Starting phenix.real_space_refine on Wed Apr 10 08:26:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txr_41704/04_2024/8txr_41704.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txr_41704/04_2024/8txr_41704.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txr_41704/04_2024/8txr_41704.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txr_41704/04_2024/8txr_41704.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txr_41704/04_2024/8txr_41704.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txr_41704/04_2024/8txr_41704.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.055 sd= 0.214 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 38 5.16 5 C 11828 2.51 5 N 3498 2.21 5 O 3656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 19020 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3432 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 18, 'TRANS': 408} Chain breaks: 2 Chain: "C" Number of atoms: 3458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3458 Classifications: {'peptide': 431} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 411} Chain breaks: 2 Chain: "i" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 482 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain: "c" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 457 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "g" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 457 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "h" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 466 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 1, 'TRANS': 57} Chain: "a" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 370 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "b" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 495 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "B" Number of atoms: 2367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2367 Classifications: {'peptide': 297} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 281} Chain breaks: 1 Chain: "o" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 431 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 1, 'TRANS': 52} Chain: "p" Number of atoms: 473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 473 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 1, 'TRANS': 58} Chain: "D" Number of atoms: 2367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2367 Classifications: {'peptide': 297} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 281} Chain breaks: 1 Chain: "m" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 470 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 1, 'TRANS': 57} Chain: "n" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 470 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 1, 'TRANS': 57} Chain: "j" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 465 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 1, 'TRANS': 57} Chain: "k" Number of atoms: 473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 473 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 1, 'TRANS': 58} Chain: "l" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 466 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 1, 'TRANS': 57} Chain: "d" Number of atoms: 473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 473 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 1, 'TRANS': 58} Chain: "e" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 482 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain: "f" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 466 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 1, 'TRANS': 57} Time building chain proxies: 9.93, per 1000 atoms: 0.52 Number of scatterers: 19020 At special positions: 0 Unit cell: (103, 106, 348, 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 38 16.00 O 3656 8.00 N 3498 7.00 C 11828 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 - 3.50 Amino acid : False - 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: 7.67 Conformation dependent library (CDL) restraints added in 3.6 seconds 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4540 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 10 sheets defined 66.4% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 12 through 27 removed outlier: 3.648A pdb=" N LEU A 21 " --> pdb=" O GLN A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 68 removed outlier: 4.354A pdb=" N ARG A 68 " --> pdb=" O ARG A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 125 removed outlier: 3.617A pdb=" N GLU A 124 " --> pdb=" O LYS A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 132 Processing helix chain 'A' and resid 150 through 164 removed outlier: 4.014A pdb=" N HIS A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 196 removed outlier: 3.757A pdb=" N GLN A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 217 removed outlier: 3.786A pdb=" N TRP A 214 " --> pdb=" O GLU A 211 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N SER A 215 " --> pdb=" O ASP A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 228 Processing helix chain 'A' and resid 243 through 249 removed outlier: 3.881A pdb=" N PHE A 247 " --> pdb=" O THR A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 264 removed outlier: 3.705A pdb=" N ALA A 260 " --> pdb=" O PRO A 256 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU A 261 " --> pdb=" O SER A 257 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL A 263 " --> pdb=" O ALA A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 306 removed outlier: 3.974A pdb=" N GLN A 305 " --> pdb=" O HIS A 301 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLN A 306 " --> pdb=" O ARG A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 350 removed outlier: 3.830A pdb=" N LYS A 335 " --> pdb=" O GLU A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 396 Processing helix chain 'C' and resid 12 through 27 Processing helix chain 'C' and resid 63 through 68 Processing helix chain 'C' and resid 110 through 125 removed outlier: 3.514A pdb=" N LYS C 120 " --> pdb=" O GLN C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 164 removed outlier: 4.183A pdb=" N HIS C 154 " --> pdb=" O GLY C 150 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP C 155 " --> pdb=" O ALA C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 196 removed outlier: 4.259A pdb=" N GLY C 183 " --> pdb=" O ASP C 179 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG C 187 " --> pdb=" O GLY C 183 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU C 190 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN C 193 " --> pdb=" O ILE C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 217 Processing helix chain 'C' and resid 218 through 228 removed outlier: 4.151A pdb=" N ALA C 222 " --> pdb=" O ASP C 218 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG C 223 " --> pdb=" O GLU C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 249 removed outlier: 3.765A pdb=" N PHE C 247 " --> pdb=" O THR C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 264 removed outlier: 3.786A pdb=" N ALA C 260 " --> pdb=" O PRO C 256 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU C 261 " --> pdb=" O SER C 257 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL C 263 " --> pdb=" O ALA C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 305 removed outlier: 3.578A pdb=" N LEU C 270 " --> pdb=" O ASN C 266 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN C 305 " --> pdb=" O HIS C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 351 removed outlier: 3.523A pdb=" N GLN C 315 " --> pdb=" O ARG C 311 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU C 322 " --> pdb=" O MET C 318 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN C 342 " --> pdb=" O GLY C 338 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU C 344 " --> pdb=" O GLN C 340 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN C 351 " --> pdb=" O ARG C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 395 removed outlier: 3.534A pdb=" N ALA C 377 " --> pdb=" O GLU C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 423 Processing helix chain 'i' and resid 10 through 28 removed outlier: 3.603A pdb=" N ALA i 14 " --> pdb=" O SER i 10 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU i 15 " --> pdb=" O PHE i 11 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER i 16 " --> pdb=" O GLU i 12 " (cutoff:3.500A) Processing helix chain 'i' and resid 31 through 65 removed outlier: 3.550A pdb=" N GLN i 44 " --> pdb=" O GLU i 40 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE i 62 " --> pdb=" O GLN i 58 " (cutoff:3.500A) Processing helix chain 'c' and resid 10 through 27 Processing helix chain 'c' and resid 31 through 34 Processing helix chain 'c' and resid 35 through 60 removed outlier: 3.539A pdb=" N GLN c 58 " --> pdb=" O GLN c 54 " (cutoff:3.500A) Processing helix chain 'c' and resid 61 through 65 Processing helix chain 'g' and resid 10 through 28 Processing helix chain 'g' and resid 31 through 54 removed outlier: 3.738A pdb=" N ASN g 37 " --> pdb=" O GLU g 33 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS g 52 " --> pdb=" O GLN g 48 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU g 53 " --> pdb=" O GLY g 49 " (cutoff:3.500A) Processing helix chain 'h' and resid 10 through 28 removed outlier: 3.523A pdb=" N GLN h 20 " --> pdb=" O SER h 16 " (cutoff:3.500A) Processing helix chain 'h' and resid 31 through 65 removed outlier: 3.548A pdb=" N GLN h 44 " --> pdb=" O GLU h 40 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS h 52 " --> pdb=" O GLN h 48 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU h 53 " --> pdb=" O GLY h 49 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE h 62 " --> pdb=" O GLN h 58 " (cutoff:3.500A) Processing helix chain 'a' and resid 10 through 27 Processing helix chain 'a' and resid 31 through 55 removed outlier: 3.951A pdb=" N LYS a 52 " --> pdb=" O GLN a 48 " (cutoff:3.500A) Processing helix chain 'b' and resid 10 through 26 Processing helix chain 'b' and resid 31 through 65 removed outlier: 3.636A pdb=" N ARG b 41 " --> pdb=" O ASN b 37 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER b 65 " --> pdb=" O GLN b 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 28 Processing helix chain 'B' and resid 63 through 68 Processing helix chain 'B' and resid 110 through 125 removed outlier: 3.623A pdb=" N LYS B 120 " --> pdb=" O GLN B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 164 removed outlier: 3.681A pdb=" N HIS B 154 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG B 162 " --> pdb=" O HIS B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 196 removed outlier: 3.780A pdb=" N GLN B 184 " --> pdb=" O ASP B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 214 Processing helix chain 'B' and resid 215 through 217 No H-bonds generated for 'chain 'B' and resid 215 through 217' Processing helix chain 'B' and resid 218 through 226 Processing helix chain 'B' and resid 243 through 249 removed outlier: 3.786A pdb=" N PHE B 247 " --> pdb=" O THR B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 264 removed outlier: 3.551A pdb=" N ALA B 260 " --> pdb=" O PRO B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 306 Processing helix chain 'o' and resid 11 through 26 Processing helix chain 'o' and resid 31 through 56 removed outlier: 3.826A pdb=" N ALA o 56 " --> pdb=" O LYS o 52 " (cutoff:3.500A) Processing helix chain 'p' and resid 10 through 27 Processing helix chain 'p' and resid 35 through 65 removed outlier: 3.592A pdb=" N GLU p 40 " --> pdb=" O LEU p 36 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ARG p 41 " --> pdb=" O ASN p 37 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL p 43 " --> pdb=" O PHE p 39 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU p 63 " --> pdb=" O ARG p 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 28 Processing helix chain 'D' and resid 63 through 68 Processing helix chain 'D' and resid 110 through 125 Processing helix chain 'D' and resid 128 through 132 Processing helix chain 'D' and resid 150 through 163 Processing helix chain 'D' and resid 180 through 196 Processing helix chain 'D' and resid 209 through 217 removed outlier: 3.648A pdb=" N PHE D 216 " --> pdb=" O ASP D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 228 Processing helix chain 'D' and resid 243 through 249 Processing helix chain 'D' and resid 255 through 264 Processing helix chain 'D' and resid 266 through 306 Processing helix chain 'm' and resid 11 through 28 removed outlier: 3.916A pdb=" N GLY m 28 " --> pdb=" O ARG m 24 " (cutoff:3.500A) Processing helix chain 'm' and resid 31 through 59 Processing helix chain 'n' and resid 11 through 28 removed outlier: 4.077A pdb=" N SER n 16 " --> pdb=" O GLU n 12 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN n 20 " --> pdb=" O SER n 16 " (cutoff:3.500A) Processing helix chain 'n' and resid 31 through 64 removed outlier: 3.723A pdb=" N GLN n 54 " --> pdb=" O GLN n 50 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU n 63 " --> pdb=" O ARG n 59 " (cutoff:3.500A) Processing helix chain 'j' and resid 10 through 27 removed outlier: 3.656A pdb=" N SER j 27 " --> pdb=" O THR j 23 " (cutoff:3.500A) Processing helix chain 'j' and resid 31 through 65 removed outlier: 3.646A pdb=" N ARG j 41 " --> pdb=" O ASN j 37 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY j 42 " --> pdb=" O GLU j 38 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS j 52 " --> pdb=" O GLN j 48 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU j 53 " --> pdb=" O GLY j 49 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE j 62 " --> pdb=" O GLN j 58 " (cutoff:3.500A) Processing helix chain 'k' and resid 10 through 27 Processing helix chain 'k' and resid 31 through 65 removed outlier: 3.869A pdb=" N GLN k 44 " --> pdb=" O GLU k 40 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU k 53 " --> pdb=" O GLY k 49 " (cutoff:3.500A) Processing helix chain 'l' and resid 10 through 28 removed outlier: 3.534A pdb=" N GLN l 20 " --> pdb=" O SER l 16 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY l 28 " --> pdb=" O ARG l 24 " (cutoff:3.500A) Processing helix chain 'l' and resid 31 through 65 removed outlier: 3.981A pdb=" N ASN l 37 " --> pdb=" O GLU l 33 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU l 40 " --> pdb=" O LEU l 36 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ARG l 41 " --> pdb=" O ASN l 37 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN l 44 " --> pdb=" O GLU l 40 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS l 52 " --> pdb=" O GLN l 48 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU l 53 " --> pdb=" O GLY l 49 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN l 58 " --> pdb=" O GLN l 54 " (cutoff:3.500A) Processing helix chain 'd' and resid 10 through 26 removed outlier: 3.697A pdb=" N GLN d 20 " --> pdb=" O SER d 16 " (cutoff:3.500A) Processing helix chain 'd' and resid 31 through 65 removed outlier: 3.510A pdb=" N LEU d 36 " --> pdb=" O LEU d 32 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN d 37 " --> pdb=" O GLU d 33 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG d 59 " --> pdb=" O GLN d 55 " (cutoff:3.500A) Processing helix chain 'e' and resid 10 through 27 removed outlier: 3.778A pdb=" N SER e 27 " --> pdb=" O THR e 23 " (cutoff:3.500A) Processing helix chain 'e' and resid 31 through 65 removed outlier: 3.770A pdb=" N ASN e 37 " --> pdb=" O GLU e 33 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU e 40 " --> pdb=" O LEU e 36 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG e 41 " --> pdb=" O ASN e 37 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS e 52 " --> pdb=" O GLN e 48 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN e 61 " --> pdb=" O GLU e 57 " (cutoff:3.500A) Processing helix chain 'f' and resid 10 through 27 Processing helix chain 'f' and resid 31 through 65 removed outlier: 3.796A pdb=" N ASN f 37 " --> pdb=" O GLU f 33 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN f 44 " --> pdb=" O GLU f 40 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU f 45 " --> pdb=" O ARG f 41 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN f 48 " --> pdb=" O GLN f 44 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 11 removed outlier: 6.840A pdb=" N LEU C 81 " --> pdb=" O MET C 102 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N MET C 102 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ARG C 83 " --> pdb=" O GLU C 100 " (cutoff:3.500A) removed outlier: 9.279A pdb=" N TYR C 95 " --> pdb=" O GLN C 57 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARG C 59 " --> pdb=" O TYR C 95 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N TYR C 48 " --> pdb=" O PHE C 39 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N PHE C 39 " --> pdb=" O TYR C 48 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU C 35 " --> pdb=" O LYS C 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 9 through 11 removed outlier: 6.520A pdb=" N TRP A 31 " --> pdb=" O PHE C 10 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU A 81 " --> pdb=" O MET A 102 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N MET A 102 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ARG A 83 " --> pdb=" O GLU A 100 " (cutoff:3.500A) removed outlier: 9.552A pdb=" N GLN A 57 " --> pdb=" O TYR A 95 " (cutoff:3.500A) removed outlier: 9.369A pdb=" N ILE A 97 " --> pdb=" O GLN A 57 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ARG A 59 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N VAL A 99 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ALA A 61 " --> pdb=" O VAL A 99 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N SER A 101 " --> pdb=" O ALA A 61 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N THR A 50 " --> pdb=" O ASN A 38 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N ASN A 38 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LYS A 52 " --> pdb=" O ILE A 36 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N ILE A 36 " --> pdb=" O LYS A 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 251 through 252 removed outlier: 6.549A pdb=" N LEU A 201 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ALA A 235 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VAL A 203 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLY A 204 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL A 142 " --> pdb=" O ILE A 170 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N TYR A 172 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL A 144 " --> pdb=" O TYR A 172 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 408 through 411 removed outlier: 4.603A pdb=" N GLU A 441 " --> pdb=" O GLU C 441 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLU C 441 " --> pdb=" O GLU A 441 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLU C 439 " --> pdb=" O LYS A 443 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ILE A 445 " --> pdb=" O TRP C 437 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N TRP C 437 " --> pdb=" O ILE A 445 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL C 408 " --> pdb=" O ARG C 432 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 408 through 411 removed outlier: 3.523A pdb=" N TRP A 437 " --> pdb=" O GLN C 446 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU A 439 " --> pdb=" O ASN C 444 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ASN C 444 " --> pdb=" O GLU A 439 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 169 through 173 removed outlier: 6.290A pdb=" N LEU C 201 " --> pdb=" O VAL C 233 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU C 251 " --> pdb=" O VAL C 232 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 9 through 11 removed outlier: 6.635A pdb=" N LEU D 81 " --> pdb=" O MET D 102 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N MET D 102 " --> pdb=" O LEU D 81 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ARG D 83 " --> pdb=" O GLU D 100 " (cutoff:3.500A) removed outlier: 9.597A pdb=" N GLN D 57 " --> pdb=" O TYR D 95 " (cutoff:3.500A) removed outlier: 9.093A pdb=" N ILE D 97 " --> pdb=" O GLN D 57 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ARG D 59 " --> pdb=" O ILE D 97 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N VAL D 99 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ALA D 61 " --> pdb=" O VAL D 99 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N SER D 101 " --> pdb=" O ALA D 61 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA D 56 " --> pdb=" O ASP D 53 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N TYR D 48 " --> pdb=" O PHE D 39 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N PHE D 39 " --> pdb=" O TYR D 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 10 through 11 removed outlier: 9.258A pdb=" N PHE D 10 " --> pdb=" O GLN B 29 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TRP B 31 " --> pdb=" O PHE D 10 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER B 101 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ASN B 85 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N VAL B 99 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR B 87 " --> pdb=" O ILE B 97 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ILE B 97 " --> pdb=" O THR B 87 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N TYR B 89 " --> pdb=" O TYR B 95 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N TYR B 95 " --> pdb=" O TYR B 89 " (cutoff:3.500A) removed outlier: 9.527A pdb=" N GLN B 57 " --> pdb=" O TYR B 95 " (cutoff:3.500A) removed outlier: 9.196A pdb=" N ILE B 97 " --> pdb=" O GLN B 57 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ARG B 59 " --> pdb=" O ILE B 97 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N VAL B 99 " --> pdb=" O ARG B 59 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ALA B 61 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N SER B 101 " --> pdb=" O ALA B 61 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N THR B 50 " --> pdb=" O ASN B 38 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N ASN B 38 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LYS B 52 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N ILE B 36 " --> pdb=" O LYS B 52 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 251 through 252 removed outlier: 3.623A pdb=" N LEU B 251 " --> pdb=" O VAL B 232 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU B 201 " --> pdb=" O VAL B 233 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N ALA B 235 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL B 203 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N GLY B 143 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N GLY B 204 " --> pdb=" O GLY B 143 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE B 145 " --> pdb=" O GLY B 204 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL B 142 " --> pdb=" O ILE B 170 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N TYR B 172 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL B 144 " --> pdb=" O TYR B 172 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN o 61 " --> pdb=" O VAL B 169 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 169 through 173 removed outlier: 6.396A pdb=" N LEU D 201 " --> pdb=" O VAL D 233 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU D 251 " --> pdb=" O VAL D 232 " (cutoff:3.500A) 1306 hydrogen bonds defined for protein. 3831 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: 6.06 Time building geometry restraints manager: 8.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6752 1.34 - 1.46: 2617 1.46 - 1.57: 9833 1.57 - 1.69: 0 1.69 - 1.81: 64 Bond restraints: 19266 Sorted by residual: bond pdb=" N SER n 10 " pdb=" CA SER n 10 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.99e+00 bond pdb=" N ALA h 9 " pdb=" CA ALA h 9 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.89e+00 bond pdb=" N SER o 10 " pdb=" CA SER o 10 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.89e+00 bond pdb=" N SER m 10 " pdb=" CA SER m 10 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.87e+00 bond pdb=" N ALA b 7 " pdb=" CA ALA b 7 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.85e+00 ... (remaining 19261 not shown) Histogram of bond angle deviations from ideal: 100.51 - 107.21: 486 107.21 - 113.90: 11007 113.90 - 120.59: 8146 120.59 - 127.28: 6210 127.28 - 133.97: 148 Bond angle restraints: 25997 Sorted by residual: angle pdb=" CA TRP B 47 " pdb=" CB TRP B 47 " pdb=" CG TRP B 47 " ideal model delta sigma weight residual 113.60 117.86 -4.26 1.90e+00 2.77e-01 5.02e+00 angle pdb=" N ASP B 53 " pdb=" CA ASP B 53 " pdb=" C ASP B 53 " ideal model delta sigma weight residual 110.80 106.99 3.81 2.13e+00 2.20e-01 3.20e+00 angle pdb=" N SER C 397 " pdb=" CA SER C 397 " pdb=" C SER C 397 " ideal model delta sigma weight residual 109.81 113.56 -3.75 2.21e+00 2.05e-01 2.88e+00 angle pdb=" N THR A 55 " pdb=" CA THR A 55 " pdb=" C THR A 55 " ideal model delta sigma weight residual 110.80 114.25 -3.45 2.13e+00 2.20e-01 2.62e+00 angle pdb=" C THR B 227 " pdb=" CA THR B 227 " pdb=" CB THR B 227 " ideal model delta sigma weight residual 111.06 108.24 2.82 1.83e+00 2.99e-01 2.38e+00 ... (remaining 25992 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 11269 17.59 - 35.18: 560 35.18 - 52.77: 121 52.77 - 70.36: 24 70.36 - 87.95: 13 Dihedral angle restraints: 11987 sinusoidal: 5049 harmonic: 6938 Sorted by residual: dihedral pdb=" CA PHE B 10 " pdb=" C PHE B 10 " pdb=" N THR B 11 " pdb=" CA THR B 11 " ideal model delta harmonic sigma weight residual 180.00 157.06 22.94 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" CA PHE C 10 " pdb=" C PHE C 10 " pdb=" N THR C 11 " pdb=" CA THR C 11 " ideal model delta harmonic sigma weight residual 180.00 157.90 22.10 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA LEU j 30 " pdb=" C LEU j 30 " pdb=" N PRO j 31 " pdb=" CA PRO j 31 " ideal model delta harmonic sigma weight residual 180.00 159.83 20.17 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 11984 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1965 0.031 - 0.061: 704 0.061 - 0.092: 162 0.092 - 0.122: 92 0.122 - 0.153: 19 Chirality restraints: 2942 Sorted by residual: chirality pdb=" CA ILE C 230 " pdb=" N ILE C 230 " pdb=" C ILE C 230 " pdb=" CB ILE C 230 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.84e-01 chirality pdb=" CA ILE A 230 " pdb=" N ILE A 230 " pdb=" C ILE A 230 " pdb=" CB ILE A 230 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.14e-01 chirality pdb=" CA ILE D 230 " pdb=" N ILE D 230 " pdb=" C ILE D 230 " pdb=" CB ILE D 230 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.54e-01 ... (remaining 2939 not shown) Planarity restraints: 3479 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN C 41 " 0.029 5.00e-02 4.00e+02 4.37e-02 3.06e+00 pdb=" N PRO C 42 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO C 42 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 42 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU o 30 " -0.023 5.00e-02 4.00e+02 3.42e-02 1.87e+00 pdb=" N PRO o 31 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO o 31 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO o 31 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 255 " 0.022 5.00e-02 4.00e+02 3.27e-02 1.71e+00 pdb=" N PRO C 256 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO C 256 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 256 " 0.019 5.00e-02 4.00e+02 ... (remaining 3476 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 111 2.52 - 3.12: 15046 3.12 - 3.71: 27050 3.71 - 4.31: 36590 4.31 - 4.90: 60372 Nonbonded interactions: 139169 Sorted by model distance: nonbonded pdb=" OG SER b 65 " pdb=" O ASP b 69 " model vdw 1.930 2.440 nonbonded pdb=" OG SER A 440 " pdb=" O GLU C 441 " model vdw 2.113 2.440 nonbonded pdb=" O PHE B 226 " pdb=" OG1 THR B 227 " model vdw 2.131 2.440 nonbonded pdb=" N ASP e 29 " pdb=" OD1 ASP e 29 " model vdw 2.146 2.520 nonbonded pdb=" NZ LYS C 132 " pdb=" O VAL C 248 " model vdw 2.148 2.520 ... (remaining 139164 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and (resid 9 through 396 or resid 406 through 448)) } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = (chain 'a' and resid 10 through 55) selection = (chain 'o' and resid 10 through 55) } ncs_group { reference = (chain 'b' and resid 10 through 65) selection = (chain 'c' and resid 10 through 65) selection = (chain 'd' and resid 10 through 65) selection = (chain 'e' and resid 10 through 65) selection = (chain 'f' and resid 10 through 65) selection = (chain 'g' and resid 10 through 65) selection = (chain 'h' and resid 10 through 65) selection = (chain 'i' and resid 10 through 65) selection = (chain 'j' and resid 10 through 65) selection = (chain 'k' and resid 10 through 65) selection = (chain 'l' and resid 10 through 65) selection = (chain 'm' and resid 10 through 65) selection = (chain 'n' and resid 10 through 65) selection = (chain 'p' and resid 10 through 65) } 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: 8.440 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: 31.490 Check model and map are aligned: 0.300 Set scattering table: 0.180 Process input model: 50.120 Find NCS groups from input model: 1.270 Set up NCS constraints: 0.100 Set refine NCS operators: 0.010 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 19266 Z= 0.265 Angle : 0.461 4.377 25997 Z= 0.247 Chirality : 0.037 0.153 2942 Planarity : 0.003 0.044 3479 Dihedral : 11.549 87.953 7447 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.59 % Allowed : 2.54 % Favored : 96.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.18), residues: 2336 helix: 0.68 (0.14), residues: 1449 sheet: 0.69 (0.33), residues: 267 loop : 0.78 (0.27), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 47 HIS 0.003 0.001 HIS C 307 PHE 0.014 0.001 PHE B 10 TYR 0.011 0.001 TYR A 406 ARG 0.003 0.000 ARG A 383 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 2050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 560 time to evaluate : 2.312 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: A 14 ARG cc_start: 0.8672 (mmm160) cc_final: 0.8315 (tpt-90) REVERT: C 187 ARG cc_start: 0.7890 (ttt-90) cc_final: 0.7677 (ttt-90) REVERT: C 339 GLN cc_start: 0.7884 (tm-30) cc_final: 0.7568 (tm-30) REVERT: i 23 THR cc_start: 0.8418 (m) cc_final: 0.8187 (p) REVERT: g 16 SER cc_start: 0.8498 (t) cc_final: 0.8003 (p) REVERT: g 21 ILE cc_start: 0.9012 (mt) cc_final: 0.8811 (mm) REVERT: h 20 GLN cc_start: 0.7937 (mt0) cc_final: 0.7668 (mt0) REVERT: a 34 GLU cc_start: 0.8440 (tp30) cc_final: 0.8051 (tp30) REVERT: b 38 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7740 (mm-30) REVERT: b 47 ARG cc_start: 0.7901 (ttm-80) cc_final: 0.7664 (ttm-80) REVERT: B 47 TRP cc_start: 0.7852 (t-100) cc_final: 0.7481 (t-100) REVERT: p 40 GLU cc_start: 0.8929 (tp30) cc_final: 0.8498 (tp30) REVERT: D 71 THR cc_start: 0.9433 (p) cc_final: 0.9168 (t) REVERT: D 282 GLU cc_start: 0.8084 (tp30) cc_final: 0.7833 (tp30) REVERT: m 47 ARG cc_start: 0.8405 (tpp-160) cc_final: 0.7681 (tpp-160) REVERT: n 17 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8529 (mt-10) REVERT: n 45 LEU cc_start: 0.7809 (mt) cc_final: 0.7390 (mt) REVERT: n 48 GLN cc_start: 0.8127 (mt0) cc_final: 0.7491 (mt0) REVERT: n 57 GLU cc_start: 0.7173 (tm-30) cc_final: 0.6948 (tm-30) REVERT: e 44 GLN cc_start: 0.7730 (mt0) cc_final: 0.7264 (mt0) outliers start: 12 outliers final: 6 residues processed: 570 average time/residue: 0.4304 time to fit residues: 334.5588 Evaluate side-chains 443 residues out of total 2050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 437 time to evaluate : 2.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain i residue 29 ASP Chi-restraints excluded: chain d residue 10 SER Chi-restraints excluded: chain e residue 29 ASP Chi-restraints excluded: chain f residue 29 ASP Chi-restraints excluded: chain f residue 37 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 3.9990 chunk 172 optimal weight: 30.0000 chunk 95 optimal weight: 0.6980 chunk 59 optimal weight: 0.0980 chunk 116 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 chunk 178 optimal weight: 30.0000 chunk 69 optimal weight: 0.7980 chunk 108 optimal weight: 0.9980 chunk 133 optimal weight: 0.7980 chunk 207 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN A 273 GLN A 279 GLN A 304 GLN A 358 HIS C 41 GLN C 422 GLN c 48 GLN g 20 GLN h 50 GLN h 54 GLN h 67 ASN a 44 GLN b 50 GLN b 54 GLN b 61 GLN B 300 HIS D 279 GLN ** D 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 61 GLN e 20 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19266 Z= 0.249 Angle : 0.617 8.925 25997 Z= 0.332 Chirality : 0.041 0.171 2942 Planarity : 0.005 0.044 3479 Dihedral : 4.761 48.295 2604 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.73 % Allowed : 10.05 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.17), residues: 2336 helix: 1.82 (0.13), residues: 1516 sheet: 0.68 (0.33), residues: 269 loop : 0.61 (0.29), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 47 HIS 0.005 0.001 HIS D 301 PHE 0.014 0.002 PHE B 10 TYR 0.021 0.001 TYR C 114 ARG 0.008 0.001 ARG B 59 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 2050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 480 time to evaluate : 2.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 ARG cc_start: 0.7523 (tpp80) cc_final: 0.7269 (tpp80) REVERT: A 335 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.7767 (ttpp) REVERT: C 68 ARG cc_start: 0.7370 (mtm110) cc_final: 0.7090 (mtm110) REVERT: C 226 PHE cc_start: 0.7779 (m-80) cc_final: 0.7356 (m-80) REVERT: C 339 GLN cc_start: 0.7451 (tm-30) cc_final: 0.7091 (tm-30) REVERT: C 419 LYS cc_start: 0.8577 (tppt) cc_final: 0.8186 (mmmm) REVERT: a 34 GLU cc_start: 0.7661 (tp30) cc_final: 0.7372 (tp30) REVERT: a 38 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8584 (mm-30) REVERT: b 41 ARG cc_start: 0.8104 (ttp-110) cc_final: 0.7475 (ttp-110) REVERT: B 47 TRP cc_start: 0.7776 (t-100) cc_final: 0.7540 (t-100) REVERT: o 20 GLN cc_start: 0.8467 (tt0) cc_final: 0.8225 (tm-30) REVERT: o 24 ARG cc_start: 0.8494 (ttm110) cc_final: 0.8190 (ttm110) REVERT: o 52 LYS cc_start: 0.9139 (ttpp) cc_final: 0.8724 (tmmt) REVERT: p 40 GLU cc_start: 0.8335 (tp30) cc_final: 0.7864 (tp30) REVERT: D 71 THR cc_start: 0.9433 (p) cc_final: 0.9108 (t) REVERT: D 272 ARG cc_start: 0.9016 (tpt170) cc_final: 0.8745 (tpm170) REVERT: D 275 GLN cc_start: 0.8765 (mm110) cc_final: 0.8403 (mm-40) REVERT: D 279 GLN cc_start: 0.8194 (mm-40) cc_final: 0.7977 (mm110) REVERT: D 285 MET cc_start: 0.8223 (tpp) cc_final: 0.7913 (tpp) REVERT: D 294 ARG cc_start: 0.8322 (ttp80) cc_final: 0.7995 (ttp80) REVERT: m 47 ARG cc_start: 0.8388 (tpp-160) cc_final: 0.7369 (tpp-160) REVERT: n 13 LYS cc_start: 0.8457 (ptmm) cc_final: 0.7811 (pptt) REVERT: n 44 GLN cc_start: 0.8499 (tp-100) cc_final: 0.8177 (tp-100) REVERT: n 45 LEU cc_start: 0.7829 (mt) cc_final: 0.7372 (mt) REVERT: n 54 GLN cc_start: 0.7746 (tp-100) cc_final: 0.7438 (tp-100) REVERT: d 38 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6868 (mp0) REVERT: e 21 ILE cc_start: 0.8718 (OUTLIER) cc_final: 0.8473 (tt) REVERT: f 21 ILE cc_start: 0.7915 (mt) cc_final: 0.7510 (mm) outliers start: 56 outliers final: 29 residues processed: 507 average time/residue: 0.4370 time to fit residues: 300.9987 Evaluate side-chains 469 residues out of total 2050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 437 time to evaluate : 2.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 HIS Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 437 TRP Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain i residue 29 ASP Chi-restraints excluded: chain c residue 36 LEU Chi-restraints excluded: chain h residue 65 SER Chi-restraints excluded: chain b residue 10 SER Chi-restraints excluded: chain b residue 54 GLN Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain p residue 60 VAL Chi-restraints excluded: chain p residue 63 LEU Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 291 ASN Chi-restraints excluded: chain k residue 21 ILE Chi-restraints excluded: chain k residue 27 SER Chi-restraints excluded: chain k residue 36 LEU Chi-restraints excluded: chain k residue 65 SER Chi-restraints excluded: chain d residue 21 ILE Chi-restraints excluded: chain d residue 38 GLU Chi-restraints excluded: chain e residue 21 ILE Chi-restraints excluded: chain e residue 29 ASP Chi-restraints excluded: chain f residue 29 ASP Chi-restraints excluded: chain f residue 37 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 172 optimal weight: 10.0000 chunk 140 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 207 optimal weight: 0.9980 chunk 224 optimal weight: 0.6980 chunk 184 optimal weight: 0.3980 chunk 205 optimal weight: 0.8980 chunk 70 optimal weight: 0.7980 chunk 166 optimal weight: 9.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN C 41 GLN C 217 ASN c 44 GLN g 20 GLN ** o 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 GLN ** m 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19266 Z= 0.264 Angle : 0.598 7.730 25997 Z= 0.321 Chirality : 0.041 0.196 2942 Planarity : 0.004 0.053 3479 Dihedral : 4.753 46.099 2603 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.27 % Allowed : 12.83 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.17), residues: 2336 helix: 2.05 (0.12), residues: 1523 sheet: 0.63 (0.32), residues: 269 loop : 0.52 (0.28), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 47 HIS 0.003 0.001 HIS B 140 PHE 0.026 0.002 PHE D 296 TYR 0.021 0.002 TYR C 114 ARG 0.009 0.001 ARG B 59 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 2050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 444 time to evaluate : 2.312 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: C 164 ASP cc_start: 0.7334 (t0) cc_final: 0.7080 (t0) REVERT: C 226 PHE cc_start: 0.7709 (m-80) cc_final: 0.7361 (m-80) REVERT: C 419 LYS cc_start: 0.8585 (tppt) cc_final: 0.8198 (mmmm) REVERT: h 34 GLU cc_start: 0.7556 (tp30) cc_final: 0.6949 (tp30) REVERT: a 34 GLU cc_start: 0.7585 (tp30) cc_final: 0.7154 (tp30) REVERT: b 50 GLN cc_start: 0.7979 (tp-100) cc_final: 0.7753 (tp-100) REVERT: o 24 ARG cc_start: 0.8532 (ttm110) cc_final: 0.8124 (ttm110) REVERT: o 52 LYS cc_start: 0.9147 (ttpp) cc_final: 0.8713 (tmmt) REVERT: D 71 THR cc_start: 0.9442 (p) cc_final: 0.9095 (t) REVERT: D 92 ARG cc_start: 0.8874 (mtp85) cc_final: 0.8621 (mtp85) REVERT: D 272 ARG cc_start: 0.9001 (tpt170) cc_final: 0.8743 (tpt170) REVERT: D 279 GLN cc_start: 0.8269 (mm-40) cc_final: 0.8063 (mm110) REVERT: D 294 ARG cc_start: 0.8377 (ttp80) cc_final: 0.8032 (ttp80) REVERT: D 305 GLN cc_start: 0.6735 (mm110) cc_final: 0.6508 (mm110) REVERT: m 24 ARG cc_start: 0.8481 (mmm-85) cc_final: 0.8242 (mmm160) REVERT: m 38 GLU cc_start: 0.7970 (tm-30) cc_final: 0.7525 (tm-30) REVERT: m 41 ARG cc_start: 0.8489 (ttp80) cc_final: 0.7740 (ttp80) REVERT: m 47 ARG cc_start: 0.8253 (tpp-160) cc_final: 0.7320 (tpp-160) REVERT: n 44 GLN cc_start: 0.8535 (tp-100) cc_final: 0.8322 (tp-100) REVERT: d 38 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.6737 (mp0) outliers start: 67 outliers final: 56 residues processed: 480 average time/residue: 0.4363 time to fit residues: 287.2559 Evaluate side-chains 472 residues out of total 2050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 415 time to evaluate : 2.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 HIS Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 435 ASP Chi-restraints excluded: chain A residue 437 TRP Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 326 MET Chi-restraints excluded: chain C residue 384 GLU Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain i residue 29 ASP Chi-restraints excluded: chain c residue 36 LEU Chi-restraints excluded: chain g residue 16 SER Chi-restraints excluded: chain h residue 10 SER Chi-restraints excluded: chain h residue 65 SER Chi-restraints excluded: chain a residue 53 LEU Chi-restraints excluded: chain b residue 10 SER Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 301 HIS Chi-restraints excluded: chain o residue 55 GLN Chi-restraints excluded: chain p residue 15 LEU Chi-restraints excluded: chain p residue 21 ILE Chi-restraints excluded: chain p residue 60 VAL Chi-restraints excluded: chain p residue 63 LEU Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain m residue 29 ASP Chi-restraints excluded: chain n residue 53 LEU Chi-restraints excluded: chain j residue 29 ASP Chi-restraints excluded: chain j residue 43 VAL Chi-restraints excluded: chain k residue 20 GLN Chi-restraints excluded: chain k residue 21 ILE Chi-restraints excluded: chain k residue 27 SER Chi-restraints excluded: chain k residue 36 LEU Chi-restraints excluded: chain k residue 65 SER Chi-restraints excluded: chain d residue 21 ILE Chi-restraints excluded: chain d residue 38 GLU Chi-restraints excluded: chain d residue 60 VAL Chi-restraints excluded: chain d residue 62 ILE Chi-restraints excluded: chain e residue 21 ILE Chi-restraints excluded: chain e residue 29 ASP Chi-restraints excluded: chain f residue 29 ASP Chi-restraints excluded: chain f residue 38 GLU Chi-restraints excluded: chain f residue 64 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 0.6980 chunk 155 optimal weight: 0.3980 chunk 107 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 139 optimal weight: 1.9990 chunk 208 optimal weight: 1.9990 chunk 220 optimal weight: 0.9990 chunk 108 optimal weight: 0.7980 chunk 197 optimal weight: 0.0010 chunk 59 optimal weight: 0.6980 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS C 41 GLN C 67 ASN c 44 GLN g 20 GLN b 50 GLN ** p 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 GLN D 275 GLN ** D 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 50 GLN ** n 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 54 GLN e 44 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19266 Z= 0.203 Angle : 0.558 6.660 25997 Z= 0.297 Chirality : 0.039 0.176 2942 Planarity : 0.004 0.058 3479 Dihedral : 4.454 39.700 2601 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.27 % Allowed : 14.54 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.17), residues: 2336 helix: 2.38 (0.13), residues: 1523 sheet: 0.51 (0.32), residues: 274 loop : 0.49 (0.28), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 214 HIS 0.003 0.001 HIS B 140 PHE 0.025 0.001 PHE D 296 TYR 0.022 0.001 TYR C 114 ARG 0.009 0.001 ARG B 73 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 2050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 440 time to evaluate : 2.324 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: C 164 ASP cc_start: 0.7247 (t0) cc_final: 0.7015 (t0) REVERT: C 226 PHE cc_start: 0.7701 (m-80) cc_final: 0.7459 (m-80) REVERT: C 294 ARG cc_start: 0.8416 (ttp80) cc_final: 0.8195 (ttp-110) REVERT: C 419 LYS cc_start: 0.8573 (tppt) cc_final: 0.8245 (mmmm) REVERT: h 34 GLU cc_start: 0.7411 (tp30) cc_final: 0.7149 (tp30) REVERT: a 34 GLU cc_start: 0.7464 (tp30) cc_final: 0.7173 (tp30) REVERT: b 50 GLN cc_start: 0.7974 (tp40) cc_final: 0.7756 (tp-100) REVERT: o 40 GLU cc_start: 0.8640 (tp30) cc_final: 0.8383 (tp30) REVERT: o 52 LYS cc_start: 0.9166 (ttpp) cc_final: 0.8739 (tmmt) REVERT: p 13 LYS cc_start: 0.8922 (tmmt) cc_final: 0.8522 (tmmt) REVERT: p 47 ARG cc_start: 0.8316 (tpp-160) cc_final: 0.8042 (tpp80) REVERT: D 71 THR cc_start: 0.9465 (p) cc_final: 0.9108 (t) REVERT: D 272 ARG cc_start: 0.8987 (tpt170) cc_final: 0.8714 (tpt170) REVERT: D 275 GLN cc_start: 0.8542 (mm110) cc_final: 0.8310 (mm-40) REVERT: D 283 MET cc_start: 0.8700 (mmm) cc_final: 0.8344 (mmt) REVERT: D 294 ARG cc_start: 0.8387 (ttp80) cc_final: 0.8049 (ttp80) REVERT: D 305 GLN cc_start: 0.6693 (mm110) cc_final: 0.6434 (mm110) REVERT: m 38 GLU cc_start: 0.8033 (tm-30) cc_final: 0.7546 (tm-30) REVERT: m 41 ARG cc_start: 0.8576 (ttp80) cc_final: 0.7827 (ttp80) REVERT: m 47 ARG cc_start: 0.8278 (tpp-160) cc_final: 0.7300 (tpp-160) REVERT: k 47 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7084 (ttp80) REVERT: d 38 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6912 (mp0) REVERT: e 26 GLU cc_start: 0.8603 (tt0) cc_final: 0.8287 (tt0) outliers start: 67 outliers final: 50 residues processed: 480 average time/residue: 0.4773 time to fit residues: 318.5906 Evaluate side-chains 463 residues out of total 2050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 411 time to evaluate : 2.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 HIS Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 437 TRP Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 384 GLU Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain i residue 29 ASP Chi-restraints excluded: chain c residue 36 LEU Chi-restraints excluded: chain g residue 16 SER Chi-restraints excluded: chain g residue 18 LEU Chi-restraints excluded: chain h residue 65 SER Chi-restraints excluded: chain a residue 53 LEU Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 301 HIS Chi-restraints excluded: chain o residue 55 GLN Chi-restraints excluded: chain p residue 15 LEU Chi-restraints excluded: chain p residue 21 ILE Chi-restraints excluded: chain p residue 55 GLN Chi-restraints excluded: chain p residue 60 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain n residue 17 GLU Chi-restraints excluded: chain n residue 53 LEU Chi-restraints excluded: chain j residue 29 ASP Chi-restraints excluded: chain j residue 43 VAL Chi-restraints excluded: chain k residue 20 GLN Chi-restraints excluded: chain k residue 21 ILE Chi-restraints excluded: chain k residue 27 SER Chi-restraints excluded: chain k residue 34 GLU Chi-restraints excluded: chain k residue 47 ARG Chi-restraints excluded: chain k residue 65 SER Chi-restraints excluded: chain d residue 38 GLU Chi-restraints excluded: chain d residue 62 ILE Chi-restraints excluded: chain e residue 29 ASP Chi-restraints excluded: chain e residue 64 LEU Chi-restraints excluded: chain f residue 29 ASP Chi-restraints excluded: chain f residue 38 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 0.6980 chunk 125 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 188 optimal weight: 0.7980 chunk 152 optimal weight: 0.0870 chunk 0 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 197 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN C 41 GLN i 61 GLN c 44 GLN c 48 GLN g 20 GLN ** p 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 54 GLN ** n 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 44 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19266 Z= 0.252 Angle : 0.596 12.314 25997 Z= 0.313 Chirality : 0.040 0.192 2942 Planarity : 0.004 0.059 3479 Dihedral : 4.521 37.021 2601 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.56 % Allowed : 15.56 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.17), residues: 2336 helix: 2.36 (0.13), residues: 1515 sheet: 0.42 (0.32), residues: 275 loop : 0.45 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 214 HIS 0.005 0.001 HIS B 140 PHE 0.016 0.002 PHE B 10 TYR 0.020 0.002 TYR C 114 ARG 0.012 0.001 ARG D 302 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 412 time to evaluate : 2.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 ARG cc_start: 0.7075 (mtt180) cc_final: 0.6838 (mtt90) REVERT: C 164 ASP cc_start: 0.7258 (t0) cc_final: 0.7055 (t0) REVERT: C 170 ILE cc_start: 0.8541 (mm) cc_final: 0.8325 (mm) REVERT: C 226 PHE cc_start: 0.7701 (m-80) cc_final: 0.7483 (m-80) REVERT: C 294 ARG cc_start: 0.8395 (ttp80) cc_final: 0.8182 (ttp-110) REVERT: C 419 LYS cc_start: 0.8569 (tppt) cc_final: 0.8259 (mmmm) REVERT: i 30 LEU cc_start: 0.8197 (tp) cc_final: 0.7825 (tp) REVERT: h 34 GLU cc_start: 0.7313 (tp30) cc_final: 0.6938 (tp30) REVERT: a 34 GLU cc_start: 0.7531 (tp30) cc_final: 0.7220 (tp30) REVERT: o 52 LYS cc_start: 0.9136 (ttpp) cc_final: 0.8713 (tmmt) REVERT: p 13 LYS cc_start: 0.8848 (tmmt) cc_final: 0.8637 (tmmt) REVERT: p 47 ARG cc_start: 0.8315 (tpp-160) cc_final: 0.8070 (tpp80) REVERT: D 71 THR cc_start: 0.9461 (p) cc_final: 0.9086 (t) REVERT: D 283 MET cc_start: 0.8675 (mmm) cc_final: 0.8371 (tpp) REVERT: m 38 GLU cc_start: 0.8016 (tm-30) cc_final: 0.7655 (tm-30) REVERT: m 41 ARG cc_start: 0.8613 (ttp80) cc_final: 0.8092 (ttp80) REVERT: m 47 ARG cc_start: 0.8289 (tpp-160) cc_final: 0.7268 (tpp-160) REVERT: n 61 GLN cc_start: 0.8637 (tp-100) cc_final: 0.8352 (tp-100) REVERT: k 47 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7125 (ttp80) REVERT: l 19 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6884 (mt-10) REVERT: d 34 GLU cc_start: 0.7378 (mm-30) cc_final: 0.7118 (mm-30) REVERT: d 38 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6843 (mp0) REVERT: e 36 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8302 (tt) outliers start: 73 outliers final: 56 residues processed: 460 average time/residue: 0.4217 time to fit residues: 267.6016 Evaluate side-chains 457 residues out of total 2050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 397 time to evaluate : 2.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 435 ASP Chi-restraints excluded: chain A residue 437 TRP Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 326 MET Chi-restraints excluded: chain C residue 384 GLU Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain i residue 29 ASP Chi-restraints excluded: chain g residue 16 SER Chi-restraints excluded: chain h residue 58 GLN Chi-restraints excluded: chain h residue 65 SER Chi-restraints excluded: chain a residue 53 LEU Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 301 HIS Chi-restraints excluded: chain p residue 15 LEU Chi-restraints excluded: chain p residue 21 ILE Chi-restraints excluded: chain p residue 55 GLN Chi-restraints excluded: chain p residue 60 VAL Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain j residue 29 ASP Chi-restraints excluded: chain j residue 43 VAL Chi-restraints excluded: chain j residue 53 LEU Chi-restraints excluded: chain k residue 20 GLN Chi-restraints excluded: chain k residue 21 ILE Chi-restraints excluded: chain k residue 27 SER Chi-restraints excluded: chain k residue 34 GLU Chi-restraints excluded: chain k residue 36 LEU Chi-restraints excluded: chain k residue 47 ARG Chi-restraints excluded: chain k residue 65 SER Chi-restraints excluded: chain l residue 19 GLU Chi-restraints excluded: chain d residue 21 ILE Chi-restraints excluded: chain d residue 38 GLU Chi-restraints excluded: chain d residue 60 VAL Chi-restraints excluded: chain d residue 62 ILE Chi-restraints excluded: chain e residue 29 ASP Chi-restraints excluded: chain e residue 36 LEU Chi-restraints excluded: chain e residue 64 LEU Chi-restraints excluded: chain f residue 29 ASP Chi-restraints excluded: chain f residue 37 ASN Chi-restraints excluded: chain f residue 38 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 0.9980 chunk 198 optimal weight: 0.0980 chunk 43 optimal weight: 0.5980 chunk 129 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 220 optimal weight: 0.5980 chunk 183 optimal weight: 0.8980 chunk 102 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 115 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN c 44 GLN g 20 GLN ** p 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 54 GLN ** n 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 44 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.4339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19266 Z= 0.215 Angle : 0.581 11.646 25997 Z= 0.305 Chirality : 0.039 0.172 2942 Planarity : 0.004 0.060 3479 Dihedral : 4.389 34.861 2601 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 4.05 % Allowed : 16.73 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.17), residues: 2336 helix: 2.47 (0.13), residues: 1516 sheet: 0.40 (0.32), residues: 275 loop : 0.39 (0.28), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 214 HIS 0.005 0.001 HIS B 140 PHE 0.013 0.001 PHE D 296 TYR 0.018 0.001 TYR C 114 ARG 0.012 0.001 ARG D 272 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 2050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 417 time to evaluate : 2.125 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: C 164 ASP cc_start: 0.7162 (t0) cc_final: 0.6922 (t0) REVERT: C 170 ILE cc_start: 0.8527 (mm) cc_final: 0.8325 (mm) REVERT: C 419 LYS cc_start: 0.8526 (tppt) cc_final: 0.8210 (mmmm) REVERT: C 444 ASN cc_start: 0.8123 (OUTLIER) cc_final: 0.7386 (p0) REVERT: h 19 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7722 (mp0) REVERT: h 34 GLU cc_start: 0.7213 (tp30) cc_final: 0.6922 (tp30) REVERT: a 24 ARG cc_start: 0.8705 (tpp80) cc_final: 0.8351 (ttm110) REVERT: a 34 GLU cc_start: 0.7435 (tp30) cc_final: 0.7110 (tp30) REVERT: b 50 GLN cc_start: 0.8016 (tp-100) cc_final: 0.7786 (tp-100) REVERT: o 52 LYS cc_start: 0.9178 (ttpp) cc_final: 0.8750 (tmmt) REVERT: p 13 LYS cc_start: 0.8869 (tmmt) cc_final: 0.8494 (tmmt) REVERT: p 26 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7364 (mt-10) REVERT: p 37 ASN cc_start: 0.8055 (p0) cc_final: 0.7612 (p0) REVERT: p 38 GLU cc_start: 0.7029 (tt0) cc_final: 0.6689 (pm20) REVERT: p 47 ARG cc_start: 0.8315 (tpp-160) cc_final: 0.8044 (tpp80) REVERT: D 71 THR cc_start: 0.9444 (p) cc_final: 0.9060 (t) REVERT: D 283 MET cc_start: 0.8627 (mmm) cc_final: 0.8300 (tpp) REVERT: D 294 ARG cc_start: 0.8488 (ttp80) cc_final: 0.8227 (ttp80) REVERT: m 24 ARG cc_start: 0.8541 (mmm-85) cc_final: 0.8217 (mmm160) REVERT: m 38 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7648 (tm-30) REVERT: m 41 ARG cc_start: 0.8607 (ttp80) cc_final: 0.8106 (ttp80) REVERT: m 47 ARG cc_start: 0.8300 (tpp-160) cc_final: 0.7211 (tpp-160) REVERT: n 59 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.6702 (tmm-80) REVERT: n 61 GLN cc_start: 0.8528 (tp-100) cc_final: 0.8202 (tp-100) REVERT: k 47 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7053 (ttp80) REVERT: l 19 GLU cc_start: 0.7102 (OUTLIER) cc_final: 0.6785 (mt-10) REVERT: d 23 THR cc_start: 0.8395 (m) cc_final: 0.8177 (m) REVERT: d 38 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6948 (mp0) REVERT: e 36 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8266 (tt) outliers start: 83 outliers final: 61 residues processed: 468 average time/residue: 0.4083 time to fit residues: 265.5303 Evaluate side-chains 474 residues out of total 2050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 407 time to evaluate : 2.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 349 ASN Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 435 ASP Chi-restraints excluded: chain A residue 437 TRP Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 326 MET Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 384 GLU Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 444 ASN Chi-restraints excluded: chain i residue 13 LYS Chi-restraints excluded: chain i residue 29 ASP Chi-restraints excluded: chain c residue 58 GLN Chi-restraints excluded: chain h residue 65 SER Chi-restraints excluded: chain a residue 29 ASP Chi-restraints excluded: chain a residue 53 LEU Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 301 HIS Chi-restraints excluded: chain o residue 44 GLN Chi-restraints excluded: chain p residue 15 LEU Chi-restraints excluded: chain p residue 20 GLN Chi-restraints excluded: chain p residue 21 ILE Chi-restraints excluded: chain p residue 55 GLN Chi-restraints excluded: chain p residue 60 VAL Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain n residue 17 GLU Chi-restraints excluded: chain n residue 59 ARG Chi-restraints excluded: chain j residue 43 VAL Chi-restraints excluded: chain j residue 53 LEU Chi-restraints excluded: chain k residue 20 GLN Chi-restraints excluded: chain k residue 21 ILE Chi-restraints excluded: chain k residue 27 SER Chi-restraints excluded: chain k residue 34 GLU Chi-restraints excluded: chain k residue 47 ARG Chi-restraints excluded: chain k residue 65 SER Chi-restraints excluded: chain l residue 19 GLU Chi-restraints excluded: chain d residue 38 GLU Chi-restraints excluded: chain d residue 60 VAL Chi-restraints excluded: chain d residue 62 ILE Chi-restraints excluded: chain e residue 36 LEU Chi-restraints excluded: chain e residue 64 LEU Chi-restraints excluded: chain f residue 29 ASP Chi-restraints excluded: chain f residue 37 ASN Chi-restraints excluded: chain f residue 38 GLU Chi-restraints excluded: chain f residue 64 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 161 optimal weight: 0.3980 chunk 124 optimal weight: 0.7980 chunk 185 optimal weight: 0.7980 chunk 123 optimal weight: 0.7980 chunk 219 optimal weight: 0.9980 chunk 137 optimal weight: 0.5980 chunk 133 optimal weight: 0.6980 chunk 101 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN C 446 GLN c 44 GLN g 20 GLN ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 44 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 19266 Z= 0.243 Angle : 0.609 11.839 25997 Z= 0.319 Chirality : 0.040 0.170 2942 Planarity : 0.004 0.056 3479 Dihedral : 4.415 34.225 2599 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.71 % Allowed : 17.85 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.17), residues: 2336 helix: 2.42 (0.13), residues: 1516 sheet: 0.49 (0.33), residues: 265 loop : 0.30 (0.27), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 214 HIS 0.006 0.001 HIS B 140 PHE 0.038 0.002 PHE C 226 TYR 0.018 0.001 TYR A 95 ARG 0.011 0.001 ARG D 272 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 2050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 404 time to evaluate : 2.365 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: A 47 TRP cc_start: 0.6627 (m-10) cc_final: 0.6392 (m-10) REVERT: A 385 ARG cc_start: 0.7070 (mtt180) cc_final: 0.6827 (mtt90) REVERT: C 164 ASP cc_start: 0.7231 (t0) cc_final: 0.7002 (t0) REVERT: C 170 ILE cc_start: 0.8550 (mm) cc_final: 0.8350 (mm) REVERT: C 252 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.6152 (tmt170) REVERT: C 419 LYS cc_start: 0.8569 (tppt) cc_final: 0.8194 (mmmm) REVERT: C 444 ASN cc_start: 0.8171 (OUTLIER) cc_final: 0.7419 (p0) REVERT: i 58 GLN cc_start: 0.8564 (tp40) cc_final: 0.8362 (tp40) REVERT: h 19 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7677 (mp0) REVERT: a 24 ARG cc_start: 0.8707 (tpp80) cc_final: 0.8405 (ttm110) REVERT: a 34 GLU cc_start: 0.7466 (tp30) cc_final: 0.7139 (tp30) REVERT: b 50 GLN cc_start: 0.7997 (tp-100) cc_final: 0.7791 (tp-100) REVERT: o 52 LYS cc_start: 0.9199 (ttpp) cc_final: 0.8768 (tmmt) REVERT: o 63 LEU cc_start: 0.5899 (OUTLIER) cc_final: 0.5509 (mp) REVERT: D 71 THR cc_start: 0.9443 (p) cc_final: 0.9052 (t) REVERT: D 294 ARG cc_start: 0.8491 (ttp80) cc_final: 0.8217 (ttp80) REVERT: m 24 ARG cc_start: 0.8560 (mmm-85) cc_final: 0.8215 (mmm160) REVERT: m 38 GLU cc_start: 0.8256 (tm-30) cc_final: 0.7641 (tm-30) REVERT: m 41 ARG cc_start: 0.8624 (ttp80) cc_final: 0.8148 (ttp80) REVERT: m 47 ARG cc_start: 0.8284 (tpp-160) cc_final: 0.7157 (tpp-160) REVERT: n 47 ARG cc_start: 0.8815 (ttp80) cc_final: 0.8548 (ttm110) REVERT: n 59 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.6901 (tmm-80) REVERT: n 61 GLN cc_start: 0.8580 (tp-100) cc_final: 0.8157 (tp-100) REVERT: k 47 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7067 (ttp80) REVERT: l 19 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6913 (mt-10) REVERT: d 38 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6976 (mp0) REVERT: e 36 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8228 (tt) outliers start: 76 outliers final: 63 residues processed: 451 average time/residue: 0.4171 time to fit residues: 260.8083 Evaluate side-chains 471 residues out of total 2050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 400 time to evaluate : 2.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 HIS Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 435 ASP Chi-restraints excluded: chain A residue 437 TRP Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 252 ARG Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 326 MET Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 384 GLU Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 444 ASN Chi-restraints excluded: chain i residue 29 ASP Chi-restraints excluded: chain g residue 16 SER Chi-restraints excluded: chain h residue 65 SER Chi-restraints excluded: chain a residue 29 ASP Chi-restraints excluded: chain a residue 53 LEU Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 301 HIS Chi-restraints excluded: chain o residue 44 GLN Chi-restraints excluded: chain o residue 63 LEU Chi-restraints excluded: chain p residue 15 LEU Chi-restraints excluded: chain p residue 20 GLN Chi-restraints excluded: chain p residue 21 ILE Chi-restraints excluded: chain p residue 53 LEU Chi-restraints excluded: chain p residue 60 VAL Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain n residue 59 ARG Chi-restraints excluded: chain j residue 43 VAL Chi-restraints excluded: chain j residue 53 LEU Chi-restraints excluded: chain k residue 20 GLN Chi-restraints excluded: chain k residue 21 ILE Chi-restraints excluded: chain k residue 27 SER Chi-restraints excluded: chain k residue 34 GLU Chi-restraints excluded: chain k residue 36 LEU Chi-restraints excluded: chain k residue 47 ARG Chi-restraints excluded: chain k residue 65 SER Chi-restraints excluded: chain l residue 19 GLU Chi-restraints excluded: chain d residue 21 ILE Chi-restraints excluded: chain d residue 38 GLU Chi-restraints excluded: chain d residue 60 VAL Chi-restraints excluded: chain d residue 62 ILE Chi-restraints excluded: chain e residue 36 LEU Chi-restraints excluded: chain e residue 64 LEU Chi-restraints excluded: chain f residue 29 ASP Chi-restraints excluded: chain f residue 37 ASN Chi-restraints excluded: chain f residue 44 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 0.9990 chunk 87 optimal weight: 0.0770 chunk 131 optimal weight: 1.9990 chunk 66 optimal weight: 0.0970 chunk 43 optimal weight: 0.2980 chunk 42 optimal weight: 0.9980 chunk 139 optimal weight: 0.0000 chunk 149 optimal weight: 0.0970 chunk 108 optimal weight: 0.0030 chunk 20 optimal weight: 0.9990 chunk 172 optimal weight: 9.9990 overall best weight: 0.0548 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN C 354 GLN c 44 GLN g 20 GLN b 50 GLN ** p 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 275 GLN ** D 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 50 GLN ** n 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 54 GLN ** n 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.5039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19266 Z= 0.182 Angle : 0.592 12.648 25997 Z= 0.304 Chirality : 0.038 0.199 2942 Planarity : 0.004 0.057 3479 Dihedral : 3.973 32.707 2599 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.39 % Allowed : 19.41 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.98 (0.18), residues: 2336 helix: 2.82 (0.13), residues: 1507 sheet: 0.40 (0.33), residues: 264 loop : 0.43 (0.28), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 47 HIS 0.006 0.001 HIS B 140 PHE 0.015 0.001 PHE C 39 TYR 0.016 0.001 TYR C 114 ARG 0.012 0.001 ARG i 47 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 2050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 474 time to evaluate : 2.303 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: C 68 ARG cc_start: 0.7543 (mtm110) cc_final: 0.7249 (mtm110) REVERT: C 162 ARG cc_start: 0.8362 (ttp-110) cc_final: 0.8151 (ttp80) REVERT: C 164 ASP cc_start: 0.7151 (t0) cc_final: 0.6922 (t0) REVERT: C 252 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.6736 (tmt170) REVERT: C 424 LYS cc_start: 0.8801 (pptt) cc_final: 0.8461 (pptt) REVERT: h 34 GLU cc_start: 0.6955 (tp30) cc_final: 0.6744 (tp30) REVERT: a 24 ARG cc_start: 0.8532 (tpp80) cc_final: 0.8250 (ttm110) REVERT: a 34 GLU cc_start: 0.7079 (tp30) cc_final: 0.6847 (tp30) REVERT: o 52 LYS cc_start: 0.9077 (ttpp) cc_final: 0.8648 (tmmt) REVERT: p 37 ASN cc_start: 0.8323 (p0) cc_final: 0.7841 (p0) REVERT: D 71 THR cc_start: 0.9385 (p) cc_final: 0.9003 (t) REVERT: D 272 ARG cc_start: 0.8762 (mmm160) cc_final: 0.8202 (mmm160) REVERT: D 294 ARG cc_start: 0.8454 (ttp80) cc_final: 0.8212 (ttp80) REVERT: m 24 ARG cc_start: 0.8454 (mmm-85) cc_final: 0.8101 (mmm160) REVERT: m 38 GLU cc_start: 0.8310 (tm-30) cc_final: 0.7689 (tm-30) REVERT: m 41 ARG cc_start: 0.8602 (ttp80) cc_final: 0.8180 (ttp80) REVERT: m 47 ARG cc_start: 0.8280 (tpp-160) cc_final: 0.7174 (tpp-160) REVERT: n 59 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.6742 (tmm-80) REVERT: j 12 GLU cc_start: 0.7901 (tt0) cc_final: 0.7582 (tt0) REVERT: l 17 GLU cc_start: 0.7766 (tp30) cc_final: 0.7504 (tp30) REVERT: l 19 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6610 (mt-10) REVERT: d 60 VAL cc_start: 0.7664 (t) cc_final: 0.7434 (t) REVERT: e 36 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8120 (tt) outliers start: 49 outliers final: 26 residues processed: 498 average time/residue: 0.4328 time to fit residues: 294.4484 Evaluate side-chains 455 residues out of total 2050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 425 time to evaluate : 2.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 437 TRP Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 252 ARG Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain a residue 53 LEU Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 301 HIS Chi-restraints excluded: chain p residue 15 LEU Chi-restraints excluded: chain p residue 20 GLN Chi-restraints excluded: chain p residue 53 LEU Chi-restraints excluded: chain p residue 55 GLN Chi-restraints excluded: chain p residue 60 VAL Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain n residue 54 GLN Chi-restraints excluded: chain n residue 59 ARG Chi-restraints excluded: chain k residue 21 ILE Chi-restraints excluded: chain k residue 65 SER Chi-restraints excluded: chain l residue 19 GLU Chi-restraints excluded: chain e residue 36 LEU Chi-restraints excluded: chain f residue 64 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 0.7980 chunk 210 optimal weight: 0.8980 chunk 192 optimal weight: 6.9990 chunk 204 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 89 optimal weight: 0.2980 chunk 160 optimal weight: 0.5980 chunk 62 optimal weight: 0.0070 chunk 185 optimal weight: 0.3980 chunk 193 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN C 354 GLN C 446 GLN i 48 GLN i 61 GLN c 44 GLN c 48 GLN g 20 GLN h 20 GLN b 67 ASN B 306 GLN o 50 GLN ** p 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 304 GLN ** D 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.4959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19266 Z= 0.210 Angle : 0.639 14.675 25997 Z= 0.323 Chirality : 0.039 0.186 2942 Planarity : 0.004 0.051 3479 Dihedral : 4.003 22.474 2593 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.80 % Allowed : 20.73 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.89 (0.17), residues: 2336 helix: 2.75 (0.13), residues: 1510 sheet: 0.56 (0.33), residues: 255 loop : 0.28 (0.27), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 31 HIS 0.004 0.001 HIS B 140 PHE 0.015 0.001 PHE A 39 TYR 0.018 0.001 TYR A 95 ARG 0.009 0.001 ARG C 223 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 424 time to evaluate : 1.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ILE cc_start: 0.8550 (mm) cc_final: 0.8290 (mm) REVERT: C 164 ASP cc_start: 0.7206 (t0) cc_final: 0.6936 (t0) REVERT: C 252 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7219 (tmt170) REVERT: a 24 ARG cc_start: 0.8631 (tpp80) cc_final: 0.8335 (ttm110) REVERT: a 34 GLU cc_start: 0.7312 (tp30) cc_final: 0.7106 (tp30) REVERT: o 52 LYS cc_start: 0.9147 (ttpp) cc_final: 0.8731 (tmmt) REVERT: p 25 LEU cc_start: 0.7676 (tt) cc_final: 0.7229 (tt) REVERT: p 38 GLU cc_start: 0.4844 (pm20) cc_final: 0.4613 (pm20) REVERT: D 71 THR cc_start: 0.9394 (p) cc_final: 0.8998 (t) REVERT: m 24 ARG cc_start: 0.8482 (mmm-85) cc_final: 0.8110 (mmm160) REVERT: m 38 GLU cc_start: 0.8302 (tm-30) cc_final: 0.7695 (tm-30) REVERT: m 41 ARG cc_start: 0.8622 (ttp80) cc_final: 0.8203 (ttp80) REVERT: n 59 ARG cc_start: 0.7432 (OUTLIER) cc_final: 0.6993 (tmm-80) REVERT: j 12 GLU cc_start: 0.7972 (tt0) cc_final: 0.7660 (tt0) REVERT: l 19 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6766 (mt-10) REVERT: e 36 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8159 (tt) outliers start: 37 outliers final: 27 residues processed: 444 average time/residue: 0.4111 time to fit residues: 253.4298 Evaluate side-chains 439 residues out of total 2050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 408 time to evaluate : 2.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 437 TRP Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 252 ARG Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain a residue 53 LEU Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain B residue 301 HIS Chi-restraints excluded: chain p residue 15 LEU Chi-restraints excluded: chain p residue 53 LEU Chi-restraints excluded: chain p residue 55 GLN Chi-restraints excluded: chain p residue 60 VAL Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain n residue 59 ARG Chi-restraints excluded: chain k residue 21 ILE Chi-restraints excluded: chain l residue 19 GLU Chi-restraints excluded: chain l residue 45 LEU Chi-restraints excluded: chain l residue 62 ILE Chi-restraints excluded: chain e residue 36 LEU Chi-restraints excluded: chain f residue 64 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 0.3980 chunk 132 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 chunk 150 optimal weight: 0.7980 chunk 227 optimal weight: 0.5980 chunk 209 optimal weight: 0.7980 chunk 180 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 chunk 139 optimal weight: 0.0040 chunk 110 optimal weight: 0.0470 chunk 143 optimal weight: 0.9990 overall best weight: 0.3290 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 96 GLN C 41 GLN c 44 GLN g 20 GLN b 50 GLN ** p 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.5050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19266 Z= 0.207 Angle : 0.661 13.548 25997 Z= 0.338 Chirality : 0.039 0.191 2942 Planarity : 0.004 0.049 3479 Dihedral : 4.022 22.510 2593 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.80 % Allowed : 21.27 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.90 (0.17), residues: 2336 helix: 2.78 (0.13), residues: 1504 sheet: 0.50 (0.33), residues: 260 loop : 0.25 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 214 HIS 0.004 0.001 HIS B 140 PHE 0.012 0.001 PHE h 11 TYR 0.016 0.001 TYR A 95 ARG 0.012 0.001 ARG p 41 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 416 time to evaluate : 2.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7411 (mm-30) REVERT: C 164 ASP cc_start: 0.7174 (t0) cc_final: 0.6929 (t0) REVERT: C 223 ARG cc_start: 0.7466 (tmm160) cc_final: 0.7038 (ttp80) REVERT: C 252 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7364 (tmt170) REVERT: h 38 GLU cc_start: 0.6860 (mt-10) cc_final: 0.6408 (mt-10) REVERT: a 24 ARG cc_start: 0.8658 (tpp80) cc_final: 0.8348 (ttm110) REVERT: a 34 GLU cc_start: 0.7305 (tp30) cc_final: 0.7101 (tp30) REVERT: o 52 LYS cc_start: 0.9092 (ttpp) cc_final: 0.8654 (tmmt) REVERT: p 50 GLN cc_start: 0.8697 (tm-30) cc_final: 0.8057 (tp40) REVERT: D 71 THR cc_start: 0.9381 (p) cc_final: 0.8990 (t) REVERT: D 294 ARG cc_start: 0.8539 (ttp80) cc_final: 0.8267 (ttp80) REVERT: m 24 ARG cc_start: 0.8471 (mmm-85) cc_final: 0.8098 (mmm160) REVERT: m 38 GLU cc_start: 0.8304 (tm-30) cc_final: 0.7716 (tm-30) REVERT: m 41 ARG cc_start: 0.8620 (ttp80) cc_final: 0.8178 (ttp80) REVERT: n 59 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.7180 (tmm-80) REVERT: j 12 GLU cc_start: 0.7949 (tt0) cc_final: 0.7622 (tt0) REVERT: l 19 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6790 (mt-10) outliers start: 37 outliers final: 30 residues processed: 436 average time/residue: 0.3684 time to fit residues: 222.0873 Evaluate side-chains 442 residues out of total 2050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 409 time to evaluate : 1.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 437 TRP Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 252 ARG Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain a residue 53 LEU Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 301 HIS Chi-restraints excluded: chain p residue 53 LEU Chi-restraints excluded: chain p residue 55 GLN Chi-restraints excluded: chain p residue 60 VAL Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain n residue 59 ARG Chi-restraints excluded: chain j residue 43 VAL Chi-restraints excluded: chain j residue 60 VAL Chi-restraints excluded: chain k residue 21 ILE Chi-restraints excluded: chain l residue 19 GLU Chi-restraints excluded: chain f residue 29 ASP Chi-restraints excluded: chain f residue 64 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 0.9990 chunk 55 optimal weight: 0.0870 chunk 166 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 50 optimal weight: 0.0060 chunk 181 optimal weight: 2.9990 chunk 75 optimal weight: 0.4980 chunk 186 optimal weight: 1.9990 chunk 22 optimal weight: 0.0370 chunk 33 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 overall best weight: 0.3254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN c 44 GLN g 20 GLN h 20 GLN B 306 GLN ** p 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.100378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.079080 restraints weight = 59977.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.077260 restraints weight = 52740.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.077100 restraints weight = 40008.027| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.5109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19266 Z= 0.204 Angle : 0.669 13.018 25997 Z= 0.342 Chirality : 0.039 0.189 2942 Planarity : 0.005 0.099 3479 Dihedral : 4.049 24.241 2593 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.66 % Allowed : 21.27 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.84 (0.18), residues: 2336 helix: 2.73 (0.13), residues: 1512 sheet: 0.52 (0.33), residues: 260 loop : 0.18 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 47 HIS 0.006 0.001 HIS B 140 PHE 0.011 0.001 PHE h 11 TYR 0.017 0.001 TYR A 95 ARG 0.009 0.001 ARG i 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5485.78 seconds wall clock time: 107 minutes 40.67 seconds (6460.67 seconds total)