Starting phenix.real_space_refine on Wed Aug 7 04:43:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txr_41704/08_2024/8txr_41704.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txr_41704/08_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_41704/08_2024/8txr_41704.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txr_41704/08_2024/8txr_41704.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txr_41704/08_2024/8txr_41704.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txr_41704/08_2024/8txr_41704.cif" } 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 12.68, per 1000 atoms: 0.67 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: 7.83 Conformation dependent library (CDL) restraints added in 3.3 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: 2.08 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: 8.29 Time building geometry restraints manager: 8.05 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 3.040 nonbonded pdb=" OG SER A 440 " pdb=" O GLU C 441 " model vdw 2.113 3.040 nonbonded pdb=" O PHE B 226 " pdb=" OG1 THR B 227 " model vdw 2.131 3.040 nonbonded pdb=" N ASP e 29 " pdb=" OD1 ASP e 29 " model vdw 2.146 3.120 nonbonded pdb=" NZ LYS C 132 " pdb=" O VAL C 248 " model vdw 2.148 3.120 ... (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 Time spend for trying shortcut: 0.00 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: 13.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.700 Check model and map are aligned: 0.120 Set scattering table: 0.180 Process input model: 55.130 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.030 ------------------------------------------------------------------------------- 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 : 2.363 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: 0.3615 time to fit residues: 281.7471 Evaluate side-chains 443 residues out of total 2050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 437 time to evaluate : 1.445 ------------------------------------------------------------------------------- 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: 6.9990 chunk 172 optimal weight: 30.0000 chunk 95 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 chunk 116 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 178 optimal weight: 40.0000 chunk 69 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 chunk 133 optimal weight: 0.6980 chunk 207 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN A 96 GLN 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 a 44 GLN b 50 GLN b 61 GLN B 300 HIS D 279 GLN ** D 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 20 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 19266 Z= 0.283 Angle : 0.648 9.124 25997 Z= 0.350 Chirality : 0.042 0.184 2942 Planarity : 0.005 0.044 3479 Dihedral : 4.822 48.256 2604 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.44 % Allowed : 9.90 % Favored : 87.66 % 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: 1.91 (0.17), residues: 2336 helix: 1.70 (0.12), residues: 1519 sheet: 0.64 (0.33), residues: 262 loop : 0.59 (0.28), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 47 HIS 0.005 0.001 HIS B 140 PHE 0.016 0.002 PHE B 10 TYR 0.022 0.002 TYR C 114 ARG 0.015 0.001 ARG D 302 *********************** 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 532 residues out of total 2050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 482 time to evaluate : 2.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 335 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.7789 (ttpp) REVERT: C 118 LYS cc_start: 0.9327 (tttm) cc_final: 0.8762 (ptmm) REVERT: C 226 PHE cc_start: 0.7746 (m-80) cc_final: 0.7351 (m-80) REVERT: C 339 GLN cc_start: 0.7474 (tm-30) cc_final: 0.7108 (tm-30) REVERT: C 419 LYS cc_start: 0.8525 (tppt) cc_final: 0.8105 (mmmm) REVERT: a 34 GLU cc_start: 0.7706 (tp30) cc_final: 0.7416 (tp30) REVERT: a 38 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8565 (mm-30) REVERT: B 47 TRP cc_start: 0.7803 (t-100) cc_final: 0.7548 (t-100) REVERT: o 20 GLN cc_start: 0.8515 (tt0) cc_final: 0.8187 (tm-30) REVERT: o 52 LYS cc_start: 0.9149 (ttpp) cc_final: 0.8721 (tmmt) REVERT: p 40 GLU cc_start: 0.8354 (tp30) cc_final: 0.7910 (tp30) REVERT: D 71 THR cc_start: 0.9437 (p) cc_final: 0.9109 (t) REVERT: D 272 ARG cc_start: 0.9022 (tpt170) cc_final: 0.8782 (tpm170) REVERT: D 275 GLN cc_start: 0.8779 (mm110) cc_final: 0.8523 (mm-40) REVERT: D 279 GLN cc_start: 0.8183 (mm-40) cc_final: 0.7971 (mm110) REVERT: D 283 MET cc_start: 0.8450 (tpp) cc_final: 0.7929 (mmt) REVERT: D 285 MET cc_start: 0.8217 (tpp) cc_final: 0.7908 (tpp) REVERT: m 37 ASN cc_start: 0.8086 (m110) cc_final: 0.7868 (m-40) REVERT: m 40 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7462 (mm-30) REVERT: m 47 ARG cc_start: 0.8364 (tpp-160) cc_final: 0.7369 (tpp-160) REVERT: n 13 LYS cc_start: 0.8400 (ptmm) cc_final: 0.7801 (pptt) REVERT: n 44 GLN cc_start: 0.8491 (tp-100) cc_final: 0.8181 (tp-100) REVERT: n 45 LEU cc_start: 0.7806 (mt) cc_final: 0.7389 (mt) REVERT: n 54 GLN cc_start: 0.7730 (tp-100) cc_final: 0.7430 (tp-100) REVERT: d 38 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6903 (mp0) REVERT: f 21 ILE cc_start: 0.7943 (mt) cc_final: 0.7573 (mm) outliers start: 50 outliers final: 28 residues processed: 506 average time/residue: 0.4205 time to fit residues: 292.0962 Evaluate side-chains 461 residues out of total 2050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 431 time to evaluate : 2.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 HIS 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 430 THR 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 384 GLU 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 36 LEU 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 291 ASN Chi-restraints excluded: chain n residue 43 VAL 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 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: 0.9980 chunk 64 optimal weight: 5.9990 chunk 172 optimal weight: 50.0000 chunk 140 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 207 optimal weight: 0.2980 chunk 224 optimal weight: 0.6980 chunk 184 optimal weight: 0.8980 chunk 205 optimal weight: 0.9990 chunk 70 optimal weight: 0.3980 chunk 166 optimal weight: 8.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS A 96 GLN C 38 ASN C 41 GLN c 44 GLN g 20 GLN b 61 GLN ** o 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 20 GLN ** n 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 20 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3739 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= 0.247 Angle : 0.592 7.429 25997 Z= 0.318 Chirality : 0.040 0.174 2942 Planarity : 0.005 0.056 3479 Dihedral : 4.701 46.255 2599 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.83 % Allowed : 12.49 % Favored : 84.68 % 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: 2.28 (0.17), residues: 2336 helix: 2.06 (0.12), residues: 1521 sheet: 0.56 (0.32), residues: 274 loop : 0.58 (0.28), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 47 HIS 0.003 0.001 HIS B 140 PHE 0.029 0.002 PHE D 296 TYR 0.020 0.002 TYR C 114 ARG 0.011 0.001 ARG n 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 506 residues out of total 2050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 448 time to evaluate : 1.951 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: C 164 ASP cc_start: 0.7218 (t0) cc_final: 0.6820 (t0) REVERT: C 419 LYS cc_start: 0.8531 (tppt) cc_final: 0.8109 (mmmm) REVERT: c 40 GLU cc_start: 0.6309 (tm-30) cc_final: 0.6104 (tm-30) REVERT: g 29 ASP cc_start: 0.8258 (p0) cc_final: 0.7949 (p0) REVERT: h 34 GLU cc_start: 0.7464 (tp30) cc_final: 0.7084 (tp30) REVERT: a 34 GLU cc_start: 0.7558 (tp30) cc_final: 0.7194 (tp30) REVERT: b 50 GLN cc_start: 0.7991 (tp-100) cc_final: 0.7783 (tp-100) REVERT: o 24 ARG cc_start: 0.8553 (ttm110) cc_final: 0.8057 (ttm110) REVERT: o 52 LYS cc_start: 0.9143 (ttpp) cc_final: 0.8704 (tmmt) REVERT: p 40 GLU cc_start: 0.8035 (tp30) cc_final: 0.7757 (tp30) REVERT: D 71 THR cc_start: 0.9437 (p) cc_final: 0.9089 (t) REVERT: D 92 ARG cc_start: 0.8834 (mtp85) cc_final: 0.8620 (mtp85) REVERT: D 272 ARG cc_start: 0.9021 (tpt170) cc_final: 0.8758 (tpt170) REVERT: m 24 ARG cc_start: 0.8656 (mmm-85) cc_final: 0.8321 (mmm160) REVERT: m 41 ARG cc_start: 0.8592 (ttp80) cc_final: 0.8308 (ttp80) REVERT: m 47 ARG cc_start: 0.8223 (tpp-160) cc_final: 0.7293 (tpp-160) REVERT: n 17 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8223 (mt-10) REVERT: n 44 GLN cc_start: 0.8515 (tp-100) cc_final: 0.8271 (tp-100) REVERT: d 38 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6771 (mp0) outliers start: 58 outliers final: 44 residues processed: 477 average time/residue: 0.4247 time to fit residues: 277.6796 Evaluate side-chains 456 residues out of total 2050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 411 time to evaluate : 2.297 ------------------------------------------------------------------------------- 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 103 GLN Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 158 HIS 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 140 HIS Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 326 MET Chi-restraints excluded: chain C residue 384 GLU 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 c residue 48 GLN Chi-restraints excluded: chain c residue 58 GLN 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 149 THR 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 n residue 53 LEU 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 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: 0.5980 chunk 107 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 139 optimal weight: 0.5980 chunk 208 optimal weight: 0.4980 chunk 220 optimal weight: 0.5980 chunk 108 optimal weight: 0.2980 chunk 197 optimal weight: 0.0670 chunk 59 optimal weight: 0.6980 overall best weight: 0.4118 ------------------------------------------------------------------------------- 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 C 67 ASN c 44 GLN g 20 GLN b 67 ASN ** p 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 GLN D 304 GLN m 37 ASN ** n 44 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: 0.7970 moved from start: 0.4139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19266 Z= 0.199 Angle : 0.559 7.796 25997 Z= 0.298 Chirality : 0.039 0.176 2942 Planarity : 0.004 0.060 3479 Dihedral : 4.409 39.748 2597 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.54 % Allowed : 14.20 % Favored : 83.27 % 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: 2.59 (0.17), residues: 2336 helix: 2.41 (0.13), residues: 1515 sheet: 0.53 (0.33), residues: 265 loop : 0.44 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 214 HIS 0.003 0.001 HIS A 76 PHE 0.012 0.001 PHE h 11 TYR 0.021 0.001 TYR C 114 ARG 0.008 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 495 residues out of total 2050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 443 time to evaluate : 2.517 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 272 ARG cc_start: 0.7562 (tpp80) cc_final: 0.6997 (mpp80) REVERT: C 164 ASP cc_start: 0.7071 (t0) cc_final: 0.6856 (t0) REVERT: C 419 LYS cc_start: 0.8551 (tppt) cc_final: 0.8102 (mmmm) REVERT: c 40 GLU cc_start: 0.6129 (tm-30) cc_final: 0.5881 (tm-30) REVERT: g 29 ASP cc_start: 0.8171 (p0) cc_final: 0.7921 (p0) REVERT: h 34 GLU cc_start: 0.7467 (tp30) cc_final: 0.6876 (tp30) REVERT: h 38 GLU cc_start: 0.7127 (mt-10) cc_final: 0.6349 (mt-10) REVERT: a 24 ARG cc_start: 0.8463 (tpp80) cc_final: 0.8190 (ttm110) REVERT: a 34 GLU cc_start: 0.7443 (tp30) cc_final: 0.7165 (tp30) REVERT: B 47 TRP cc_start: 0.7319 (t-100) cc_final: 0.7069 (m-90) REVERT: o 52 LYS cc_start: 0.9165 (ttpp) cc_final: 0.8731 (tmmt) REVERT: p 13 LYS cc_start: 0.8881 (tmmt) cc_final: 0.8519 (tmmt) REVERT: p 40 GLU cc_start: 0.7837 (tp30) cc_final: 0.7517 (tp30) REVERT: p 47 ARG cc_start: 0.8326 (tpp-160) cc_final: 0.8073 (tpp80) REVERT: D 71 THR cc_start: 0.9462 (p) cc_final: 0.9097 (t) REVERT: D 272 ARG cc_start: 0.9013 (tpt170) cc_final: 0.8737 (tpt170) REVERT: D 283 MET cc_start: 0.8628 (tpp) cc_final: 0.7865 (mmt) REVERT: m 24 ARG cc_start: 0.8635 (mmm-85) cc_final: 0.8384 (mmm160) REVERT: m 41 ARG cc_start: 0.8611 (ttp80) cc_final: 0.8175 (ttp80) REVERT: n 44 GLN cc_start: 0.8449 (tp-100) cc_final: 0.8199 (tp-100) REVERT: k 47 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7084 (ttp80) REVERT: l 17 GLU cc_start: 0.7881 (tp30) cc_final: 0.7666 (tp30) REVERT: d 38 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.6885 (mp0) REVERT: e 21 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8499 (tt) REVERT: e 26 GLU cc_start: 0.8555 (tt0) cc_final: 0.8228 (tt0) outliers start: 52 outliers final: 38 residues processed: 474 average time/residue: 0.4617 time to fit residues: 303.4672 Evaluate side-chains 449 residues out of total 2050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 408 time to evaluate : 2.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 HIS 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 335 LYS Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 413 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 326 MET 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 c residue 48 GLN Chi-restraints excluded: chain c residue 58 GLN 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 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 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 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 21 ILE Chi-restraints excluded: chain f residue 38 GLU Chi-restraints excluded: chain f residue 64 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 188 optimal weight: 0.5980 chunk 152 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 197 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 i 61 GLN c 44 GLN g 20 GLN ** p 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 275 GLN D 304 GLN m 50 GLN ** n 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 54 GLN e 44 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19266 Z= 0.272 Angle : 0.617 12.158 25997 Z= 0.326 Chirality : 0.041 0.172 2942 Planarity : 0.005 0.105 3479 Dihedral : 4.580 38.089 2597 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.37 % Allowed : 15.12 % Favored : 81.51 % 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: 2.39 (0.17), residues: 2336 helix: 2.24 (0.13), residues: 1514 sheet: 0.48 (0.32), residues: 273 loop : 0.41 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 214 HIS 0.005 0.001 HIS B 140 PHE 0.024 0.002 PHE C 226 TYR 0.020 0.002 TYR C 114 ARG 0.008 0.001 ARG h 24 *********************** 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 478 residues out of total 2050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 409 time to evaluate : 2.289 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: 0.7185 (t0) cc_final: 0.6966 (t0) REVERT: C 226 PHE cc_start: 0.7612 (m-80) cc_final: 0.7243 (m-80) REVERT: C 419 LYS cc_start: 0.8546 (tppt) cc_final: 0.8105 (mmmm) REVERT: i 30 LEU cc_start: 0.8235 (tp) cc_final: 0.7912 (tp) REVERT: c 40 GLU cc_start: 0.6290 (tm-30) cc_final: 0.6055 (tm-30) REVERT: g 29 ASP cc_start: 0.8229 (p0) cc_final: 0.7905 (p0) REVERT: h 34 GLU cc_start: 0.7653 (tp30) cc_final: 0.7313 (tp30) REVERT: a 34 GLU cc_start: 0.7504 (tp30) cc_final: 0.7197 (tp30) REVERT: b 38 GLU cc_start: 0.7506 (mm-30) cc_final: 0.7253 (mm-30) REVERT: B 47 TRP cc_start: 0.7317 (t-100) cc_final: 0.7030 (m-90) REVERT: o 52 LYS cc_start: 0.9148 (ttpp) cc_final: 0.8731 (tmmt) REVERT: p 40 GLU cc_start: 0.7763 (tp30) cc_final: 0.7502 (tp30) REVERT: D 71 THR cc_start: 0.9463 (p) cc_final: 0.9087 (t) REVERT: D 272 ARG cc_start: 0.9017 (tpt170) cc_final: 0.8802 (mmm160) REVERT: D 283 MET cc_start: 0.8658 (tpp) cc_final: 0.8077 (mmt) REVERT: D 305 GLN cc_start: 0.6880 (mm110) cc_final: 0.6566 (mm110) REVERT: m 24 ARG cc_start: 0.8709 (mmm-85) cc_final: 0.8413 (mmm160) REVERT: m 41 ARG cc_start: 0.8613 (ttp80) cc_final: 0.8289 (ttp80) REVERT: n 61 GLN cc_start: 0.8787 (tp-100) cc_final: 0.8533 (tp-100) REVERT: j 30 LEU cc_start: 0.8498 (mp) cc_final: 0.8282 (mt) REVERT: k 47 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7104 (ttp80) REVERT: l 19 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6843 (mt-10) REVERT: d 34 GLU cc_start: 0.7396 (mm-30) cc_final: 0.7140 (mm-30) REVERT: d 38 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6809 (mp0) REVERT: e 21 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8466 (tt) outliers start: 69 outliers final: 51 residues processed: 454 average time/residue: 0.3956 time to fit residues: 249.9670 Evaluate side-chains 453 residues out of total 2050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 398 time to evaluate : 2.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 HIS Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 116 GLN 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 437 TRP Chi-restraints excluded: chain C residue 41 GLN 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 167 LEU 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 30 LEU 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 60 VAL Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 36 ILE 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 60 VAL Chi-restraints excluded: chain k residue 65 SER Chi-restraints excluded: chain l residue 16 SER Chi-restraints excluded: chain l residue 19 GLU Chi-restraints excluded: chain l residue 45 LEU 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 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: 0.6980 chunk 43 optimal weight: 0.4980 chunk 129 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 220 optimal weight: 0.9990 chunk 183 optimal weight: 0.5980 chunk 102 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 115 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 44 GLN g 20 GLN b 50 GLN D 304 GLN ** D 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 48 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19266 Z= 0.245 Angle : 0.611 11.373 25997 Z= 0.323 Chirality : 0.040 0.172 2942 Planarity : 0.004 0.060 3479 Dihedral : 4.501 37.618 2597 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.41 % Allowed : 16.24 % Favored : 80.34 % 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: 2.42 (0.17), residues: 2336 helix: 2.28 (0.13), residues: 1514 sheet: 0.47 (0.32), residues: 273 loop : 0.36 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 47 HIS 0.005 0.001 HIS B 140 PHE 0.016 0.002 PHE C 226 TYR 0.019 0.002 TYR A 95 ARG 0.009 0.001 ARG f 41 *********************** 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 473 residues out of total 2050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 403 time to evaluate : 2.192 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: C 164 ASP cc_start: 0.7123 (t0) cc_final: 0.6912 (t0) REVERT: C 226 PHE cc_start: 0.7554 (m-80) cc_final: 0.7122 (m-80) REVERT: C 419 LYS cc_start: 0.8505 (tppt) cc_final: 0.8058 (mmmm) REVERT: C 424 LYS cc_start: 0.8777 (pptt) cc_final: 0.8550 (pptt) REVERT: c 40 GLU cc_start: 0.6293 (tm-30) cc_final: 0.6009 (tm-30) REVERT: g 29 ASP cc_start: 0.8191 (p0) cc_final: 0.7880 (p0) REVERT: a 24 ARG cc_start: 0.8713 (tpp80) cc_final: 0.8365 (ttm110) REVERT: a 34 GLU cc_start: 0.7446 (tp30) cc_final: 0.7133 (tp30) REVERT: B 47 TRP cc_start: 0.7469 (t-100) cc_final: 0.7138 (m-90) REVERT: B 179 ASP cc_start: 0.7669 (p0) cc_final: 0.7421 (p0) REVERT: o 40 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8318 (mm-30) REVERT: o 52 LYS cc_start: 0.9154 (ttpp) cc_final: 0.8737 (tmmt) REVERT: p 37 ASN cc_start: 0.8070 (p0) cc_final: 0.7422 (p0) REVERT: p 38 GLU cc_start: 0.7086 (tt0) cc_final: 0.6880 (pm20) REVERT: D 71 THR cc_start: 0.9451 (p) cc_final: 0.9065 (t) REVERT: D 283 MET cc_start: 0.8611 (tpp) cc_final: 0.8115 (mmt) REVERT: D 305 GLN cc_start: 0.6951 (mm110) cc_final: 0.6655 (mm110) REVERT: m 24 ARG cc_start: 0.8703 (mmm-85) cc_final: 0.8399 (mmm160) REVERT: m 41 ARG cc_start: 0.8631 (ttp80) cc_final: 0.8336 (ttp80) REVERT: n 47 ARG cc_start: 0.8838 (ttp80) cc_final: 0.8566 (ttm110) REVERT: n 61 GLN cc_start: 0.8773 (tp-100) cc_final: 0.8495 (tp-100) REVERT: j 17 GLU cc_start: 0.6920 (mm-30) cc_final: 0.6664 (mm-30) REVERT: k 47 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7130 (ttp80) REVERT: d 38 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.6898 (mp0) REVERT: e 21 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8495 (tt) REVERT: e 36 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8291 (tt) outliers start: 70 outliers final: 57 residues processed: 447 average time/residue: 0.3897 time to fit residues: 242.3293 Evaluate side-chains 456 residues out of total 2050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 395 time to evaluate : 2.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 HIS Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 158 HIS 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 82 VAL 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 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 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 30 LEU 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 p residue 15 LEU Chi-restraints excluded: chain p residue 21 ILE 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 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 30 LEU 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 60 VAL Chi-restraints excluded: chain k residue 65 SER Chi-restraints excluded: chain l residue 16 SER Chi-restraints excluded: chain l residue 45 LEU 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 36 LEU Chi-restraints excluded: chain e residue 64 LEU Chi-restraints excluded: chain f residue 37 ASN Chi-restraints excluded: chain f residue 38 GLU Chi-restraints excluded: chain f residue 44 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 0.9980 chunk 24 optimal weight: 0.4980 chunk 125 optimal weight: 0.8980 chunk 161 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 185 optimal weight: 0.5980 chunk 123 optimal weight: 0.6980 chunk 219 optimal weight: 0.7980 chunk 137 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 101 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 C 217 ASN c 44 GLN g 20 GLN D 304 GLN 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: 0.8007 moved from start: 0.4414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 19266 Z= 0.251 Angle : 0.632 11.579 25997 Z= 0.333 Chirality : 0.040 0.209 2942 Planarity : 0.005 0.079 3479 Dihedral : 4.510 35.007 2597 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.66 % Allowed : 17.22 % Favored : 79.12 % 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: 2.39 (0.17), residues: 2336 helix: 2.28 (0.13), residues: 1515 sheet: 0.47 (0.32), residues: 273 loop : 0.29 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 47 HIS 0.005 0.001 HIS B 140 PHE 0.015 0.001 PHE A 39 TYR 0.019 0.001 TYR A 95 ARG 0.013 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 474 residues out of total 2050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 399 time to evaluate : 2.454 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: 0.7217 (t0) cc_final: 0.6977 (t0) REVERT: C 170 ILE cc_start: 0.8570 (mm) cc_final: 0.8360 (mm) REVERT: C 419 LYS cc_start: 0.8527 (tppt) cc_final: 0.8081 (mmmm) REVERT: C 424 LYS cc_start: 0.8791 (pptt) cc_final: 0.8585 (pptt) REVERT: i 58 GLN cc_start: 0.8588 (tp40) cc_final: 0.8370 (tp40) REVERT: c 40 GLU cc_start: 0.6257 (tm-30) cc_final: 0.6018 (tm-30) REVERT: g 29 ASP cc_start: 0.8211 (p0) cc_final: 0.7900 (p0) REVERT: a 24 ARG cc_start: 0.8708 (tpp80) cc_final: 0.8386 (ttm110) REVERT: a 34 GLU cc_start: 0.7441 (tp30) cc_final: 0.7131 (tp30) REVERT: b 38 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7164 (mm-30) REVERT: B 47 TRP cc_start: 0.7534 (t-100) cc_final: 0.7188 (m-90) REVERT: B 179 ASP cc_start: 0.7661 (p0) cc_final: 0.7451 (p0) REVERT: o 52 LYS cc_start: 0.9165 (ttpp) cc_final: 0.8744 (tmmt) REVERT: o 63 LEU cc_start: 0.5937 (OUTLIER) cc_final: 0.5526 (mp) REVERT: p 26 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7378 (mt-10) REVERT: p 37 ASN cc_start: 0.8228 (p0) cc_final: 0.7425 (p0) REVERT: p 38 GLU cc_start: 0.7082 (tt0) cc_final: 0.6643 (pm20) REVERT: D 71 THR cc_start: 0.9446 (p) cc_final: 0.9048 (t) REVERT: D 283 MET cc_start: 0.8555 (tpp) cc_final: 0.8108 (mmt) REVERT: D 305 GLN cc_start: 0.6906 (mm110) cc_final: 0.6606 (mm110) REVERT: m 24 ARG cc_start: 0.8714 (mmm-85) cc_final: 0.8405 (mmm160) REVERT: m 41 ARG cc_start: 0.8643 (ttp80) cc_final: 0.8331 (ttp80) REVERT: n 61 GLN cc_start: 0.8778 (tp-100) cc_final: 0.8519 (tp-100) REVERT: k 47 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7135 (ttp80) REVERT: l 19 GLU cc_start: 0.7087 (mt-10) cc_final: 0.6830 (mt-10) REVERT: d 38 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.6969 (mp0) REVERT: e 21 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8476 (tt) REVERT: e 36 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8267 (tt) outliers start: 75 outliers final: 63 residues processed: 453 average time/residue: 0.3969 time to fit residues: 250.1504 Evaluate side-chains 456 residues out of total 2050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 388 time to evaluate : 1.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 HIS 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 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 437 TRP Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 82 VAL 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 167 LEU 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 382 THR 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 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 67 ASN 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 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 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 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 30 LEU 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 60 VAL Chi-restraints excluded: chain k residue 65 SER Chi-restraints excluded: chain l residue 16 SER Chi-restraints excluded: chain l residue 45 LEU 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 36 LEU Chi-restraints excluded: chain e residue 64 LEU 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.5235 > 50: distance: 29 - 33: 8.902 distance: 33 - 34: 26.633 distance: 34 - 35: 5.031 distance: 35 - 36: 5.079 distance: 35 - 37: 23.429 distance: 37 - 38: 17.996 distance: 38 - 39: 12.560 distance: 38 - 41: 15.858 distance: 39 - 40: 22.429 distance: 39 - 45: 34.086 distance: 41 - 42: 15.342 distance: 42 - 43: 5.706 distance: 42 - 44: 11.020 distance: 45 - 46: 19.970 distance: 46 - 47: 17.733 distance: 46 - 49: 7.143 distance: 47 - 48: 25.268 distance: 47 - 53: 11.742 distance: 49 - 50: 25.471 distance: 50 - 51: 17.167 distance: 50 - 52: 28.295 distance: 53 - 54: 9.572 distance: 53 - 59: 13.387 distance: 54 - 55: 3.295 distance: 54 - 57: 17.574 distance: 55 - 56: 32.495 distance: 55 - 60: 16.869 distance: 56 - 86: 28.220 distance: 57 - 58: 9.395 distance: 58 - 59: 15.345 distance: 60 - 61: 7.601 distance: 61 - 62: 7.639 distance: 61 - 64: 7.955 distance: 62 - 63: 17.060 distance: 62 - 68: 19.016 distance: 63 - 91: 31.820 distance: 64 - 65: 17.871 distance: 65 - 66: 9.481 distance: 65 - 67: 7.172 distance: 68 - 69: 4.463 distance: 69 - 70: 7.560 distance: 69 - 72: 7.084 distance: 70 - 71: 9.561 distance: 70 - 77: 5.154 distance: 71 - 99: 22.115 distance: 72 - 73: 12.770 distance: 73 - 74: 8.932 distance: 74 - 75: 3.720 distance: 74 - 76: 9.498 distance: 77 - 78: 4.270 distance: 78 - 79: 9.549 distance: 78 - 81: 3.956 distance: 79 - 80: 9.049 distance: 79 - 86: 3.632 distance: 80 - 107: 6.968 distance: 81 - 82: 6.418 distance: 82 - 83: 5.457 distance: 83 - 84: 3.189 distance: 83 - 85: 5.715 distance: 86 - 87: 6.700 distance: 87 - 88: 11.322 distance: 87 - 90: 5.035 distance: 88 - 89: 10.577 distance: 88 - 91: 8.403 distance: 89 - 116: 11.259 distance: 91 - 92: 9.611 distance: 92 - 93: 3.127 distance: 92 - 95: 11.599 distance: 93 - 94: 11.655 distance: 93 - 99: 9.071 distance: 94 - 123: 18.082 distance: 95 - 96: 11.532 distance: 96 - 97: 16.949 distance: 96 - 98: 4.937 distance: 99 - 100: 3.330 distance: 100 - 101: 12.972 distance: 100 - 103: 16.865 distance: 101 - 102: 10.596 distance: 101 - 107: 10.727 distance: 102 - 129: 25.322 distance: 103 - 104: 21.310 distance: 104 - 105: 7.002 distance: 104 - 106: 5.046