342 (tp) REVERT: k 150 LEU cc_start: 0.9003 (tt) cc_final: 0.8707 (mt) REVERT: l 48 ARG cc_start: 0.8900 (ptp-110) cc_final: 0.8546 (ptp-110) REVERT: l 54 LYS cc_start: 0.8920 (mttt) cc_final: 0.8141 (mmtt) REVERT: l 61 MET cc_start: 0.9176 (mmm) cc_final: 0.8279 (mmm) REVERT: l 68 TYR cc_start: 0.8944 (m-80) cc_final: 0.8583 (m-80) REVERT: l 118 VAL cc_start: 0.9745 (t) cc_final: 0.9397 (m) REVERT: l 123 GLN cc_start: 0.8760 (mp10) cc_final: 0.8511 (mp10) REVERT: l 131 MET cc_start: 0.8946 (ttp) cc_final: 0.8695 (ttp) REVERT: m 21 SER cc_start: 0.9327 (m) cc_final: 0.8853 (p) REVERT: m 25 PHE cc_start: 0.8879 (m-80) cc_final: 0.8440 (m-80) REVERT: m 47 MET cc_start: 0.8340 (tpp) cc_final: 0.7627 (tpp) REVERT: m 48 ARG cc_start: 0.8746 (mmm-85) cc_final: 0.8118 (mmm-85) REVERT: m 52 ILE cc_start: 0.9425 (mt) cc_final: 0.9187 (mt) REVERT: m 61 MET cc_start: 0.9482 (mmm) cc_final: 0.9249 (mmm) REVERT: m 80 LEU cc_start: 0.9348 (mt) cc_final: 0.9079 (mt) REVERT: m 86 LEU cc_start: 0.9087 (tp) cc_final: 0.8742 (tp) REVERT: m 90 PHE cc_start: 0.9325 (m-10) cc_final: 0.8688 (m-80) REVERT: m 92 GLN cc_start: 0.9074 (mt0) cc_final: 0.8781 (mt0) REVERT: n 13 PHE cc_start: 0.8634 (t80) cc_final: 0.8003 (t80) REVERT: n 17 MET cc_start: 0.9030 (mmt) cc_final: 0.8726 (mmm) REVERT: n 36 LYS cc_start: 0.8665 (mmtt) cc_final: 0.8245 (mmtp) REVERT: n 45 SER cc_start: 0.9129 (m) cc_final: 0.8615 (p) REVERT: n 53 MET cc_start: 0.9361 (mmm) cc_final: 0.9103 (mmm) REVERT: n 57 ILE cc_start: 0.9357 (mm) cc_final: 0.9057 (mm) REVERT: n 60 VAL cc_start: 0.9260 (t) cc_final: 0.9050 (t) REVERT: n 61 MET cc_start: 0.9013 (mmp) cc_final: 0.8702 (mmm) REVERT: n 68 TYR cc_start: 0.9640 (m-80) cc_final: 0.9051 (m-80) REVERT: n 75 LEU cc_start: 0.8969 (mt) cc_final: 0.8694 (mt) REVERT: n 88 ARG cc_start: 0.8299 (ttm-80) cc_final: 0.7226 (mmm160) REVERT: n 90 PHE cc_start: 0.9644 (m-80) cc_final: 0.9383 (m-80) REVERT: n 124 GLN cc_start: 0.9019 (tp-100) cc_final: 0.8145 (tm-30) REVERT: n 127 LEU cc_start: 0.9514 (tp) cc_final: 0.9293 (tp) REVERT: n 140 VAL cc_start: 0.9535 (t) cc_final: 0.9172 (t) REVERT: n 141 LEU cc_start: 0.9604 (mt) cc_final: 0.9315 (mt) REVERT: n 144 TYR cc_start: 0.9102 (m-10) cc_final: 0.8562 (m-10) REVERT: o 32 TYR cc_start: 0.8321 (t80) cc_final: 0.8019 (t80) REVERT: o 44 MET cc_start: 0.8138 (ttp) cc_final: 0.7766 (ttp) REVERT: o 50 GLU cc_start: 0.8140 (mp0) cc_final: 0.7485 (tp30) REVERT: o 61 MET cc_start: 0.8982 (mmm) cc_final: 0.8441 (mmp) REVERT: o 65 ILE cc_start: 0.9681 (mt) cc_final: 0.9428 (mt) REVERT: o 90 PHE cc_start: 0.9105 (m-10) cc_final: 0.8482 (m-10) REVERT: p 308 ASN cc_start: 0.9276 (t0) cc_final: 0.8980 (t0) REVERT: p 313 ILE cc_start: 0.9437 (mt) cc_final: 0.9024 (mt) REVERT: p 338 ILE cc_start: 0.8732 (pt) cc_final: 0.8206 (pt) REVERT: p 339 ILE cc_start: 0.7330 (mm) cc_final: 0.6800 (mt) outliers start: 2 outliers final: 0 residues processed: 1051 average time/residue: 0.1340 time to fit residues: 227.0730 Evaluate side-chains 910 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 910 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 35 optimal weight: 0.0470 chunk 68 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 chunk 22 optimal weight: 0.0970 chunk 33 optimal weight: 0.5980 chunk 267 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 180 optimal weight: 0.7980 chunk 137 optimal weight: 1.9990 chunk 139 optimal weight: 0.8980 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 85 GLN a 524 ASN ** a 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 130 HIS ** d 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 33 ASN ** e 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 92 GLN j 92 GLN j 124 GLN m 7 ASN n 92 GLN o 7 ASN ** p 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 330 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.087634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.075234 restraints weight = 72036.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.077993 restraints weight = 40199.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.079946 restraints weight = 25643.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.081317 restraints weight = 17744.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.082292 restraints weight = 13015.310| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.6725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 21366 Z= 0.165 Angle : 0.727 11.255 28966 Z= 0.378 Chirality : 0.044 0.224 3430 Planarity : 0.005 0.053 3602 Dihedral : 4.267 19.939 2978 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.18 % Favored : 96.79 % Rotamer: Outliers : 0.09 % Allowed : 0.47 % Favored : 99.44 % 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 aren not related in a simple way. whole: 1.47 (0.16), residues: 2771 helix: 1.60 (0.11), residues: 2092 sheet: -1.08 (1.20), residues: 18 loop : -0.93 (0.25), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 126 TYR 0.031 0.002 TYR o 68 PHE 0.032 0.002 PHE c 431 TRP 0.041 0.002 TRP b 16 HIS 0.004 0.001 HIS H 111 Details of bonding type rmsd covalent geometry : bond 0.00357 (21366) covalent geometry : angle 0.72697 (28966) hydrogen bonds : bond 0.05178 ( 1744) hydrogen bonds : angle 4.62772 ( 5124) ********************** 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 1069 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1067 time to evaluate : 0.792 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 56 MET cc_start: 0.9034 (tmm) cc_final: 0.8618 (tmm) REVERT: H 57 LEU cc_start: 0.9413 (tt) cc_final: 0.9100 (tt) REVERT: H 58 MET cc_start: 0.9431 (tmm) cc_final: 0.9146 (tmm) REVERT: H 64 GLU cc_start: 0.8460 (tp30) cc_final: 0.8017 (tp30) REVERT: H 68 SER cc_start: 0.9401 (m) cc_final: 0.8945 (t) REVERT: H 91 GLN cc_start: 0.9088 (tt0) cc_final: 0.8599 (tt0) REVERT: H 137 ASN cc_start: 0.8994 (m-40) cc_final: 0.8498 (m110) REVERT: H 140 LYS cc_start: 0.9375 (tttt) cc_final: 0.8998 (ttpt) REVERT: L 22 LEU cc_start: 0.9432 (mt) cc_final: 0.9145 (mt) REVERT: L 36 PHE cc_start: 0.8953 (p90) cc_final: 0.8752 (p90) REVERT: L 49 GLU cc_start: 0.8856 (pt0) cc_final: 0.8002 (pp20) REVERT: L 58 ARG cc_start: 0.8538 (mtm110) cc_final: 0.7749 (ttm110) REVERT: L 73 MET cc_start: 0.8626 (mtm) cc_final: 0.8282 (ptp) REVERT: L 95 GLU cc_start: 0.8428 (tm-30) cc_final: 0.8108 (tm-30) REVERT: L 99 ASP cc_start: 0.6213 (p0) cc_final: 0.5977 (t0) REVERT: a 388 GLU cc_start: 0.8032 (tp30) cc_final: 0.7821 (tt0) REVERT: a 397 ILE cc_start: 0.9287 (mm) cc_final: 0.8932 (tp) REVERT: a 401 PHE cc_start: 0.9090 (t80) cc_final: 0.8486 (t80) REVERT: a 403 PHE cc_start: 0.9049 (t80) cc_final: 0.8752 (t80) REVERT: a 414 ILE cc_start: 0.8817 (mm) cc_final: 0.8526 (mm) REVERT: a 423 MET cc_start: 0.9275 (mpp) cc_final: 0.8945 (mpp) REVERT: a 449 ILE cc_start: 0.9404 (mt) cc_final: 0.8927 (mt) REVERT: a 453 MET cc_start: 0.8982 (mtp) cc_final: 0.8421 (mtp) REVERT: a 467 CYS cc_start: 0.6232 (t) cc_final: 0.5970 (t) REVERT: a 538 MET cc_start: 0.7860 (ttt) cc_final: 0.7556 (ttt) REVERT: a 540 MET cc_start: 0.9164 (mmm) cc_final: 0.8785 (mmm) REVERT: a 549 MET cc_start: 0.9439 (mmm) cc_final: 0.9161 (mmm) REVERT: a 576 GLU cc_start: 0.9008 (pm20) cc_final: 0.8675 (pm20) REVERT: a 580 MET cc_start: 0.8927 (mmm) cc_final: 0.8553 (mmm) REVERT: a 616 MET cc_start: 0.9132 (ttp) cc_final: 0.8835 (tmm) REVERT: a 636 ILE cc_start: 0.9343 (mm) cc_final: 0.9061 (tp) REVERT: a 641 ILE cc_start: 0.9335 (mp) cc_final: 0.8397 (mp) REVERT: a 651 MET cc_start: 0.8994 (mmm) cc_final: 0.8407 (mmm) REVERT: a 721 GLN cc_start: 0.9206 (tp40) cc_final: 0.8698 (tp40) REVERT: a 743 TRP cc_start: 0.9089 (t60) cc_final: 0.8721 (t60) REVERT: a 759 MET cc_start: 0.8002 (mmm) cc_final: 0.7446 (tmm) REVERT: a 810 GLU cc_start: 0.7660 (mp0) cc_final: 0.6891 (mp0) REVERT: b 19 MET cc_start: 0.8910 (mtp) cc_final: 0.8410 (mtt) REVERT: b 25 CYS cc_start: 0.9209 (m) cc_final: 0.8833 (t) REVERT: b 30 ASP cc_start: 0.8628 (t70) cc_final: 0.8383 (t0) REVERT: b 34 ARG cc_start: 0.8390 (mmm160) cc_final: 0.6656 (tpt170) REVERT: b 36 ASP cc_start: 0.7904 (t70) cc_final: 0.7325 (t0) REVERT: b 48 MET cc_start: 0.8698 (ttt) cc_final: 0.8214 (tmm) REVERT: b 52 LEU cc_start: 0.9505 (mt) cc_final: 0.9104 (mt) REVERT: b 70 TYR cc_start: 0.8946 (p90) cc_final: 0.8451 (p90) REVERT: b 71 ILE cc_start: 0.9597 (mm) cc_final: 0.9180 (mm) REVERT: b 74 SER cc_start: 0.9498 (m) cc_final: 0.9161 (t) REVERT: b 75 SER cc_start: 0.9587 (m) cc_final: 0.9305 (p) REVERT: b 82 LYS cc_start: 0.9024 (mmtt) cc_final: 0.8587 (mmtp) REVERT: b 90 ASN cc_start: 0.8440 (m110) cc_final: 0.8183 (m110) REVERT: b 98 GLU cc_start: 0.8793 (mm-30) cc_final: 0.8445 (mm-30) REVERT: b 130 ASN cc_start: 0.9052 (m-40) cc_final: 0.8810 (m-40) REVERT: b 135 TYR cc_start: 0.8894 (m-80) cc_final: 0.8441 (m-10) REVERT: b 137 MET cc_start: 0.9346 (ttt) cc_final: 0.8909 (tpp) REVERT: b 148 ASN cc_start: 0.9597 (m110) cc_final: 0.9260 (m110) REVERT: b 169 ASN cc_start: 0.9091 (t0) cc_final: 0.8304 (t0) REVERT: b 172 LEU cc_start: 0.8554 (mt) cc_final: 0.7808 (mt) REVERT: b 203 MET cc_start: 0.8506 (mpp) cc_final: 0.8047 (mtp) REVERT: c 439 MET cc_start: 0.9186 (mmm) cc_final: 0.8732 (mmm) REVERT: c 442 SER cc_start: 0.8555 (t) cc_final: 0.8310 (t) REVERT: d 23 LEU cc_start: 0.9257 (mm) cc_final: 0.9010 (mm) REVERT: d 40 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7926 (mp0) REVERT: d 76 GLU cc_start: 0.8612 (tt0) cc_final: 0.8060 (tp30) REVERT: d 85 MET cc_start: 0.9235 (mtp) cc_final: 0.8969 (ttp) REVERT: d 98 ASP cc_start: 0.8755 (m-30) cc_final: 0.8191 (t0) REVERT: d 105 MET cc_start: 0.8948 (ttm) cc_final: 0.8372 (ttm) REVERT: d 110 ILE cc_start: 0.9398 (mm) cc_final: 0.9188 (mm) REVERT: d 124 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8474 (mt-10) REVERT: d 128 LYS cc_start: 0.9267 (mmtt) cc_final: 0.8589 (mttt) REVERT: d 176 MET cc_start: 0.8091 (mtt) cc_final: 0.7879 (mtp) REVERT: d 191 GLU cc_start: 0.8864 (mm-30) cc_final: 0.8261 (mm-30) REVERT: d 214 PHE cc_start: 0.9090 (t80) cc_final: 0.8657 (t80) REVERT: d 241 PHE cc_start: 0.8697 (m-80) cc_final: 0.8434 (m-80) REVERT: d 244 CYS cc_start: 0.8069 (m) cc_final: 0.7343 (m) REVERT: d 257 ARG cc_start: 0.9565 (mmm-85) cc_final: 0.9021 (mtp-110) REVERT: d 269 ASP cc_start: 0.9255 (m-30) cc_final: 0.9005 (m-30) REVERT: d 297 HIS cc_start: 0.8902 (t-90) cc_final: 0.8305 (t-90) REVERT: d 298 GLU cc_start: 0.9195 (tt0) cc_final: 0.8922 (tm-30) REVERT: d 332 ILE cc_start: 0.9623 (mm) cc_final: 0.9420 (tt) REVERT: d 335 CYS cc_start: 0.8584 (m) cc_final: 0.8003 (t) REVERT: e 9 PRO cc_start: 0.8193 (Cg_exo) cc_final: 0.7789 (Cg_endo) REVERT: e 13 PHE cc_start: 0.8049 (m-80) cc_final: 0.7459 (m-80) REVERT: e 47 CYS cc_start: 0.8370 (p) cc_final: 0.7580 (p) REVERT: e 54 ILE cc_start: 0.9372 (mt) cc_final: 0.9091 (mt) REVERT: e 68 LEU cc_start: 0.8678 (tp) cc_final: 0.8424 (tp) REVERT: f 67 TYR cc_start: 0.8684 (m-80) cc_final: 0.8236 (m-80) REVERT: g 25 PHE cc_start: 0.8953 (m-80) cc_final: 0.8683 (m-80) REVERT: g 45 SER cc_start: 0.9601 (p) cc_final: 0.9332 (p) REVERT: g 51 LEU cc_start: 0.9139 (mt) cc_final: 0.8912 (mt) REVERT: g 61 MET cc_start: 0.8147 (mmt) cc_final: 0.7709 (mmt) REVERT: g 88 ARG cc_start: 0.8660 (mmm160) cc_final: 0.8181 (tpm170) REVERT: g 90 PHE cc_start: 0.7735 (m-80) cc_final: 0.7414 (m-80) REVERT: g 91 LEU cc_start: 0.9037 (mt) cc_final: 0.8799 (mt) REVERT: g 108 PHE cc_start: 0.9037 (m-80) cc_final: 0.8338 (m-80) REVERT: g 131 MET cc_start: 0.9405 (ttt) cc_final: 0.9069 (ttt) REVERT: g 137 PHE cc_start: 0.8712 (m-10) cc_final: 0.8436 (m-80) REVERT: g 141 LEU cc_start: 0.9155 (mt) cc_final: 0.8892 (mt) REVERT: g 144 TYR cc_start: 0.9082 (m-80) cc_final: 0.8531 (m-80) REVERT: g 152 LEU cc_start: 0.9500 (mt) cc_final: 0.9271 (mt) REVERT: h 54 LYS cc_start: 0.8749 (mmmt) cc_final: 0.8508 (mmmt) REVERT: h 97 LEU cc_start: 0.9349 (mm) cc_final: 0.9082 (mm) REVERT: h 146 LEU cc_start: 0.9550 (tp) cc_final: 0.9341 (tp) REVERT: h 150 LEU cc_start: 0.9269 (mt) cc_final: 0.9028 (mt) REVERT: i 11 SER cc_start: 0.9217 (p) cc_final: 0.8977 (m) REVERT: i 14 PHE cc_start: 0.8969 (m-10) cc_final: 0.8544 (m-10) REVERT: i 50 GLU cc_start: 0.8934 (pm20) cc_final: 0.8716 (pm20) REVERT: i 61 MET cc_start: 0.9242 (mtm) cc_final: 0.8847 (ptp) REVERT: i 64 ILE cc_start: 0.8906 (mt) cc_final: 0.8324 (mt) REVERT: i 65 ILE cc_start: 0.9211 (mm) cc_final: 0.8708 (mm) REVERT: i 68 TYR cc_start: 0.9056 (m-10) cc_final: 0.8566 (m-80) REVERT: i 86 LEU cc_start: 0.9386 (tt) cc_final: 0.8767 (tp) REVERT: i 90 PHE cc_start: 0.7764 (m-10) cc_final: 0.7459 (m-80) REVERT: i 135 LEU cc_start: 0.9205 (mm) cc_final: 0.8891 (mm) REVERT: i 139 GLU cc_start: 0.9099 (tp30) cc_final: 0.7952 (tp30) REVERT: j 17 MET cc_start: 0.8660 (tpt) cc_final: 0.8302 (tpt) REVERT: j 61 MET cc_start: 0.8887 (tpp) cc_final: 0.8578 (tpp) REVERT: j 70 LEU cc_start: 0.9643 (tp) cc_final: 0.9311 (tp) REVERT: j 84 ILE cc_start: 0.8255 (mm) cc_final: 0.7860 (mm) REVERT: j 124 GLN cc_start: 0.8716 (tm130) cc_final: 0.8415 (tm-30) REVERT: j 136 ILE cc_start: 0.9208 (mm) cc_final: 0.8931 (mm) REVERT: k 28 MET cc_start: 0.9007 (mtt) cc_final: 0.8384 (mmm) REVERT: k 32 TYR cc_start: 0.8804 (t80) cc_final: 0.8321 (t80) REVERT: k 47 MET cc_start: 0.8723 (mpp) cc_final: 0.8351 (mpp) REVERT: k 54 LYS cc_start: 0.8170 (mttt) cc_final: 0.7349 (ttpt) REVERT: k 57 ILE cc_start: 0.9308 (mm) cc_final: 0.8641 (mm) REVERT: k 76 ILE cc_start: 0.9448 (mt) cc_final: 0.8542 (tt) REVERT: k 80 LEU cc_start: 0.9168 (mt) cc_final: 0.8870 (mt) REVERT: k 90 PHE cc_start: 0.8621 (m-10) cc_final: 0.8229 (m-80) REVERT: k 92 GLN cc_start: 0.9120 (mt0) cc_final: 0.8866 (mt0) REVERT: k 123 GLN cc_start: 0.8930 (tp40) cc_final: 0.8344 (tp40) REVERT: k 124 GLN cc_start: 0.9004 (tm-30) cc_final: 0.8670 (tm-30) REVERT: k 133 LEU cc_start: 0.9230 (mt) cc_final: 0.8877 (mt) REVERT: k 137 PHE cc_start: 0.9049 (m-80) cc_final: 0.8452 (m-80) REVERT: k 147 ILE cc_start: 0.9595 (mt) cc_final: 0.9296 (tp) REVERT: k 150 LEU cc_start: 0.9045 (tt) cc_final: 0.8751 (mt) REVERT: l 54 LYS cc_start: 0.8847 (mttt) cc_final: 0.8044 (mmtt) REVERT: l 61 MET cc_start: 0.9072 (mmm) cc_final: 0.8177 (mmm) REVERT: l 68 TYR cc_start: 0.8958 (m-80) cc_final: 0.8654 (m-80) REVERT: l 108 PHE cc_start: 0.9117 (m-80) cc_final: 0.8165 (m-80) REVERT: l 118 VAL cc_start: 0.9732 (t) cc_final: 0.9368 (m) REVERT: l 123 GLN cc_start: 0.8709 (mp10) cc_final: 0.8440 (mp10) REVERT: l 131 MET cc_start: 0.8930 (ttp) cc_final: 0.8681 (ttp) REVERT: m 21 SER cc_start: 0.9292 (m) cc_final: 0.8755 (p) REVERT: m 25 PHE cc_start: 0.8847 (m-80) cc_final: 0.8383 (m-80) REVERT: m 45 SER cc_start: 0.9486 (p) cc_final: 0.9266 (p) REVERT: m 47 MET cc_start: 0.8303 (tpp) cc_final: 0.7581 (tpp) REVERT: m 48 ARG cc_start: 0.8717 (mmm-85) cc_final: 0.8087 (mmm-85) REVERT: m 52 ILE cc_start: 0.9400 (mt) cc_final: 0.9149 (mt) REVERT: m 57 ILE cc_start: 0.8251 (mp) cc_final: 0.7934 (mm) REVERT: m 61 MET cc_start: 0.9501 (mmm) cc_final: 0.9222 (mmm) REVERT: m 80 LEU cc_start: 0.9284 (mt) cc_final: 0.9041 (mt) REVERT: m 86 LEU cc_start: 0.9039 (tp) cc_final: 0.8771 (tp) REVERT: m 90 PHE cc_start: 0.9222 (m-10) cc_final: 0.8666 (m-80) REVERT: m 92 GLN cc_start: 0.9092 (mt0) cc_final: 0.8888 (mt0) REVERT: n 36 LYS cc_start: 0.8609 (mmtt) cc_final: 0.8174 (mmtp) REVERT: n 54 LYS cc_start: 0.8356 (mttt) cc_final: 0.7920 (ttmm) REVERT: n 57 ILE cc_start: 0.9304 (mm) cc_final: 0.9000 (mm) REVERT: n 60 VAL cc_start: 0.9251 (t) cc_final: 0.9026 (t) REVERT: n 61 MET cc_start: 0.8984 (mmp) cc_final: 0.8629 (mmm) REVERT: n 68 TYR cc_start: 0.9577 (m-80) cc_final: 0.9026 (m-80) REVERT: n 75 LEU cc_start: 0.8946 (mt) cc_final: 0.8675 (mt) REVERT: n 88 ARG cc_start: 0.8269 (ttm-80) cc_final: 0.7342 (mmm160) REVERT: n 90 PHE cc_start: 0.9630 (m-80) cc_final: 0.9388 (m-80) REVERT: n 124 GLN cc_start: 0.8942 (tp-100) cc_final: 0.8063 (tm-30) REVERT: n 140 VAL cc_start: 0.9523 (t) cc_final: 0.9172 (t) REVERT: n 141 LEU cc_start: 0.9605 (mt) cc_final: 0.9321 (mt) REVERT: n 144 TYR cc_start: 0.9059 (m-10) cc_final: 0.8553 (m-10) REVERT: o 24 VAL cc_start: 0.9416 (m) cc_final: 0.9170 (p) REVERT: o 32 TYR cc_start: 0.8376 (t80) cc_final: 0.8091 (t80) REVERT: o 44 MET cc_start: 0.8106 (ttp) cc_final: 0.7724 (ttp) REVERT: o 50 GLU cc_start: 0.8194 (mp0) cc_final: 0.7299 (tp30) REVERT: o 61 MET cc_start: 0.8788 (mmm) cc_final: 0.8367 (mmp) REVERT: o 68 TYR cc_start: 0.8743 (m-80) cc_final: 0.8437 (m-80) REVERT: o 90 PHE cc_start: 0.9010 (m-10) cc_final: 0.8427 (m-80) REVERT: o 92 GLN cc_start: 0.9166 (mp10) cc_final: 0.8945 (mp10) REVERT: o 131 MET cc_start: 0.9467 (ttt) cc_final: 0.9048 (ttt) REVERT: o 133 LEU cc_start: 0.8924 (tp) cc_final: 0.8585 (tp) REVERT: o 151 ILE cc_start: 0.9636 (mm) cc_final: 0.9434 (tp) REVERT: p 308 ASN cc_start: 0.9209 (t0) cc_final: 0.8970 (t0) REVERT: p 313 ILE cc_start: 0.9465 (mt) cc_final: 0.9047 (mt) REVERT: p 339 ILE cc_start: 0.7473 (mm) cc_final: 0.7199 (mt) outliers start: 2 outliers final: 0 residues processed: 1068 average time/residue: 0.1308 time to fit residues: 226.9934 Evaluate side-chains 938 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 938 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 29 optimal weight: 0.6980 chunk 214 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 184 optimal weight: 0.9990 chunk 33 optimal weight: 9.9990 chunk 66 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 238 optimal weight: 0.7980 chunk 101 optimal weight: 0.0060 chunk 216 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 108 ASN d 130 HIS ** d 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 124 GLN m 7 ASN n 92 GLN o 7 ASN ** p 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.088731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.076186 restraints weight = 74736.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.078833 restraints weight = 43095.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.080710 restraints weight = 28338.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.082032 restraints weight = 19964.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.082882 restraints weight = 14932.314| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.6892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 21366 Z= 0.166 Angle : 0.742 13.421 28966 Z= 0.380 Chirality : 0.045 0.320 3430 Planarity : 0.005 0.055 3602 Dihedral : 4.264 20.424 2978 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.00 % Favored : 96.97 % Rotamer: Outliers : 0.09 % Allowed : 0.42 % Favored : 99.48 % 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 aren not related in a simple way. whole: 1.40 (0.16), residues: 2771 helix: 1.54 (0.11), residues: 2094 sheet: -0.99 (1.24), residues: 18 loop : -0.93 (0.25), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 63 TYR 0.046 0.002 TYR m 144 PHE 0.028 0.002 PHE b 189 TRP 0.041 0.002 TRP b 16 HIS 0.004 0.001 HIS H 111 Details of bonding type rmsd covalent geometry : bond 0.00368 (21366) covalent geometry : angle 0.74184 (28966) hydrogen bonds : bond 0.05126 ( 1744) hydrogen bonds : angle 4.61686 ( 5124) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4846.27 seconds wall clock time: 84 minutes 7.32 seconds (5047.32 seconds total)