Starting phenix.real_space_refine on Tue Aug 26 20:25:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pvg_17965/08_2025/8pvg_17965.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pvg_17965/08_2025/8pvg_17965.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8pvg_17965/08_2025/8pvg_17965.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pvg_17965/08_2025/8pvg_17965.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8pvg_17965/08_2025/8pvg_17965.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pvg_17965/08_2025/8pvg_17965.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 252 5.16 5 C 25752 2.51 5 N 6960 2.21 5 O 7764 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 252 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40728 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3394 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} Chain breaks: 1 Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L Time building chain proxies: 4.92, per 1000 atoms: 0.12 Number of scatterers: 40728 At special positions: 0 Unit cell: (151.434, 159.894, 115.902, 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 252 16.00 O 7764 8.00 N 6960 7.00 C 25752 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.45 Conformation dependent library (CDL) restraints added in 1.9 seconds Enol-peptide restraints added in 953.7 nanoseconds 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9720 Finding SS restraints... Secondary structure from input PDB file: 204 helices and 36 sheets defined 42.1% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 2 through 14 removed outlier: 3.714A pdb=" N VAL A 6 " --> pdb=" O SER A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 42 through 47 Processing helix chain 'A' and resid 72 through 75 removed outlier: 3.589A pdb=" N ALA A 75 " --> pdb=" O ALA A 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 72 through 75' Processing helix chain 'A' and resid 104 through 120 removed outlier: 3.514A pdb=" N GLY A 120 " --> pdb=" O LEU A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 203 Processing helix chain 'A' and resid 229 through 250 Processing helix chain 'A' and resid 287 through 291 Processing helix chain 'A' and resid 292 through 305 Processing helix chain 'A' and resid 305 through 314 removed outlier: 3.904A pdb=" N LEU A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 321 Processing helix chain 'A' and resid 367 through 385 Processing helix chain 'A' and resid 414 through 425 Processing helix chain 'A' and resid 426 through 431 Processing helix chain 'A' and resid 432 through 434 No H-bonds generated for 'chain 'A' and resid 432 through 434' Processing helix chain 'A' and resid 436 through 456 removed outlier: 3.968A pdb=" N GLU A 450 " --> pdb=" O LEU A 446 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG A 453 " --> pdb=" O GLU A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 467 Processing helix chain 'B' and resid 2 through 14 removed outlier: 3.714A pdb=" N VAL B 6 " --> pdb=" O SER B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 39 No H-bonds generated for 'chain 'B' and resid 37 through 39' Processing helix chain 'B' and resid 42 through 47 Processing helix chain 'B' and resid 72 through 75 removed outlier: 3.589A pdb=" N ALA B 75 " --> pdb=" O ALA B 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 72 through 75' Processing helix chain 'B' and resid 104 through 120 removed outlier: 3.515A pdb=" N GLY B 120 " --> pdb=" O LEU B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 203 Processing helix chain 'B' and resid 229 through 250 Processing helix chain 'B' and resid 287 through 291 Processing helix chain 'B' and resid 292 through 305 Processing helix chain 'B' and resid 305 through 314 removed outlier: 3.903A pdb=" N LEU B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 321 Processing helix chain 'B' and resid 367 through 385 Processing helix chain 'B' and resid 414 through 425 Processing helix chain 'B' and resid 426 through 431 Processing helix chain 'B' and resid 432 through 434 No H-bonds generated for 'chain 'B' and resid 432 through 434' Processing helix chain 'B' and resid 436 through 456 removed outlier: 3.968A pdb=" N GLU B 450 " --> pdb=" O LEU B 446 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG B 453 " --> pdb=" O GLU B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 467 Processing helix chain 'C' and resid 2 through 14 removed outlier: 3.714A pdb=" N VAL C 6 " --> pdb=" O SER C 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 42 through 47 Processing helix chain 'C' and resid 72 through 75 removed outlier: 3.588A pdb=" N ALA C 75 " --> pdb=" O ALA C 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 72 through 75' Processing helix chain 'C' and resid 104 through 120 removed outlier: 3.515A pdb=" N GLY C 120 " --> pdb=" O LEU C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 203 Processing helix chain 'C' and resid 229 through 250 Processing helix chain 'C' and resid 287 through 291 Processing helix chain 'C' and resid 292 through 305 Processing helix chain 'C' and resid 305 through 314 removed outlier: 3.903A pdb=" N LEU C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 321 Processing helix chain 'C' and resid 367 through 385 Processing helix chain 'C' and resid 414 through 425 Processing helix chain 'C' and resid 426 through 431 Processing helix chain 'C' and resid 432 through 434 No H-bonds generated for 'chain 'C' and resid 432 through 434' Processing helix chain 'C' and resid 436 through 456 removed outlier: 3.968A pdb=" N GLU C 450 " --> pdb=" O LEU C 446 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG C 453 " --> pdb=" O GLU C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 467 Processing helix chain 'D' and resid 2 through 14 removed outlier: 3.714A pdb=" N VAL D 6 " --> pdb=" O SER D 2 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 42 through 47 Processing helix chain 'D' and resid 72 through 75 removed outlier: 3.589A pdb=" N ALA D 75 " --> pdb=" O ALA D 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 72 through 75' Processing helix chain 'D' and resid 104 through 120 removed outlier: 3.514A pdb=" N GLY D 120 " --> pdb=" O LEU D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 203 Processing helix chain 'D' and resid 229 through 250 Processing helix chain 'D' and resid 287 through 291 Processing helix chain 'D' and resid 292 through 305 Processing helix chain 'D' and resid 305 through 314 removed outlier: 3.904A pdb=" N LEU D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 321 Processing helix chain 'D' and resid 367 through 385 Processing helix chain 'D' and resid 414 through 425 Processing helix chain 'D' and resid 426 through 431 Processing helix chain 'D' and resid 432 through 434 No H-bonds generated for 'chain 'D' and resid 432 through 434' Processing helix chain 'D' and resid 436 through 456 removed outlier: 3.968A pdb=" N GLU D 450 " --> pdb=" O LEU D 446 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG D 453 " --> pdb=" O GLU D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 467 Processing helix chain 'E' and resid 2 through 14 removed outlier: 3.714A pdb=" N VAL E 6 " --> pdb=" O SER E 2 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 39 No H-bonds generated for 'chain 'E' and resid 37 through 39' Processing helix chain 'E' and resid 42 through 47 Processing helix chain 'E' and resid 72 through 75 removed outlier: 3.589A pdb=" N ALA E 75 " --> pdb=" O ALA E 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 72 through 75' Processing helix chain 'E' and resid 104 through 120 removed outlier: 3.515A pdb=" N GLY E 120 " --> pdb=" O LEU E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 203 Processing helix chain 'E' and resid 229 through 250 Processing helix chain 'E' and resid 287 through 291 Processing helix chain 'E' and resid 292 through 305 Processing helix chain 'E' and resid 305 through 314 removed outlier: 3.903A pdb=" N LEU E 312 " --> pdb=" O ALA E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 321 Processing helix chain 'E' and resid 367 through 385 Processing helix chain 'E' and resid 414 through 425 Processing helix chain 'E' and resid 426 through 431 Processing helix chain 'E' and resid 432 through 434 No H-bonds generated for 'chain 'E' and resid 432 through 434' Processing helix chain 'E' and resid 436 through 456 removed outlier: 3.968A pdb=" N GLU E 450 " --> pdb=" O LEU E 446 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG E 453 " --> pdb=" O GLU E 449 " (cutoff:3.500A) Processing helix chain 'E' and resid 459 through 467 Processing helix chain 'F' and resid 2 through 14 removed outlier: 3.714A pdb=" N VAL F 6 " --> pdb=" O SER F 2 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 39 No H-bonds generated for 'chain 'F' and resid 37 through 39' Processing helix chain 'F' and resid 42 through 47 Processing helix chain 'F' and resid 72 through 75 removed outlier: 3.588A pdb=" N ALA F 75 " --> pdb=" O ALA F 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 72 through 75' Processing helix chain 'F' and resid 104 through 120 removed outlier: 3.515A pdb=" N GLY F 120 " --> pdb=" O LEU F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 203 Processing helix chain 'F' and resid 229 through 250 Processing helix chain 'F' and resid 287 through 291 Processing helix chain 'F' and resid 292 through 305 Processing helix chain 'F' and resid 305 through 314 removed outlier: 3.903A pdb=" N LEU F 312 " --> pdb=" O ALA F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 321 Processing helix chain 'F' and resid 367 through 385 Processing helix chain 'F' and resid 414 through 425 Processing helix chain 'F' and resid 426 through 431 Processing helix chain 'F' and resid 432 through 434 No H-bonds generated for 'chain 'F' and resid 432 through 434' Processing helix chain 'F' and resid 436 through 456 removed outlier: 3.968A pdb=" N GLU F 450 " --> pdb=" O LEU F 446 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG F 453 " --> pdb=" O GLU F 449 " (cutoff:3.500A) Processing helix chain 'F' and resid 459 through 467 Processing helix chain 'G' and resid 2 through 14 removed outlier: 3.714A pdb=" N VAL G 6 " --> pdb=" O SER G 2 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 39 No H-bonds generated for 'chain 'G' and resid 37 through 39' Processing helix chain 'G' and resid 42 through 47 Processing helix chain 'G' and resid 72 through 75 removed outlier: 3.589A pdb=" N ALA G 75 " --> pdb=" O ALA G 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 72 through 75' Processing helix chain 'G' and resid 104 through 120 removed outlier: 3.514A pdb=" N GLY G 120 " --> pdb=" O LEU G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 203 Processing helix chain 'G' and resid 229 through 250 Processing helix chain 'G' and resid 287 through 291 Processing helix chain 'G' and resid 292 through 305 Processing helix chain 'G' and resid 305 through 314 removed outlier: 3.904A pdb=" N LEU G 312 " --> pdb=" O ALA G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 317 through 321 Processing helix chain 'G' and resid 367 through 385 Processing helix chain 'G' and resid 414 through 425 Processing helix chain 'G' and resid 426 through 431 Processing helix chain 'G' and resid 432 through 434 No H-bonds generated for 'chain 'G' and resid 432 through 434' Processing helix chain 'G' and resid 436 through 456 removed outlier: 3.968A pdb=" N GLU G 450 " --> pdb=" O LEU G 446 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG G 453 " --> pdb=" O GLU G 449 " (cutoff:3.500A) Processing helix chain 'G' and resid 459 through 467 Processing helix chain 'H' and resid 2 through 14 removed outlier: 3.714A pdb=" N VAL H 6 " --> pdb=" O SER H 2 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 39 No H-bonds generated for 'chain 'H' and resid 37 through 39' Processing helix chain 'H' and resid 42 through 47 Processing helix chain 'H' and resid 72 through 75 removed outlier: 3.589A pdb=" N ALA H 75 " --> pdb=" O ALA H 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 72 through 75' Processing helix chain 'H' and resid 104 through 120 removed outlier: 3.515A pdb=" N GLY H 120 " --> pdb=" O LEU H 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 190 through 203 Processing helix chain 'H' and resid 229 through 250 Processing helix chain 'H' and resid 287 through 291 Processing helix chain 'H' and resid 292 through 305 Processing helix chain 'H' and resid 305 through 314 removed outlier: 3.903A pdb=" N LEU H 312 " --> pdb=" O ALA H 308 " (cutoff:3.500A) Processing helix chain 'H' and resid 317 through 321 Processing helix chain 'H' and resid 367 through 385 Processing helix chain 'H' and resid 414 through 425 Processing helix chain 'H' and resid 426 through 431 Processing helix chain 'H' and resid 432 through 434 No H-bonds generated for 'chain 'H' and resid 432 through 434' Processing helix chain 'H' and resid 436 through 456 removed outlier: 3.968A pdb=" N GLU H 450 " --> pdb=" O LEU H 446 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG H 453 " --> pdb=" O GLU H 449 " (cutoff:3.500A) Processing helix chain 'H' and resid 459 through 467 Processing helix chain 'I' and resid 2 through 14 removed outlier: 3.714A pdb=" N VAL I 6 " --> pdb=" O SER I 2 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 39 No H-bonds generated for 'chain 'I' and resid 37 through 39' Processing helix chain 'I' and resid 42 through 47 Processing helix chain 'I' and resid 72 through 75 removed outlier: 3.588A pdb=" N ALA I 75 " --> pdb=" O ALA I 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 72 through 75' Processing helix chain 'I' and resid 104 through 120 removed outlier: 3.515A pdb=" N GLY I 120 " --> pdb=" O LEU I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 190 through 203 Processing helix chain 'I' and resid 229 through 250 Processing helix chain 'I' and resid 287 through 291 Processing helix chain 'I' and resid 292 through 305 Processing helix chain 'I' and resid 305 through 314 removed outlier: 3.903A pdb=" N LEU I 312 " --> pdb=" O ALA I 308 " (cutoff:3.500A) Processing helix chain 'I' and resid 317 through 321 Processing helix chain 'I' and resid 367 through 385 Processing helix chain 'I' and resid 414 through 425 Processing helix chain 'I' and resid 426 through 431 Processing helix chain 'I' and resid 432 through 434 No H-bonds generated for 'chain 'I' and resid 432 through 434' Processing helix chain 'I' and resid 436 through 456 removed outlier: 3.968A pdb=" N GLU I 450 " --> pdb=" O LEU I 446 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG I 453 " --> pdb=" O GLU I 449 " (cutoff:3.500A) Processing helix chain 'I' and resid 459 through 467 Processing helix chain 'J' and resid 2 through 14 removed outlier: 3.714A pdb=" N VAL J 6 " --> pdb=" O SER J 2 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 39 No H-bonds generated for 'chain 'J' and resid 37 through 39' Processing helix chain 'J' and resid 42 through 47 Processing helix chain 'J' and resid 72 through 75 removed outlier: 3.589A pdb=" N ALA J 75 " --> pdb=" O ALA J 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 72 through 75' Processing helix chain 'J' and resid 104 through 120 removed outlier: 3.514A pdb=" N GLY J 120 " --> pdb=" O LEU J 116 " (cutoff:3.500A) Processing helix chain 'J' and resid 190 through 203 Processing helix chain 'J' and resid 229 through 250 Processing helix chain 'J' and resid 287 through 291 Processing helix chain 'J' and resid 292 through 305 Processing helix chain 'J' and resid 305 through 314 removed outlier: 3.904A pdb=" N LEU J 312 " --> pdb=" O ALA J 308 " (cutoff:3.500A) Processing helix chain 'J' and resid 317 through 321 Processing helix chain 'J' and resid 367 through 385 Processing helix chain 'J' and resid 414 through 425 Processing helix chain 'J' and resid 426 through 431 Processing helix chain 'J' and resid 432 through 434 No H-bonds generated for 'chain 'J' and resid 432 through 434' Processing helix chain 'J' and resid 436 through 456 removed outlier: 3.968A pdb=" N GLU J 450 " --> pdb=" O LEU J 446 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG J 453 " --> pdb=" O GLU J 449 " (cutoff:3.500A) Processing helix chain 'J' and resid 459 through 467 Processing helix chain 'K' and resid 2 through 14 removed outlier: 3.714A pdb=" N VAL K 6 " --> pdb=" O SER K 2 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 39 No H-bonds generated for 'chain 'K' and resid 37 through 39' Processing helix chain 'K' and resid 42 through 47 Processing helix chain 'K' and resid 72 through 75 removed outlier: 3.588A pdb=" N ALA K 75 " --> pdb=" O ALA K 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 72 through 75' Processing helix chain 'K' and resid 104 through 120 removed outlier: 3.515A pdb=" N GLY K 120 " --> pdb=" O LEU K 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 190 through 203 Processing helix chain 'K' and resid 229 through 250 Processing helix chain 'K' and resid 287 through 291 Processing helix chain 'K' and resid 292 through 305 Processing helix chain 'K' and resid 305 through 314 removed outlier: 3.903A pdb=" N LEU K 312 " --> pdb=" O ALA K 308 " (cutoff:3.500A) Processing helix chain 'K' and resid 317 through 321 Processing helix chain 'K' and resid 367 through 385 Processing helix chain 'K' and resid 414 through 425 Processing helix chain 'K' and resid 426 through 431 Processing helix chain 'K' and resid 432 through 434 No H-bonds generated for 'chain 'K' and resid 432 through 434' Processing helix chain 'K' and resid 436 through 456 removed outlier: 3.968A pdb=" N GLU K 450 " --> pdb=" O LEU K 446 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG K 453 " --> pdb=" O GLU K 449 " (cutoff:3.500A) Processing helix chain 'K' and resid 459 through 467 Processing helix chain 'L' and resid 2 through 14 removed outlier: 3.714A pdb=" N VAL L 6 " --> pdb=" O SER L 2 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 39 No H-bonds generated for 'chain 'L' and resid 37 through 39' Processing helix chain 'L' and resid 42 through 47 Processing helix chain 'L' and resid 72 through 75 removed outlier: 3.589A pdb=" N ALA L 75 " --> pdb=" O ALA L 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 72 through 75' Processing helix chain 'L' and resid 104 through 120 removed outlier: 3.515A pdb=" N GLY L 120 " --> pdb=" O LEU L 116 " (cutoff:3.500A) Processing helix chain 'L' and resid 190 through 203 Processing helix chain 'L' and resid 229 through 250 Processing helix chain 'L' and resid 287 through 291 Processing helix chain 'L' and resid 292 through 305 Processing helix chain 'L' and resid 305 through 314 removed outlier: 3.903A pdb=" N LEU L 312 " --> pdb=" O ALA L 308 " (cutoff:3.500A) Processing helix chain 'L' and resid 317 through 321 Processing helix chain 'L' and resid 367 through 385 Processing helix chain 'L' and resid 414 through 425 Processing helix chain 'L' and resid 426 through 431 Processing helix chain 'L' and resid 432 through 434 No H-bonds generated for 'chain 'L' and resid 432 through 434' Processing helix chain 'L' and resid 436 through 456 removed outlier: 3.968A pdb=" N GLU L 450 " --> pdb=" O LEU L 446 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG L 453 " --> pdb=" O GLU L 449 " (cutoff:3.500A) Processing helix chain 'L' and resid 459 through 467 Processing sheet with id=1, first strand: chain 'A' and resid 17 through 23 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 29 through 35 current: chain 'A' and resid 66 through 70 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 66 through 70 current: chain 'A' and resid 85 through 93 Processing sheet with id=2, first strand: chain 'A' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 124 through 136 current: chain 'A' and resid 219 through 224 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 219 through 224 current: chain 'A' and resid 280 through 281 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 280 through 281 current: chain 'A' and resid 342 through 345 Processing sheet with id=3, first strand: chain 'A' and resid 138 through 144 removed outlier: 3.766A pdb=" N GLY A 147 " --> pdb=" O SER A 144 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'B' and resid 17 through 23 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 29 through 35 current: chain 'B' and resid 66 through 70 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 66 through 70 current: chain 'B' and resid 85 through 93 Processing sheet with id=5, first strand: chain 'B' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 124 through 136 current: chain 'B' and resid 219 through 224 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 219 through 224 current: chain 'B' and resid 280 through 281 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 280 through 281 current: chain 'B' and resid 342 through 345 Processing sheet with id=6, first strand: chain 'B' and resid 138 through 144 removed outlier: 3.766A pdb=" N GLY B 147 " --> pdb=" O SER B 144 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'C' and resid 17 through 23 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 29 through 35 current: chain 'C' and resid 66 through 70 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 66 through 70 current: chain 'C' and resid 85 through 93 Processing sheet with id=8, first strand: chain 'C' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 124 through 136 current: chain 'C' and resid 219 through 224 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 219 through 224 current: chain 'C' and resid 280 through 281 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 280 through 281 current: chain 'C' and resid 342 through 345 Processing sheet with id=9, first strand: chain 'C' and resid 138 through 144 removed outlier: 3.766A pdb=" N GLY C 147 " --> pdb=" O SER C 144 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'D' and resid 17 through 23 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 29 through 35 current: chain 'D' and resid 66 through 70 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 66 through 70 current: chain 'D' and resid 85 through 93 Processing sheet with id=11, first strand: chain 'D' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 124 through 136 current: chain 'D' and resid 219 through 224 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 219 through 224 current: chain 'D' and resid 280 through 281 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 280 through 281 current: chain 'D' and resid 342 through 345 Processing sheet with id=12, first strand: chain 'D' and resid 138 through 144 removed outlier: 3.766A pdb=" N GLY D 147 " --> pdb=" O SER D 144 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'E' and resid 17 through 23 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 29 through 35 current: chain 'E' and resid 66 through 70 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 66 through 70 current: chain 'E' and resid 85 through 93 Processing sheet with id=14, first strand: chain 'E' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 124 through 136 current: chain 'E' and resid 219 through 224 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 219 through 224 current: chain 'E' and resid 280 through 281 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 280 through 281 current: chain 'E' and resid 342 through 345 Processing sheet with id=15, first strand: chain 'E' and resid 138 through 144 removed outlier: 3.766A pdb=" N GLY E 147 " --> pdb=" O SER E 144 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'F' and resid 17 through 23 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 29 through 35 current: chain 'F' and resid 66 through 70 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 66 through 70 current: chain 'F' and resid 85 through 93 Processing sheet with id=17, first strand: chain 'F' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 124 through 136 current: chain 'F' and resid 219 through 224 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 219 through 224 current: chain 'F' and resid 280 through 281 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 280 through 281 current: chain 'F' and resid 342 through 345 Processing sheet with id=18, first strand: chain 'F' and resid 138 through 144 removed outlier: 3.766A pdb=" N GLY F 147 " --> pdb=" O SER F 144 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'G' and resid 17 through 23 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 29 through 35 current: chain 'G' and resid 66 through 70 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 66 through 70 current: chain 'G' and resid 85 through 93 Processing sheet with id=20, first strand: chain 'G' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 124 through 136 current: chain 'G' and resid 219 through 224 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 219 through 224 current: chain 'G' and resid 280 through 281 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 280 through 281 current: chain 'G' and resid 342 through 345 Processing sheet with id=21, first strand: chain 'G' and resid 138 through 144 removed outlier: 3.766A pdb=" N GLY G 147 " --> pdb=" O SER G 144 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'H' and resid 17 through 23 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 29 through 35 current: chain 'H' and resid 66 through 70 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 66 through 70 current: chain 'H' and resid 85 through 93 Processing sheet with id=23, first strand: chain 'H' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 124 through 136 current: chain 'H' and resid 219 through 224 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 219 through 224 current: chain 'H' and resid 280 through 281 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 280 through 281 current: chain 'H' and resid 342 through 345 Processing sheet with id=24, first strand: chain 'H' and resid 138 through 144 removed outlier: 3.766A pdb=" N GLY H 147 " --> pdb=" O SER H 144 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'I' and resid 17 through 23 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 29 through 35 current: chain 'I' and resid 66 through 70 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 66 through 70 current: chain 'I' and resid 85 through 93 Processing sheet with id=26, first strand: chain 'I' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 124 through 136 current: chain 'I' and resid 219 through 224 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 219 through 224 current: chain 'I' and resid 280 through 281 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 280 through 281 current: chain 'I' and resid 342 through 345 Processing sheet with id=27, first strand: chain 'I' and resid 138 through 144 removed outlier: 3.766A pdb=" N GLY I 147 " --> pdb=" O SER I 144 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'J' and resid 17 through 23 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 29 through 35 current: chain 'J' and resid 66 through 70 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 66 through 70 current: chain 'J' and resid 85 through 93 Processing sheet with id=29, first strand: chain 'J' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 124 through 136 current: chain 'J' and resid 219 through 224 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 219 through 224 current: chain 'J' and resid 280 through 281 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 280 through 281 current: chain 'J' and resid 342 through 345 Processing sheet with id=30, first strand: chain 'J' and resid 138 through 144 removed outlier: 3.766A pdb=" N GLY J 147 " --> pdb=" O SER J 144 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'K' and resid 17 through 23 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 29 through 35 current: chain 'K' and resid 66 through 70 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 66 through 70 current: chain 'K' and resid 85 through 93 Processing sheet with id=32, first strand: chain 'K' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 124 through 136 current: chain 'K' and resid 219 through 224 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 219 through 224 current: chain 'K' and resid 280 through 281 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 280 through 281 current: chain 'K' and resid 342 through 345 Processing sheet with id=33, first strand: chain 'K' and resid 138 through 144 removed outlier: 3.766A pdb=" N GLY K 147 " --> pdb=" O SER K 144 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'L' and resid 17 through 23 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 29 through 35 current: chain 'L' and resid 66 through 70 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 66 through 70 current: chain 'L' and resid 85 through 93 Processing sheet with id=35, first strand: chain 'L' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 124 through 136 current: chain 'L' and resid 219 through 224 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 219 through 224 current: chain 'L' and resid 280 through 281 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 280 through 281 current: chain 'L' and resid 342 through 345 Processing sheet with id=36, first strand: chain 'L' and resid 138 through 144 removed outlier: 3.766A pdb=" N GLY L 147 " --> pdb=" O SER L 144 " (cutoff:3.500A) 1548 hydrogen bonds defined for protein. 4464 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: 9.16 Time building geometry restraints manager: 4.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8984 1.34 - 1.46: 13432 1.46 - 1.58: 18756 1.58 - 1.71: 0 1.71 - 1.83: 456 Bond restraints: 41628 Sorted by residual: bond pdb=" C ILE I 408 " pdb=" N PRO I 409 " ideal model delta sigma weight residual 1.332 1.371 -0.040 1.30e-02 5.92e+03 9.26e+00 bond pdb=" C ILE C 408 " pdb=" N PRO C 409 " ideal model delta sigma weight residual 1.332 1.371 -0.040 1.30e-02 5.92e+03 9.26e+00 bond pdb=" C ILE A 408 " pdb=" N PRO A 409 " ideal model delta sigma weight residual 1.332 1.371 -0.040 1.30e-02 5.92e+03 9.24e+00 bond pdb=" C ILE J 408 " pdb=" N PRO J 409 " ideal model delta sigma weight residual 1.332 1.371 -0.040 1.30e-02 5.92e+03 9.24e+00 bond pdb=" C ILE G 408 " pdb=" N PRO G 409 " ideal model delta sigma weight residual 1.332 1.371 -0.040 1.30e-02 5.92e+03 9.24e+00 ... (remaining 41623 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 43782 1.72 - 3.43: 10622 3.43 - 5.15: 1544 5.15 - 6.87: 248 6.87 - 8.58: 108 Bond angle restraints: 56304 Sorted by residual: angle pdb=" CA PHE F 398 " pdb=" CB PHE F 398 " pdb=" CG PHE F 398 " ideal model delta sigma weight residual 113.80 121.44 -7.64 1.00e+00 1.00e+00 5.84e+01 angle pdb=" CA PHE K 398 " pdb=" CB PHE K 398 " pdb=" CG PHE K 398 " ideal model delta sigma weight residual 113.80 121.44 -7.64 1.00e+00 1.00e+00 5.84e+01 angle pdb=" CA PHE I 398 " pdb=" CB PHE I 398 " pdb=" CG PHE I 398 " ideal model delta sigma weight residual 113.80 121.44 -7.64 1.00e+00 1.00e+00 5.84e+01 angle pdb=" CA PHE C 398 " pdb=" CB PHE C 398 " pdb=" CG PHE C 398 " ideal model delta sigma weight residual 113.80 121.44 -7.64 1.00e+00 1.00e+00 5.84e+01 angle pdb=" CA PHE H 398 " pdb=" CB PHE H 398 " pdb=" CG PHE H 398 " ideal model delta sigma weight residual 113.80 121.41 -7.61 1.00e+00 1.00e+00 5.79e+01 ... (remaining 56299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.66: 22668 16.66 - 33.33: 1920 33.33 - 49.99: 444 49.99 - 66.66: 96 66.66 - 83.32: 36 Dihedral angle restraints: 25164 sinusoidal: 10080 harmonic: 15084 Sorted by residual: dihedral pdb=" CA SER F 64 " pdb=" C SER F 64 " pdb=" N ASP F 65 " pdb=" CA ASP F 65 " ideal model delta harmonic sigma weight residual -180.00 -152.44 -27.56 0 5.00e+00 4.00e-02 3.04e+01 dihedral pdb=" CA SER C 64 " pdb=" C SER C 64 " pdb=" N ASP C 65 " pdb=" CA ASP C 65 " ideal model delta harmonic sigma weight residual 180.00 -152.44 -27.56 0 5.00e+00 4.00e-02 3.04e+01 dihedral pdb=" CA SER I 64 " pdb=" C SER I 64 " pdb=" N ASP I 65 " pdb=" CA ASP I 65 " ideal model delta harmonic sigma weight residual 180.00 -152.44 -27.56 0 5.00e+00 4.00e-02 3.04e+01 ... (remaining 25161 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 3160 0.048 - 0.095: 1604 0.095 - 0.143: 968 0.143 - 0.190: 328 0.190 - 0.238: 72 Chirality restraints: 6132 Sorted by residual: chirality pdb=" CA HIS F 210 " pdb=" N HIS F 210 " pdb=" C HIS F 210 " pdb=" CB HIS F 210 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA HIS I 210 " pdb=" N HIS I 210 " pdb=" C HIS I 210 " pdb=" CB HIS I 210 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA HIS C 210 " pdb=" N HIS C 210 " pdb=" C HIS C 210 " pdb=" CB HIS C 210 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 6129 not shown) Planarity restraints: 7452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE G 398 " 0.038 2.00e-02 2.50e+03 2.48e-02 1.08e+01 pdb=" CG PHE G 398 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE G 398 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE G 398 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE G 398 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 PHE G 398 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE G 398 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE J 398 " 0.038 2.00e-02 2.50e+03 2.48e-02 1.08e+01 pdb=" CG PHE J 398 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE J 398 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE J 398 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE J 398 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 PHE J 398 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE J 398 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 398 " -0.038 2.00e-02 2.50e+03 2.48e-02 1.08e+01 pdb=" CG PHE D 398 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE D 398 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE D 398 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE D 398 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 PHE D 398 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE D 398 " -0.019 2.00e-02 2.50e+03 ... (remaining 7449 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 1140 2.70 - 3.25: 38776 3.25 - 3.80: 63084 3.80 - 4.35: 92496 4.35 - 4.90: 148930 Nonbonded interactions: 344426 Sorted by model distance: nonbonded pdb=" O LEU I 282 " pdb=" OG SER I 292 " model vdw 2.147 3.040 nonbonded pdb=" O LEU C 282 " pdb=" OG SER C 292 " model vdw 2.147 3.040 nonbonded pdb=" O LEU F 282 " pdb=" OG SER F 292 " model vdw 2.147 3.040 nonbonded pdb=" O LEU K 282 " pdb=" OG SER K 292 " model vdw 2.147 3.040 nonbonded pdb=" O LEU J 282 " pdb=" OG SER J 292 " model vdw 2.148 3.040 ... (remaining 344421 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: 0.15 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.710 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 33.350 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.100 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:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 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 : 0.009 0.043 41628 Z= 0.588 Angle : 1.543 8.585 56304 Z= 1.023 Chirality : 0.076 0.238 6132 Planarity : 0.007 0.047 7452 Dihedral : 14.003 83.322 15444 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.10 % Allowed : 4.14 % Favored : 94.75 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.11), residues: 5172 helix: 0.02 (0.11), residues: 1944 sheet: -0.47 (0.15), residues: 1140 loop : -1.22 (0.13), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.006 ARG J 193 TYR 0.022 0.006 TYR C 101 PHE 0.038 0.006 PHE B 398 TRP 0.013 0.006 TRP I 58 HIS 0.028 0.005 HIS J 210 Details of bonding type rmsd covalent geometry : bond 0.00916 (41628) covalent geometry : angle 1.54314 (56304) hydrogen bonds : bond 0.16188 ( 1548) hydrogen bonds : angle 6.88151 ( 4464) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1100 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 1052 time to evaluate : 1.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 9 MET cc_start: 0.9255 (ttm) cc_final: 0.9005 (ttm) REVERT: A 14 GLU cc_start: 0.8512 (tp30) cc_final: 0.7734 (tm-30) REVERT: A 19 ASP cc_start: 0.8368 (t70) cc_final: 0.7832 (t0) REVERT: A 28 LYS cc_start: 0.8073 (tptm) cc_final: 0.7859 (ttpp) REVERT: A 30 GLN cc_start: 0.8025 (mm-40) cc_final: 0.7340 (mp10) REVERT: A 38 GLN cc_start: 0.8659 (mm110) cc_final: 0.8374 (mm110) REVERT: A 69 MET cc_start: 0.8601 (tpp) cc_final: 0.8100 (mmm) REVERT: A 94 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8204 (mp0) REVERT: A 208 GLU cc_start: 0.7981 (pt0) cc_final: 0.7702 (mt-10) REVERT: A 216 THR cc_start: 0.8643 (m) cc_final: 0.8325 (p) REVERT: A 229 MET cc_start: 0.8964 (ttm) cc_final: 0.8636 (ttm) REVERT: A 353 LYS cc_start: 0.9514 (mttt) cc_final: 0.9288 (tppt) REVERT: A 393 MET cc_start: 0.8904 (mmt) cc_final: 0.8678 (mmm) REVERT: A 437 ASP cc_start: 0.8320 (m-30) cc_final: 0.8097 (m-30) REVERT: B 14 GLU cc_start: 0.8495 (tp30) cc_final: 0.7838 (tm-30) REVERT: B 19 ASP cc_start: 0.8202 (t70) cc_final: 0.7878 (t0) REVERT: B 30 GLN cc_start: 0.7955 (mm-40) cc_final: 0.7335 (mp10) REVERT: B 38 GLN cc_start: 0.8578 (mm110) cc_final: 0.8277 (mm110) REVERT: B 69 MET cc_start: 0.8562 (tpp) cc_final: 0.8056 (tpt) REVERT: B 94 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8051 (mp0) REVERT: B 99 GLN cc_start: 0.8477 (mm-40) cc_final: 0.8145 (tt0) REVERT: B 137 ASP cc_start: 0.8665 (t0) cc_final: 0.8458 (m-30) REVERT: B 208 GLU cc_start: 0.7953 (pt0) cc_final: 0.7388 (mt-10) REVERT: B 216 THR cc_start: 0.8605 (m) cc_final: 0.8165 (p) REVERT: B 353 LYS cc_start: 0.9517 (mttt) cc_final: 0.9307 (tppt) REVERT: B 437 ASP cc_start: 0.8385 (m-30) cc_final: 0.8174 (m-30) REVERT: C 14 GLU cc_start: 0.8480 (tp30) cc_final: 0.7775 (tm-30) REVERT: C 28 LYS cc_start: 0.8139 (tptm) cc_final: 0.7936 (ttpp) REVERT: C 30 GLN cc_start: 0.7988 (mm-40) cc_final: 0.7252 (mp10) REVERT: C 38 GLN cc_start: 0.8533 (mm110) cc_final: 0.8275 (mm110) REVERT: C 69 MET cc_start: 0.8644 (tpp) cc_final: 0.8157 (tpt) REVERT: C 94 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8152 (mp0) REVERT: C 137 ASP cc_start: 0.8651 (t0) cc_final: 0.8424 (m-30) REVERT: C 208 GLU cc_start: 0.7995 (pt0) cc_final: 0.7567 (mt-10) REVERT: C 216 THR cc_start: 0.8604 (m) cc_final: 0.8240 (p) REVERT: C 353 LYS cc_start: 0.9533 (mttt) cc_final: 0.9285 (tppt) REVERT: C 393 MET cc_start: 0.8921 (mmt) cc_final: 0.8704 (mmm) REVERT: D 9 MET cc_start: 0.9255 (ttm) cc_final: 0.9006 (ttm) REVERT: D 14 GLU cc_start: 0.8510 (tp30) cc_final: 0.7733 (tm-30) REVERT: D 19 ASP cc_start: 0.8367 (t70) cc_final: 0.7830 (t0) REVERT: D 28 LYS cc_start: 0.8070 (tptm) cc_final: 0.7860 (ttpp) REVERT: D 30 GLN cc_start: 0.8023 (mm-40) cc_final: 0.7340 (mp10) REVERT: D 38 GLN cc_start: 0.8659 (mm110) cc_final: 0.8373 (mm110) REVERT: D 69 MET cc_start: 0.8598 (tpp) cc_final: 0.8097 (mmm) REVERT: D 94 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8203 (mp0) REVERT: D 208 GLU cc_start: 0.7982 (pt0) cc_final: 0.7701 (mt-10) REVERT: D 216 THR cc_start: 0.8646 (m) cc_final: 0.8329 (p) REVERT: D 229 MET cc_start: 0.8967 (ttm) cc_final: 0.8639 (ttm) REVERT: D 353 LYS cc_start: 0.9515 (mttt) cc_final: 0.9291 (tppt) REVERT: D 393 MET cc_start: 0.8901 (mmt) cc_final: 0.8677 (mmm) REVERT: D 437 ASP cc_start: 0.8326 (m-30) cc_final: 0.8102 (m-30) REVERT: E 14 GLU cc_start: 0.8496 (tp30) cc_final: 0.7839 (tm-30) REVERT: E 19 ASP cc_start: 0.8204 (t70) cc_final: 0.7876 (t0) REVERT: E 30 GLN cc_start: 0.7953 (mm-40) cc_final: 0.7330 (mp10) REVERT: E 38 GLN cc_start: 0.8575 (mm110) cc_final: 0.8273 (mm110) REVERT: E 69 MET cc_start: 0.8561 (tpp) cc_final: 0.8053 (tpt) REVERT: E 94 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8049 (mp0) REVERT: E 99 GLN cc_start: 0.8477 (mm-40) cc_final: 0.8147 (tt0) REVERT: E 137 ASP cc_start: 0.8662 (t0) cc_final: 0.8458 (m-30) REVERT: E 208 GLU cc_start: 0.7950 (pt0) cc_final: 0.7386 (mt-10) REVERT: E 216 THR cc_start: 0.8607 (m) cc_final: 0.8164 (p) REVERT: E 353 LYS cc_start: 0.9516 (mttt) cc_final: 0.9306 (tppt) REVERT: E 437 ASP cc_start: 0.8383 (m-30) cc_final: 0.8172 (m-30) REVERT: F 14 GLU cc_start: 0.8481 (tp30) cc_final: 0.7775 (tm-30) REVERT: F 28 LYS cc_start: 0.8141 (tptm) cc_final: 0.7939 (ttpp) REVERT: F 30 GLN cc_start: 0.7989 (mm-40) cc_final: 0.7254 (mp10) REVERT: F 38 GLN cc_start: 0.8534 (mm110) cc_final: 0.8276 (mm110) REVERT: F 69 MET cc_start: 0.8642 (tpp) cc_final: 0.8154 (tpt) REVERT: F 94 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8153 (mp0) REVERT: F 137 ASP cc_start: 0.8653 (t0) cc_final: 0.8425 (m-30) REVERT: F 208 GLU cc_start: 0.7998 (pt0) cc_final: 0.7569 (mt-10) REVERT: F 216 THR cc_start: 0.8600 (m) cc_final: 0.8236 (p) REVERT: F 353 LYS cc_start: 0.9533 (mttt) cc_final: 0.9286 (tppt) REVERT: F 393 MET cc_start: 0.8923 (mmt) cc_final: 0.8705 (mmm) REVERT: G 9 MET cc_start: 0.9254 (ttm) cc_final: 0.9005 (ttm) REVERT: G 14 GLU cc_start: 0.8510 (tp30) cc_final: 0.7733 (tm-30) REVERT: G 19 ASP cc_start: 0.8371 (t70) cc_final: 0.7830 (t0) REVERT: G 28 LYS cc_start: 0.8071 (tptm) cc_final: 0.7859 (ttpp) REVERT: G 30 GLN cc_start: 0.8025 (mm-40) cc_final: 0.7337 (mp10) REVERT: G 38 GLN cc_start: 0.8656 (mm110) cc_final: 0.8371 (mm110) REVERT: G 69 MET cc_start: 0.8595 (tpp) cc_final: 0.8096 (mmm) REVERT: G 94 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8203 (mp0) REVERT: G 208 GLU cc_start: 0.7983 (pt0) cc_final: 0.7701 (mt-10) REVERT: G 216 THR cc_start: 0.8646 (m) cc_final: 0.8327 (p) REVERT: G 229 MET cc_start: 0.8962 (ttm) cc_final: 0.8633 (ttm) REVERT: G 353 LYS cc_start: 0.9515 (mttt) cc_final: 0.9290 (tppt) REVERT: G 393 MET cc_start: 0.8902 (mmt) cc_final: 0.8678 (mmm) REVERT: G 437 ASP cc_start: 0.8321 (m-30) cc_final: 0.8099 (m-30) REVERT: H 14 GLU cc_start: 0.8496 (tp30) cc_final: 0.7839 (tm-30) REVERT: H 19 ASP cc_start: 0.8203 (t70) cc_final: 0.7881 (t0) REVERT: H 30 GLN cc_start: 0.7953 (mm-40) cc_final: 0.7333 (mp10) REVERT: H 38 GLN cc_start: 0.8575 (mm110) cc_final: 0.8275 (mm110) REVERT: H 69 MET cc_start: 0.8565 (tpp) cc_final: 0.8056 (tpt) REVERT: H 94 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8050 (mp0) REVERT: H 99 GLN cc_start: 0.8475 (mm-40) cc_final: 0.8146 (tt0) REVERT: H 137 ASP cc_start: 0.8666 (t0) cc_final: 0.8456 (m-30) REVERT: H 208 GLU cc_start: 0.7947 (pt0) cc_final: 0.7383 (mt-10) REVERT: H 216 THR cc_start: 0.8608 (m) cc_final: 0.8167 (p) REVERT: H 353 LYS cc_start: 0.9516 (mttt) cc_final: 0.9308 (tppt) REVERT: H 437 ASP cc_start: 0.8382 (m-30) cc_final: 0.8173 (m-30) REVERT: I 14 GLU cc_start: 0.8481 (tp30) cc_final: 0.7776 (tm-30) REVERT: I 28 LYS cc_start: 0.8143 (tptm) cc_final: 0.7942 (ttpp) REVERT: I 30 GLN cc_start: 0.7991 (mm-40) cc_final: 0.7254 (mp10) REVERT: I 38 GLN cc_start: 0.8532 (mm110) cc_final: 0.8274 (mm110) REVERT: I 69 MET cc_start: 0.8642 (tpp) cc_final: 0.8155 (tpt) REVERT: I 94 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8154 (mp0) REVERT: I 137 ASP cc_start: 0.8652 (t0) cc_final: 0.8425 (m-30) REVERT: I 208 GLU cc_start: 0.7997 (pt0) cc_final: 0.7566 (mt-10) REVERT: I 216 THR cc_start: 0.8604 (m) cc_final: 0.8240 (p) REVERT: I 353 LYS cc_start: 0.9532 (mttt) cc_final: 0.9287 (tppt) REVERT: I 393 MET cc_start: 0.8923 (mmt) cc_final: 0.8705 (mmm) REVERT: J 9 MET cc_start: 0.9255 (ttm) cc_final: 0.9005 (ttm) REVERT: J 14 GLU cc_start: 0.8511 (tp30) cc_final: 0.7733 (tm-30) REVERT: J 19 ASP cc_start: 0.8367 (t70) cc_final: 0.7831 (t0) REVERT: J 28 LYS cc_start: 0.8072 (tptm) cc_final: 0.7861 (ttpp) REVERT: J 30 GLN cc_start: 0.8022 (mm-40) cc_final: 0.7340 (mp10) REVERT: J 38 GLN cc_start: 0.8661 (mm110) cc_final: 0.8376 (mm110) REVERT: J 69 MET cc_start: 0.8595 (tpp) cc_final: 0.8095 (mmm) REVERT: J 94 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8204 (mp0) REVERT: J 208 GLU cc_start: 0.7984 (pt0) cc_final: 0.7707 (mt-10) REVERT: J 216 THR cc_start: 0.8648 (m) cc_final: 0.8331 (p) REVERT: J 229 MET cc_start: 0.8963 (ttm) cc_final: 0.8636 (ttm) REVERT: J 353 LYS cc_start: 0.9515 (mttt) cc_final: 0.9290 (tppt) REVERT: J 393 MET cc_start: 0.8903 (mmt) cc_final: 0.8679 (mmm) REVERT: J 437 ASP cc_start: 0.8321 (m-30) cc_final: 0.8099 (m-30) REVERT: K 14 GLU cc_start: 0.8480 (tp30) cc_final: 0.7774 (tm-30) REVERT: K 30 GLN cc_start: 0.7985 (mm-40) cc_final: 0.7252 (mp10) REVERT: K 38 GLN cc_start: 0.8533 (mm110) cc_final: 0.8275 (mm110) REVERT: K 69 MET cc_start: 0.8642 (tpp) cc_final: 0.8154 (tpt) REVERT: K 94 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8152 (mp0) REVERT: K 137 ASP cc_start: 0.8651 (t0) cc_final: 0.8425 (m-30) REVERT: K 208 GLU cc_start: 0.7997 (pt0) cc_final: 0.7568 (mt-10) REVERT: K 216 THR cc_start: 0.8601 (m) cc_final: 0.8237 (p) REVERT: K 353 LYS cc_start: 0.9534 (mttt) cc_final: 0.9288 (tppt) REVERT: K 393 MET cc_start: 0.8923 (mmt) cc_final: 0.8704 (mmm) REVERT: L 14 GLU cc_start: 0.8495 (tp30) cc_final: 0.7838 (tm-30) REVERT: L 19 ASP cc_start: 0.8197 (t70) cc_final: 0.7874 (t0) REVERT: L 30 GLN cc_start: 0.7946 (mm-40) cc_final: 0.7328 (mp10) REVERT: L 38 GLN cc_start: 0.8576 (mm110) cc_final: 0.8275 (mm110) REVERT: L 69 MET cc_start: 0.8563 (tpp) cc_final: 0.8052 (tpt) REVERT: L 94 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8049 (mp0) REVERT: L 99 GLN cc_start: 0.8474 (mm-40) cc_final: 0.8146 (tt0) REVERT: L 137 ASP cc_start: 0.8662 (t0) cc_final: 0.8456 (m-30) REVERT: L 208 GLU cc_start: 0.7948 (pt0) cc_final: 0.7384 (mt-10) REVERT: L 216 THR cc_start: 0.8602 (m) cc_final: 0.8163 (p) REVERT: L 353 LYS cc_start: 0.9517 (mttt) cc_final: 0.9307 (tppt) REVERT: L 437 ASP cc_start: 0.8382 (m-30) cc_final: 0.8172 (m-30) outliers start: 48 outliers final: 16 residues processed: 1088 average time/residue: 0.2733 time to fit residues: 478.3563 Evaluate side-chains 697 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 681 time to evaluate : 1.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 HIS Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 210 HIS Chi-restraints excluded: chain D residue 210 HIS Chi-restraints excluded: chain E residue 210 HIS Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 210 HIS Chi-restraints excluded: chain G residue 210 HIS Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain I residue 55 ILE Chi-restraints excluded: chain I residue 210 HIS Chi-restraints excluded: chain J residue 210 HIS Chi-restraints excluded: chain K residue 55 ILE Chi-restraints excluded: chain K residue 210 HIS Chi-restraints excluded: chain L residue 210 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 394 optimal weight: 0.9980 chunk 430 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 265 optimal weight: 0.9990 chunk 497 optimal weight: 2.9990 chunk 414 optimal weight: 0.7980 chunk 310 optimal weight: 2.9990 chunk 488 optimal weight: 0.9990 chunk 366 optimal weight: 0.6980 chunk 223 optimal weight: 0.9990 chunk 142 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN B 30 GLN B 278 ASN D 278 ASN E 30 GLN E 278 ASN G 278 ASN H 30 GLN H 278 ASN J 278 ASN K 30 GLN L 30 GLN L 278 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.097260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.075396 restraints weight = 86404.861| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 3.33 r_work: 0.3011 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 41628 Z= 0.126 Angle : 0.600 9.549 56304 Z= 0.308 Chirality : 0.044 0.133 6132 Planarity : 0.005 0.048 7452 Dihedral : 5.178 26.012 5660 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.13 % Allowed : 8.03 % Favored : 90.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.12), residues: 5172 helix: 2.00 (0.12), residues: 1788 sheet: -0.19 (0.15), residues: 1236 loop : -0.77 (0.13), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 249 TYR 0.016 0.002 TYR C 239 PHE 0.044 0.002 PHE C 398 TRP 0.002 0.000 TRP E 58 HIS 0.006 0.001 HIS B 210 Details of bonding type rmsd covalent geometry : bond 0.00284 (41628) covalent geometry : angle 0.59986 (56304) hydrogen bonds : bond 0.03624 ( 1548) hydrogen bonds : angle 4.77425 ( 4464) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 786 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 737 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLN cc_start: 0.8642 (mm-40) cc_final: 0.8309 (mp10) REVERT: A 208 GLU cc_start: 0.8427 (pt0) cc_final: 0.8143 (tm-30) REVERT: A 437 ASP cc_start: 0.8692 (m-30) cc_final: 0.8067 (m-30) REVERT: A 441 ASP cc_start: 0.8838 (m-30) cc_final: 0.8473 (m-30) REVERT: B 208 GLU cc_start: 0.8376 (pt0) cc_final: 0.7907 (tm-30) REVERT: B 437 ASP cc_start: 0.8722 (m-30) cc_final: 0.8012 (m-30) REVERT: B 441 ASP cc_start: 0.8715 (m-30) cc_final: 0.8354 (m-30) REVERT: C 14 GLU cc_start: 0.8603 (tp30) cc_final: 0.8322 (tm-30) REVERT: C 30 GLN cc_start: 0.8576 (mm-40) cc_final: 0.8220 (mp10) REVERT: C 208 GLU cc_start: 0.8407 (pt0) cc_final: 0.8133 (tm-30) REVERT: C 216 THR cc_start: 0.8967 (m) cc_final: 0.8764 (p) REVERT: C 441 ASP cc_start: 0.8763 (m-30) cc_final: 0.8318 (m-30) REVERT: D 30 GLN cc_start: 0.8603 (mm-40) cc_final: 0.8280 (mp10) REVERT: D 208 GLU cc_start: 0.8425 (pt0) cc_final: 0.8150 (tm-30) REVERT: D 437 ASP cc_start: 0.8705 (m-30) cc_final: 0.8068 (m-30) REVERT: D 441 ASP cc_start: 0.8850 (m-30) cc_final: 0.8489 (m-30) REVERT: E 208 GLU cc_start: 0.8356 (pt0) cc_final: 0.7900 (tm-30) REVERT: E 437 ASP cc_start: 0.8732 (m-30) cc_final: 0.8029 (m-30) REVERT: E 441 ASP cc_start: 0.8713 (m-30) cc_final: 0.8357 (m-30) REVERT: F 14 GLU cc_start: 0.8597 (tp30) cc_final: 0.8315 (tm-30) REVERT: F 30 GLN cc_start: 0.8582 (mm-40) cc_final: 0.8222 (mp10) REVERT: F 208 GLU cc_start: 0.8409 (pt0) cc_final: 0.8133 (tm-30) REVERT: F 441 ASP cc_start: 0.8755 (m-30) cc_final: 0.8310 (m-30) REVERT: G 30 GLN cc_start: 0.8620 (mm-40) cc_final: 0.8292 (mp10) REVERT: G 208 GLU cc_start: 0.8422 (pt0) cc_final: 0.8144 (tm-30) REVERT: G 437 ASP cc_start: 0.8703 (m-30) cc_final: 0.8079 (m-30) REVERT: G 441 ASP cc_start: 0.8845 (m-30) cc_final: 0.8483 (m-30) REVERT: H 208 GLU cc_start: 0.8366 (pt0) cc_final: 0.7903 (tm-30) REVERT: H 437 ASP cc_start: 0.8725 (m-30) cc_final: 0.8017 (m-30) REVERT: H 441 ASP cc_start: 0.8703 (m-30) cc_final: 0.8338 (m-30) REVERT: I 14 GLU cc_start: 0.8599 (tp30) cc_final: 0.8318 (tm-30) REVERT: I 30 GLN cc_start: 0.8591 (mm-40) cc_final: 0.8237 (mp10) REVERT: I 208 GLU cc_start: 0.8376 (pt0) cc_final: 0.8119 (tm-30) REVERT: I 216 THR cc_start: 0.8963 (m) cc_final: 0.8763 (p) REVERT: I 441 ASP cc_start: 0.8771 (m-30) cc_final: 0.8325 (m-30) REVERT: I 462 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8600 (mt-10) REVERT: J 30 GLN cc_start: 0.8640 (mm-40) cc_final: 0.8307 (mp10) REVERT: J 208 GLU cc_start: 0.8428 (pt0) cc_final: 0.8148 (tm-30) REVERT: J 437 ASP cc_start: 0.8682 (m-30) cc_final: 0.8047 (m-30) REVERT: J 441 ASP cc_start: 0.8841 (m-30) cc_final: 0.8480 (m-30) REVERT: K 14 GLU cc_start: 0.8607 (tp30) cc_final: 0.8324 (tm-30) REVERT: K 28 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8520 (mtpp) REVERT: K 30 GLN cc_start: 0.8504 (mm110) cc_final: 0.8177 (mp10) REVERT: K 208 GLU cc_start: 0.8404 (pt0) cc_final: 0.8127 (tm-30) REVERT: K 441 ASP cc_start: 0.8763 (m-30) cc_final: 0.8315 (m-30) REVERT: K 462 GLU cc_start: 0.8842 (mt-10) cc_final: 0.8614 (mt-10) REVERT: L 208 GLU cc_start: 0.8383 (pt0) cc_final: 0.7902 (tm-30) REVERT: L 216 THR cc_start: 0.8974 (m) cc_final: 0.8774 (p) REVERT: L 437 ASP cc_start: 0.8721 (m-30) cc_final: 0.8014 (m-30) REVERT: L 441 ASP cc_start: 0.8716 (m-30) cc_final: 0.8364 (m-30) outliers start: 49 outliers final: 24 residues processed: 778 average time/residue: 0.2232 time to fit residues: 289.0595 Evaluate side-chains 582 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 557 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 278 ASN Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 140 ARG Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 278 ASN Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 140 ARG Chi-restraints excluded: chain H residue 205 LEU Chi-restraints excluded: chain H residue 278 ASN Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain K residue 28 LYS Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 140 ARG Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain L residue 278 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 427 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 196 optimal weight: 0.0980 chunk 301 optimal weight: 10.0000 chunk 198 optimal weight: 0.8980 chunk 350 optimal weight: 10.0000 chunk 153 optimal weight: 1.9990 chunk 148 optimal weight: 7.9990 chunk 348 optimal weight: 0.7980 chunk 472 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 219 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.095758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.073483 restraints weight = 86680.908| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 3.32 r_work: 0.2984 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 41628 Z= 0.120 Angle : 0.578 8.773 56304 Z= 0.290 Chirality : 0.042 0.135 6132 Planarity : 0.005 0.052 7452 Dihedral : 4.382 18.353 5628 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.36 % Allowed : 11.99 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.12), residues: 5172 helix: 2.49 (0.12), residues: 1788 sheet: -0.13 (0.14), residues: 1260 loop : -0.67 (0.14), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 338 TYR 0.019 0.001 TYR B 239 PHE 0.027 0.001 PHE C 398 TRP 0.003 0.000 TRP F 58 HIS 0.004 0.000 HIS K 210 Details of bonding type rmsd covalent geometry : bond 0.00275 (41628) covalent geometry : angle 0.57818 (56304) hydrogen bonds : bond 0.03252 ( 1548) hydrogen bonds : angle 4.31130 ( 4464) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 647 time to evaluate : 1.590 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: A 30 GLN cc_start: 0.8564 (mm-40) cc_final: 0.8284 (mp10) REVERT: A 208 GLU cc_start: 0.8357 (pt0) cc_final: 0.7943 (tm-30) REVERT: A 421 GLU cc_start: 0.8881 (mm-30) cc_final: 0.8492 (mm-30) REVERT: A 437 ASP cc_start: 0.8689 (m-30) cc_final: 0.8120 (m-30) REVERT: A 441 ASP cc_start: 0.8785 (m-30) cc_final: 0.8344 (m-30) REVERT: B 4 GLU cc_start: 0.8201 (mp0) cc_final: 0.7795 (tp30) REVERT: B 5 HIS cc_start: 0.8638 (m-70) cc_final: 0.8305 (t-90) REVERT: B 208 GLU cc_start: 0.8325 (pt0) cc_final: 0.7684 (tm-30) REVERT: B 332 MET cc_start: 0.8711 (mmt) cc_final: 0.8401 (mmt) REVERT: C 5 HIS cc_start: 0.8583 (m-70) cc_final: 0.8350 (t-90) REVERT: C 30 GLN cc_start: 0.8534 (mm-40) cc_final: 0.8207 (mp10) REVERT: C 69 MET cc_start: 0.8801 (tpt) cc_final: 0.8484 (tpt) REVERT: C 203 MET cc_start: 0.9202 (mmm) cc_final: 0.8945 (mmm) REVERT: C 208 GLU cc_start: 0.8399 (pt0) cc_final: 0.8067 (tm-30) REVERT: C 216 THR cc_start: 0.8963 (m) cc_final: 0.8725 (p) REVERT: C 421 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8594 (mm-30) REVERT: C 441 ASP cc_start: 0.8771 (m-30) cc_final: 0.8313 (m-30) REVERT: D 30 GLN cc_start: 0.8534 (mm-40) cc_final: 0.8255 (mp10) REVERT: D 208 GLU cc_start: 0.8338 (pt0) cc_final: 0.7945 (tm-30) REVERT: D 421 GLU cc_start: 0.8894 (mm-30) cc_final: 0.8510 (mm-30) REVERT: D 437 ASP cc_start: 0.8688 (m-30) cc_final: 0.8116 (m-30) REVERT: D 441 ASP cc_start: 0.8768 (m-30) cc_final: 0.8277 (m-30) REVERT: E 4 GLU cc_start: 0.8207 (mp0) cc_final: 0.7796 (tp30) REVERT: E 5 HIS cc_start: 0.8616 (m-70) cc_final: 0.8298 (t-90) REVERT: E 208 GLU cc_start: 0.8382 (pt0) cc_final: 0.7752 (tm-30) REVERT: E 332 MET cc_start: 0.8709 (mmt) cc_final: 0.8395 (mmt) REVERT: F 5 HIS cc_start: 0.8557 (m-70) cc_final: 0.8338 (t-90) REVERT: F 30 GLN cc_start: 0.8553 (mm-40) cc_final: 0.8226 (mp10) REVERT: F 69 MET cc_start: 0.8782 (tpt) cc_final: 0.8466 (tpt) REVERT: F 203 MET cc_start: 0.9198 (mmm) cc_final: 0.8944 (mmm) REVERT: F 208 GLU cc_start: 0.8395 (pt0) cc_final: 0.8051 (tm-30) REVERT: F 421 GLU cc_start: 0.8815 (mm-30) cc_final: 0.8601 (mm-30) REVERT: F 441 ASP cc_start: 0.8753 (m-30) cc_final: 0.8298 (m-30) REVERT: G 30 GLN cc_start: 0.8548 (mm-40) cc_final: 0.8260 (mp10) REVERT: G 208 GLU cc_start: 0.8324 (pt0) cc_final: 0.7941 (tm-30) REVERT: G 421 GLU cc_start: 0.8908 (mm-30) cc_final: 0.8518 (mm-30) REVERT: G 437 ASP cc_start: 0.8681 (m-30) cc_final: 0.8125 (m-30) REVERT: G 441 ASP cc_start: 0.8782 (m-30) cc_final: 0.8342 (m-30) REVERT: H 4 GLU cc_start: 0.8193 (mp0) cc_final: 0.7790 (tp30) REVERT: H 5 HIS cc_start: 0.8640 (m-70) cc_final: 0.8300 (t-90) REVERT: H 30 GLN cc_start: 0.8509 (mp10) cc_final: 0.8309 (mp10) REVERT: H 208 GLU cc_start: 0.8349 (pt0) cc_final: 0.7736 (tm-30) REVERT: H 332 MET cc_start: 0.8706 (mmt) cc_final: 0.8391 (mmt) REVERT: I 5 HIS cc_start: 0.8554 (m-70) cc_final: 0.8299 (t-90) REVERT: I 30 GLN cc_start: 0.8539 (mm-40) cc_final: 0.8215 (mp10) REVERT: I 69 MET cc_start: 0.8823 (tpt) cc_final: 0.8509 (tpt) REVERT: I 203 MET cc_start: 0.9199 (mmm) cc_final: 0.8942 (mmm) REVERT: I 208 GLU cc_start: 0.8402 (pt0) cc_final: 0.8071 (tm-30) REVERT: I 216 THR cc_start: 0.8962 (m) cc_final: 0.8729 (p) REVERT: I 421 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8600 (mm-30) REVERT: I 441 ASP cc_start: 0.8782 (m-30) cc_final: 0.8323 (m-30) REVERT: J 30 GLN cc_start: 0.8566 (mm-40) cc_final: 0.8278 (mp10) REVERT: J 208 GLU cc_start: 0.8334 (pt0) cc_final: 0.7945 (tm-30) REVERT: J 421 GLU cc_start: 0.8908 (mm-30) cc_final: 0.8520 (mm-30) REVERT: J 437 ASP cc_start: 0.8694 (m-30) cc_final: 0.8121 (m-30) REVERT: J 441 ASP cc_start: 0.8751 (m-30) cc_final: 0.8256 (m-30) REVERT: K 5 HIS cc_start: 0.8550 (m-70) cc_final: 0.8305 (t-90) REVERT: K 28 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8476 (mtpp) REVERT: K 30 GLN cc_start: 0.8380 (mm110) cc_final: 0.8176 (mp10) REVERT: K 69 MET cc_start: 0.8816 (tpt) cc_final: 0.8504 (tpt) REVERT: K 203 MET cc_start: 0.9198 (mmm) cc_final: 0.8941 (mmm) REVERT: K 208 GLU cc_start: 0.8387 (pt0) cc_final: 0.8049 (tm-30) REVERT: K 421 GLU cc_start: 0.8804 (mm-30) cc_final: 0.8591 (mm-30) REVERT: K 441 ASP cc_start: 0.8765 (m-30) cc_final: 0.8302 (m-30) REVERT: L 4 GLU cc_start: 0.8206 (mp0) cc_final: 0.7798 (tp30) REVERT: L 5 HIS cc_start: 0.8638 (m-70) cc_final: 0.8303 (t-90) REVERT: L 30 GLN cc_start: 0.8489 (mp10) cc_final: 0.8284 (mp10) REVERT: L 208 GLU cc_start: 0.8366 (pt0) cc_final: 0.7747 (tm-30) REVERT: L 216 THR cc_start: 0.8967 (m) cc_final: 0.8741 (p) REVERT: L 332 MET cc_start: 0.8693 (mmt) cc_final: 0.8381 (mmt) outliers start: 59 outliers final: 42 residues processed: 696 average time/residue: 0.2155 time to fit residues: 254.1958 Evaluate side-chains 600 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 557 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 327 TYR Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 278 ASN Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 140 ARG Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 278 ASN Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 238 ILE Chi-restraints excluded: chain G residue 327 TYR Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain H residue 140 ARG Chi-restraints excluded: chain H residue 205 LEU Chi-restraints excluded: chain H residue 278 ASN Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 205 LEU Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 77 ILE Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 238 ILE Chi-restraints excluded: chain K residue 28 LYS Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 205 LEU Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 140 ARG Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain L residue 278 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 371 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 366 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 478 optimal weight: 7.9990 chunk 275 optimal weight: 7.9990 chunk 497 optimal weight: 4.9990 chunk 132 optimal weight: 7.9990 chunk 113 optimal weight: 0.8980 chunk 233 optimal weight: 8.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 202 GLN E 202 GLN F 318 ASN H 202 GLN L 202 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.093622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.071442 restraints weight = 86611.540| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 3.29 r_work: 0.2941 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 41628 Z= 0.160 Angle : 0.590 9.589 56304 Z= 0.289 Chirality : 0.042 0.155 6132 Planarity : 0.005 0.053 7452 Dihedral : 4.273 19.324 5628 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.27 % Allowed : 13.37 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.12), residues: 5172 helix: 2.61 (0.12), residues: 1800 sheet: 0.18 (0.15), residues: 1260 loop : -0.58 (0.14), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 338 TYR 0.016 0.002 TYR L 239 PHE 0.018 0.001 PHE G 398 TRP 0.001 0.000 TRP I 58 HIS 0.005 0.001 HIS F 459 Details of bonding type rmsd covalent geometry : bond 0.00364 (41628) covalent geometry : angle 0.58984 (56304) hydrogen bonds : bond 0.03358 ( 1548) hydrogen bonds : angle 4.13156 ( 4464) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 571 time to evaluate : 1.597 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: A 1 MET cc_start: 0.6348 (tpp) cc_final: 0.6092 (tpp) REVERT: A 30 GLN cc_start: 0.8678 (mm-40) cc_final: 0.8291 (mp10) REVERT: A 208 GLU cc_start: 0.8308 (pt0) cc_final: 0.7867 (tm-30) REVERT: A 249 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.8547 (ttm170) REVERT: A 393 MET cc_start: 0.8634 (mmm) cc_final: 0.8114 (mmt) REVERT: A 421 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8503 (mm-30) REVERT: B 30 GLN cc_start: 0.8511 (mp10) cc_final: 0.8289 (mp10) REVERT: B 208 GLU cc_start: 0.8365 (pt0) cc_final: 0.7957 (tm-30) REVERT: B 332 MET cc_start: 0.8690 (mmt) cc_final: 0.8272 (mmt) REVERT: B 410 GLN cc_start: 0.8266 (mm-40) cc_final: 0.7683 (mm-40) REVERT: C 5 HIS cc_start: 0.8608 (m-70) cc_final: 0.8279 (t-90) REVERT: C 30 GLN cc_start: 0.8594 (mm-40) cc_final: 0.8194 (mp10) REVERT: C 69 MET cc_start: 0.8860 (tpt) cc_final: 0.8615 (tpt) REVERT: C 208 GLU cc_start: 0.8318 (pt0) cc_final: 0.7925 (tm-30) REVERT: C 216 THR cc_start: 0.8982 (m) cc_final: 0.8743 (p) REVERT: C 421 GLU cc_start: 0.8801 (mm-30) cc_final: 0.8547 (mm-30) REVERT: C 441 ASP cc_start: 0.8820 (m-30) cc_final: 0.8350 (m-30) REVERT: D 1 MET cc_start: 0.6369 (tpp) cc_final: 0.6122 (tpp) REVERT: D 30 GLN cc_start: 0.8680 (mm-40) cc_final: 0.8294 (mp10) REVERT: D 208 GLU cc_start: 0.8335 (pt0) cc_final: 0.7882 (tm-30) REVERT: D 249 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.8531 (ttm170) REVERT: D 393 MET cc_start: 0.8721 (mmm) cc_final: 0.8066 (mmt) REVERT: D 421 GLU cc_start: 0.8882 (mm-30) cc_final: 0.8539 (mm-30) REVERT: E 30 GLN cc_start: 0.8494 (mp10) cc_final: 0.8277 (mp10) REVERT: E 208 GLU cc_start: 0.8359 (pt0) cc_final: 0.8006 (tm-30) REVERT: E 332 MET cc_start: 0.8683 (mmt) cc_final: 0.8266 (mmt) REVERT: E 410 GLN cc_start: 0.8256 (mm-40) cc_final: 0.7678 (mm-40) REVERT: F 5 HIS cc_start: 0.8605 (m-70) cc_final: 0.8277 (t-90) REVERT: F 30 GLN cc_start: 0.8610 (mm-40) cc_final: 0.8200 (mp10) REVERT: F 69 MET cc_start: 0.8858 (tpt) cc_final: 0.8617 (tpt) REVERT: F 208 GLU cc_start: 0.8334 (pt0) cc_final: 0.7943 (tm-30) REVERT: F 421 GLU cc_start: 0.8815 (mm-30) cc_final: 0.8561 (mm-30) REVERT: F 441 ASP cc_start: 0.8782 (m-30) cc_final: 0.8314 (m-30) REVERT: G 1 MET cc_start: 0.6358 (tpp) cc_final: 0.6105 (tpp) REVERT: G 30 GLN cc_start: 0.8674 (mm-40) cc_final: 0.8290 (mp10) REVERT: G 208 GLU cc_start: 0.8295 (pt0) cc_final: 0.7865 (tm-30) REVERT: G 249 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8525 (ttm170) REVERT: G 393 MET cc_start: 0.8611 (mmm) cc_final: 0.8093 (mmt) REVERT: G 421 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8522 (mm-30) REVERT: H 30 GLN cc_start: 0.8607 (mp10) cc_final: 0.8360 (mp10) REVERT: H 208 GLU cc_start: 0.8383 (pt0) cc_final: 0.8026 (tm-30) REVERT: H 332 MET cc_start: 0.8710 (mmt) cc_final: 0.8296 (mmt) REVERT: H 410 GLN cc_start: 0.8260 (mm-40) cc_final: 0.7672 (mm-40) REVERT: I 5 HIS cc_start: 0.8598 (m-70) cc_final: 0.8297 (t-90) REVERT: I 30 GLN cc_start: 0.8610 (mm-40) cc_final: 0.8210 (mp10) REVERT: I 69 MET cc_start: 0.8868 (tpt) cc_final: 0.8627 (tpt) REVERT: I 208 GLU cc_start: 0.8326 (pt0) cc_final: 0.7936 (tm-30) REVERT: I 216 THR cc_start: 0.8982 (m) cc_final: 0.8742 (p) REVERT: I 421 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8566 (mm-30) REVERT: I 441 ASP cc_start: 0.8812 (m-30) cc_final: 0.8352 (m-30) REVERT: J 1 MET cc_start: 0.6379 (tpp) cc_final: 0.6128 (tpp) REVERT: J 30 GLN cc_start: 0.8702 (mm-40) cc_final: 0.8303 (mp10) REVERT: J 208 GLU cc_start: 0.8326 (pt0) cc_final: 0.7883 (tm-30) REVERT: J 249 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.8544 (ttm170) REVERT: J 393 MET cc_start: 0.8708 (mmm) cc_final: 0.8056 (mmt) REVERT: J 421 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8537 (mm-30) REVERT: K 5 HIS cc_start: 0.8568 (m-70) cc_final: 0.8296 (t-90) REVERT: K 28 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8419 (mtpp) REVERT: K 30 GLN cc_start: 0.8444 (mm110) cc_final: 0.8107 (mp10) REVERT: K 69 MET cc_start: 0.8866 (tpt) cc_final: 0.8626 (tpt) REVERT: K 208 GLU cc_start: 0.8345 (pt0) cc_final: 0.7943 (tm-30) REVERT: K 421 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8542 (mm-30) REVERT: K 441 ASP cc_start: 0.8795 (m-30) cc_final: 0.8335 (m-30) REVERT: L 30 GLN cc_start: 0.8589 (mp10) cc_final: 0.8344 (mp10) REVERT: L 208 GLU cc_start: 0.8359 (pt0) cc_final: 0.8003 (tm-30) REVERT: L 216 THR cc_start: 0.8995 (m) cc_final: 0.8760 (p) REVERT: L 332 MET cc_start: 0.8678 (mmt) cc_final: 0.8259 (mmt) REVERT: L 410 GLN cc_start: 0.8255 (mm-40) cc_final: 0.7672 (mm-40) outliers start: 55 outliers final: 20 residues processed: 618 average time/residue: 0.2055 time to fit residues: 216.5429 Evaluate side-chains 560 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 535 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 249 ARG Chi-restraints excluded: chain E residue 140 ARG Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain F residue 436 THR Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 249 ARG Chi-restraints excluded: chain H residue 140 ARG Chi-restraints excluded: chain H residue 205 LEU Chi-restraints excluded: chain I residue 436 THR Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 249 ARG Chi-restraints excluded: chain K residue 28 LYS Chi-restraints excluded: chain K residue 436 THR Chi-restraints excluded: chain L residue 140 ARG Chi-restraints excluded: chain L residue 205 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 319 optimal weight: 9.9990 chunk 146 optimal weight: 7.9990 chunk 206 optimal weight: 3.9990 chunk 200 optimal weight: 3.9990 chunk 111 optimal weight: 9.9990 chunk 294 optimal weight: 3.9990 chunk 219 optimal weight: 4.9990 chunk 401 optimal weight: 6.9990 chunk 180 optimal weight: 4.9990 chunk 158 optimal weight: 0.3980 chunk 16 optimal weight: 0.8980 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 202 GLN C 318 ASN E 202 GLN H 202 GLN I 318 ASN L 202 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.091565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.069587 restraints weight = 88013.708| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 3.29 r_work: 0.2896 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 41628 Z= 0.219 Angle : 0.619 10.802 56304 Z= 0.303 Chirality : 0.044 0.164 6132 Planarity : 0.005 0.056 7452 Dihedral : 4.376 19.665 5628 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.69 % Allowed : 14.00 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.12), residues: 5172 helix: 2.51 (0.12), residues: 1812 sheet: 0.30 (0.15), residues: 1260 loop : -0.46 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 140 TYR 0.022 0.002 TYR G 239 PHE 0.016 0.001 PHE C 398 TRP 0.001 0.000 TRP H 58 HIS 0.003 0.001 HIS D 210 Details of bonding type rmsd covalent geometry : bond 0.00501 (41628) covalent geometry : angle 0.61856 (56304) hydrogen bonds : bond 0.03595 ( 1548) hydrogen bonds : angle 4.22062 ( 4464) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 544 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLN cc_start: 0.8838 (mm-40) cc_final: 0.8451 (mp10) REVERT: A 208 GLU cc_start: 0.8315 (pt0) cc_final: 0.7817 (tm-30) REVERT: A 249 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.8541 (ttm170) REVERT: A 353 LYS cc_start: 0.9296 (mptt) cc_final: 0.9052 (tppt) REVERT: B 30 GLN cc_start: 0.8650 (mp10) cc_final: 0.8366 (mp10) REVERT: B 138 ASP cc_start: 0.8711 (t0) cc_final: 0.8501 (t70) REVERT: B 208 GLU cc_start: 0.8365 (pt0) cc_final: 0.7959 (tm-30) REVERT: B 410 GLN cc_start: 0.8275 (mm-40) cc_final: 0.8042 (mm-40) REVERT: C 30 GLN cc_start: 0.8731 (mm-40) cc_final: 0.8203 (mp10) REVERT: C 69 MET cc_start: 0.8888 (tpt) cc_final: 0.8639 (tpt) REVERT: C 208 GLU cc_start: 0.8348 (pt0) cc_final: 0.7872 (tm-30) REVERT: C 216 THR cc_start: 0.9011 (m) cc_final: 0.8809 (p) REVERT: C 421 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8548 (mm-30) REVERT: C 441 ASP cc_start: 0.8816 (m-30) cc_final: 0.8387 (m-30) REVERT: D 30 GLN cc_start: 0.8821 (mm-40) cc_final: 0.8433 (mp10) REVERT: D 208 GLU cc_start: 0.8336 (pt0) cc_final: 0.7839 (tm-30) REVERT: D 249 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.8532 (ttm170) REVERT: D 353 LYS cc_start: 0.9299 (mptt) cc_final: 0.9060 (tppt) REVERT: E 30 GLN cc_start: 0.8616 (mp10) cc_final: 0.8333 (mp10) REVERT: E 138 ASP cc_start: 0.8718 (t0) cc_final: 0.8507 (t70) REVERT: E 208 GLU cc_start: 0.8330 (pt0) cc_final: 0.7909 (tm-30) REVERT: E 410 GLN cc_start: 0.8259 (mm-40) cc_final: 0.8026 (mm-40) REVERT: F 30 GLN cc_start: 0.8725 (mm-40) cc_final: 0.8190 (mp10) REVERT: F 69 MET cc_start: 0.8881 (tpt) cc_final: 0.8635 (tpt) REVERT: F 208 GLU cc_start: 0.8344 (pt0) cc_final: 0.7864 (tm-30) REVERT: F 421 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8558 (mm-30) REVERT: F 441 ASP cc_start: 0.8798 (m-30) cc_final: 0.8373 (m-30) REVERT: G 30 GLN cc_start: 0.8827 (mm-40) cc_final: 0.8443 (mp10) REVERT: G 208 GLU cc_start: 0.8299 (pt0) cc_final: 0.7827 (tm-30) REVERT: G 249 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.8532 (ttm170) REVERT: G 353 LYS cc_start: 0.9303 (mptt) cc_final: 0.9059 (tppt) REVERT: H 30 GLN cc_start: 0.8692 (mp10) cc_final: 0.8379 (mp10) REVERT: H 138 ASP cc_start: 0.8710 (t0) cc_final: 0.8500 (t70) REVERT: H 208 GLU cc_start: 0.8367 (pt0) cc_final: 0.8009 (tm-30) REVERT: H 410 GLN cc_start: 0.8258 (mm-40) cc_final: 0.8016 (mm-40) REVERT: I 30 GLN cc_start: 0.8740 (mm-40) cc_final: 0.8211 (mp10) REVERT: I 69 MET cc_start: 0.8893 (tpt) cc_final: 0.8644 (tpt) REVERT: I 208 GLU cc_start: 0.8339 (pt0) cc_final: 0.7874 (tm-30) REVERT: I 216 THR cc_start: 0.9013 (m) cc_final: 0.8805 (p) REVERT: I 421 GLU cc_start: 0.8840 (mm-30) cc_final: 0.8550 (mm-30) REVERT: I 441 ASP cc_start: 0.8818 (m-30) cc_final: 0.8387 (m-30) REVERT: J 30 GLN cc_start: 0.8845 (mm-40) cc_final: 0.8450 (mp10) REVERT: J 208 GLU cc_start: 0.8312 (pt0) cc_final: 0.7822 (tm-30) REVERT: J 249 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.8530 (ttm170) REVERT: J 353 LYS cc_start: 0.9286 (mptt) cc_final: 0.9054 (tppt) REVERT: K 30 GLN cc_start: 0.8591 (mm110) cc_final: 0.8121 (mp10) REVERT: K 69 MET cc_start: 0.8894 (tpt) cc_final: 0.8644 (tpt) REVERT: K 208 GLU cc_start: 0.8332 (pt0) cc_final: 0.7862 (tm-30) REVERT: K 421 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8545 (mm-30) REVERT: K 441 ASP cc_start: 0.8819 (m-30) cc_final: 0.8387 (m-30) REVERT: L 30 GLN cc_start: 0.8678 (mp10) cc_final: 0.8366 (mp10) REVERT: L 138 ASP cc_start: 0.8703 (t0) cc_final: 0.8490 (t70) REVERT: L 208 GLU cc_start: 0.8319 (pt0) cc_final: 0.7908 (tm-30) REVERT: L 410 GLN cc_start: 0.8266 (mm-40) cc_final: 0.8035 (mm-40) outliers start: 30 outliers final: 20 residues processed: 574 average time/residue: 0.2051 time to fit residues: 200.3648 Evaluate side-chains 551 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 527 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 249 ARG Chi-restraints excluded: chain E residue 140 ARG Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 436 THR Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 249 ARG Chi-restraints excluded: chain H residue 140 ARG Chi-restraints excluded: chain H residue 205 LEU Chi-restraints excluded: chain I residue 205 LEU Chi-restraints excluded: chain I residue 436 THR Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 249 ARG Chi-restraints excluded: chain K residue 205 LEU Chi-restraints excluded: chain K residue 436 THR Chi-restraints excluded: chain L residue 140 ARG Chi-restraints excluded: chain L residue 205 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 269 optimal weight: 10.0000 chunk 282 optimal weight: 2.9990 chunk 491 optimal weight: 2.9990 chunk 79 optimal weight: 9.9990 chunk 226 optimal weight: 0.9980 chunk 55 optimal weight: 0.0030 chunk 512 optimal weight: 8.9990 chunk 168 optimal weight: 2.9990 chunk 365 optimal weight: 1.9990 chunk 342 optimal weight: 6.9990 chunk 240 optimal weight: 8.9990 overall best weight: 1.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 202 GLN E 202 GLN H 202 GLN L 219 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.092445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.070567 restraints weight = 87936.955| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 3.31 r_work: 0.2916 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 41628 Z= 0.160 Angle : 0.582 10.054 56304 Z= 0.282 Chirality : 0.043 0.148 6132 Planarity : 0.004 0.058 7452 Dihedral : 4.229 18.496 5628 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.64 % Allowed : 14.94 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.12), residues: 5172 helix: 2.75 (0.12), residues: 1740 sheet: 0.26 (0.15), residues: 1260 loop : -0.37 (0.14), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 249 TYR 0.017 0.001 TYR D 239 PHE 0.014 0.001 PHE A 398 TRP 0.001 0.000 TRP L 58 HIS 0.003 0.001 HIS L 210 Details of bonding type rmsd covalent geometry : bond 0.00372 (41628) covalent geometry : angle 0.58247 (56304) hydrogen bonds : bond 0.03286 ( 1548) hydrogen bonds : angle 4.08434 ( 4464) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 543 time to evaluate : 1.169 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 30 GLN cc_start: 0.8813 (mm-40) cc_final: 0.8430 (mp10) REVERT: A 208 GLU cc_start: 0.8262 (pt0) cc_final: 0.7809 (tm-30) REVERT: A 249 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.8625 (ttm170) REVERT: A 353 LYS cc_start: 0.9272 (mptt) cc_final: 0.9034 (tppt) REVERT: B 30 GLN cc_start: 0.8614 (mp10) cc_final: 0.8319 (mp10) REVERT: B 69 MET cc_start: 0.8831 (tpt) cc_final: 0.8491 (tpt) REVERT: B 208 GLU cc_start: 0.8384 (pt0) cc_final: 0.7942 (tm-30) REVERT: C 30 GLN cc_start: 0.8711 (mm-40) cc_final: 0.8217 (mp10) REVERT: C 69 MET cc_start: 0.8897 (tpt) cc_final: 0.8667 (tpt) REVERT: C 208 GLU cc_start: 0.8309 (pt0) cc_final: 0.7859 (tm-30) REVERT: C 421 GLU cc_start: 0.8807 (mm-30) cc_final: 0.8513 (mm-30) REVERT: C 441 ASP cc_start: 0.8836 (m-30) cc_final: 0.8384 (m-30) REVERT: D 30 GLN cc_start: 0.8817 (mm-40) cc_final: 0.8432 (mp10) REVERT: D 208 GLU cc_start: 0.8269 (pt0) cc_final: 0.7831 (tm-30) REVERT: D 249 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8627 (ttm170) REVERT: D 353 LYS cc_start: 0.9272 (mptt) cc_final: 0.9027 (tppt) REVERT: E 30 GLN cc_start: 0.8592 (mp10) cc_final: 0.8303 (mp10) REVERT: E 69 MET cc_start: 0.8838 (tpt) cc_final: 0.8503 (tpt) REVERT: E 208 GLU cc_start: 0.8274 (pt0) cc_final: 0.7887 (tm-30) REVERT: F 30 GLN cc_start: 0.8715 (mm-40) cc_final: 0.8212 (mp10) REVERT: F 69 MET cc_start: 0.8876 (tpt) cc_final: 0.8645 (tpt) REVERT: F 208 GLU cc_start: 0.8314 (pt0) cc_final: 0.7868 (tm-30) REVERT: F 421 GLU cc_start: 0.8832 (mm-30) cc_final: 0.8540 (mm-30) REVERT: F 441 ASP cc_start: 0.8805 (m-30) cc_final: 0.8354 (m-30) REVERT: G 30 GLN cc_start: 0.8819 (mm-40) cc_final: 0.8470 (mp10) REVERT: G 208 GLU cc_start: 0.8241 (pt0) cc_final: 0.7805 (tm-30) REVERT: G 249 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.8616 (ttm170) REVERT: G 353 LYS cc_start: 0.9282 (mptt) cc_final: 0.9041 (tppt) REVERT: H 30 GLN cc_start: 0.8666 (mp10) cc_final: 0.8378 (mp10) REVERT: H 69 MET cc_start: 0.8849 (tpt) cc_final: 0.8516 (tpt) REVERT: H 208 GLU cc_start: 0.8398 (pt0) cc_final: 0.8008 (tm-30) REVERT: I 30 GLN cc_start: 0.8720 (mm-40) cc_final: 0.8223 (mp10) REVERT: I 69 MET cc_start: 0.8910 (tpt) cc_final: 0.8663 (tpt) REVERT: I 208 GLU cc_start: 0.8307 (pt0) cc_final: 0.7868 (tm-30) REVERT: I 288 TYR cc_start: 0.8085 (t80) cc_final: 0.7788 (t80) REVERT: I 421 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8546 (mm-30) REVERT: I 441 ASP cc_start: 0.8834 (m-30) cc_final: 0.8379 (m-30) REVERT: J 30 GLN cc_start: 0.8823 (mm-40) cc_final: 0.8441 (mp10) REVERT: J 208 GLU cc_start: 0.8276 (pt0) cc_final: 0.7838 (tm-30) REVERT: J 249 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8633 (ttm170) REVERT: J 353 LYS cc_start: 0.9263 (mptt) cc_final: 0.9024 (tppt) REVERT: K 30 GLN cc_start: 0.8543 (mm110) cc_final: 0.8090 (mp10) REVERT: K 69 MET cc_start: 0.8913 (tpt) cc_final: 0.8667 (tpt) REVERT: K 208 GLU cc_start: 0.8307 (pt0) cc_final: 0.7871 (tm-30) REVERT: K 288 TYR cc_start: 0.8074 (t80) cc_final: 0.7774 (t80) REVERT: K 421 GLU cc_start: 0.8832 (mm-30) cc_final: 0.8539 (mm-30) REVERT: K 441 ASP cc_start: 0.8847 (m-30) cc_final: 0.8391 (m-30) REVERT: L 30 GLN cc_start: 0.8642 (mp10) cc_final: 0.8355 (mp10) REVERT: L 69 MET cc_start: 0.8842 (tpt) cc_final: 0.8511 (tpt) REVERT: L 208 GLU cc_start: 0.8263 (pt0) cc_final: 0.7886 (tm-30) outliers start: 28 outliers final: 18 residues processed: 571 average time/residue: 0.2079 time to fit residues: 201.8121 Evaluate side-chains 524 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 502 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 249 ARG Chi-restraints excluded: chain E residue 140 ARG Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain F residue 436 THR Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 249 ARG Chi-restraints excluded: chain H residue 140 ARG Chi-restraints excluded: chain H residue 205 LEU Chi-restraints excluded: chain I residue 436 THR Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 249 ARG Chi-restraints excluded: chain K residue 436 THR Chi-restraints excluded: chain L residue 140 ARG Chi-restraints excluded: chain L residue 205 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 227 optimal weight: 0.0980 chunk 512 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 7 optimal weight: 0.5980 chunk 143 optimal weight: 5.9990 chunk 405 optimal weight: 0.7980 chunk 139 optimal weight: 2.9990 chunk 144 optimal weight: 0.7980 chunk 430 optimal weight: 10.0000 chunk 359 optimal weight: 4.9990 chunk 303 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 318 ASN E 202 GLN F 318 ASN I 318 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.093239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.070848 restraints weight = 87485.845| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 3.43 r_work: 0.2916 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.4587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 41628 Z= 0.098 Angle : 0.546 10.862 56304 Z= 0.264 Chirality : 0.041 0.143 6132 Planarity : 0.004 0.060 7452 Dihedral : 3.936 16.368 5628 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.74 % Allowed : 16.02 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.12), residues: 5172 helix: 2.77 (0.12), residues: 1740 sheet: 0.41 (0.15), residues: 1212 loop : -0.42 (0.13), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 249 TYR 0.014 0.001 TYR H 239 PHE 0.013 0.001 PHE G 398 TRP 0.001 0.000 TRP H 58 HIS 0.003 0.000 HIS G 210 Details of bonding type rmsd covalent geometry : bond 0.00230 (41628) covalent geometry : angle 0.54620 (56304) hydrogen bonds : bond 0.02854 ( 1548) hydrogen bonds : angle 3.85161 ( 4464) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 562 time to evaluate : 1.055 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: A 30 GLN cc_start: 0.8709 (mm-40) cc_final: 0.8247 (mp10) REVERT: A 208 GLU cc_start: 0.8248 (pt0) cc_final: 0.7771 (tm-30) REVERT: A 353 LYS cc_start: 0.9264 (mptt) cc_final: 0.8996 (tppt) REVERT: B 30 GLN cc_start: 0.8470 (mp10) cc_final: 0.8204 (mp10) REVERT: B 69 MET cc_start: 0.8838 (tpt) cc_final: 0.8521 (tpt) REVERT: B 208 GLU cc_start: 0.8368 (pt0) cc_final: 0.7867 (tm-30) REVERT: B 332 MET cc_start: 0.8712 (mmt) cc_final: 0.8430 (mmt) REVERT: B 441 ASP cc_start: 0.8827 (m-30) cc_final: 0.8415 (m-30) REVERT: C 30 GLN cc_start: 0.8637 (mm-40) cc_final: 0.8114 (mp10) REVERT: C 208 GLU cc_start: 0.8272 (pt0) cc_final: 0.7885 (tm-30) REVERT: C 421 GLU cc_start: 0.8774 (mm-30) cc_final: 0.8475 (mm-30) REVERT: C 441 ASP cc_start: 0.8816 (m-30) cc_final: 0.8336 (m-30) REVERT: D 30 GLN cc_start: 0.8723 (mm-40) cc_final: 0.8239 (mp10) REVERT: D 208 GLU cc_start: 0.8262 (pt0) cc_final: 0.7904 (tm-30) REVERT: D 353 LYS cc_start: 0.9263 (mptt) cc_final: 0.9004 (tppt) REVERT: E 30 GLN cc_start: 0.8480 (mp10) cc_final: 0.8212 (mp10) REVERT: E 69 MET cc_start: 0.8856 (tpt) cc_final: 0.8547 (tpt) REVERT: E 208 GLU cc_start: 0.8288 (pt0) cc_final: 0.7963 (tm-30) REVERT: E 332 MET cc_start: 0.8738 (mmt) cc_final: 0.8457 (mmt) REVERT: E 441 ASP cc_start: 0.8816 (m-30) cc_final: 0.8408 (m-30) REVERT: F 30 GLN cc_start: 0.8645 (mm-40) cc_final: 0.8125 (mp10) REVERT: F 208 GLU cc_start: 0.8305 (pt0) cc_final: 0.7927 (tm-30) REVERT: F 421 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8475 (mm-30) REVERT: F 441 ASP cc_start: 0.8806 (m-30) cc_final: 0.8326 (m-30) REVERT: G 30 GLN cc_start: 0.8721 (mm-40) cc_final: 0.8269 (mp10) REVERT: G 208 GLU cc_start: 0.8260 (pt0) cc_final: 0.7787 (tm-30) REVERT: G 353 LYS cc_start: 0.9268 (mptt) cc_final: 0.8998 (tppt) REVERT: H 30 GLN cc_start: 0.8504 (mp10) cc_final: 0.8199 (mp10) REVERT: H 69 MET cc_start: 0.8838 (tpt) cc_final: 0.8521 (tpt) REVERT: H 208 GLU cc_start: 0.8384 (pt0) cc_final: 0.7903 (tm-30) REVERT: H 332 MET cc_start: 0.8731 (mmt) cc_final: 0.8464 (mmt) REVERT: H 441 ASP cc_start: 0.8825 (m-30) cc_final: 0.8413 (m-30) REVERT: I 30 GLN cc_start: 0.8641 (mm-40) cc_final: 0.8115 (mp10) REVERT: I 208 GLU cc_start: 0.8304 (pt0) cc_final: 0.7909 (tm-30) REVERT: I 421 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8503 (mm-30) REVERT: I 441 ASP cc_start: 0.8804 (m-30) cc_final: 0.8324 (m-30) REVERT: J 30 GLN cc_start: 0.8710 (mm-40) cc_final: 0.8266 (mp10) REVERT: J 208 GLU cc_start: 0.8245 (pt0) cc_final: 0.7874 (tm-30) REVERT: J 353 LYS cc_start: 0.9254 (mptt) cc_final: 0.8998 (tppt) REVERT: K 30 GLN cc_start: 0.8372 (mm110) cc_final: 0.7994 (mp10) REVERT: K 208 GLU cc_start: 0.8278 (pt0) cc_final: 0.7916 (tm-30) REVERT: K 421 GLU cc_start: 0.8780 (mm-30) cc_final: 0.8485 (mm-30) REVERT: K 441 ASP cc_start: 0.8827 (m-30) cc_final: 0.8352 (m-30) REVERT: L 30 GLN cc_start: 0.8495 (mp10) cc_final: 0.8195 (mp10) REVERT: L 69 MET cc_start: 0.8870 (tpt) cc_final: 0.8565 (tpt) REVERT: L 208 GLU cc_start: 0.8308 (pt0) cc_final: 0.7977 (tm-30) REVERT: L 332 MET cc_start: 0.8717 (mmt) cc_final: 0.8435 (mmt) REVERT: L 441 ASP cc_start: 0.8829 (m-30) cc_final: 0.8419 (m-30) outliers start: 32 outliers final: 18 residues processed: 588 average time/residue: 0.2074 time to fit residues: 206.6884 Evaluate side-chains 534 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 516 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain E residue 140 ARG Chi-restraints excluded: chain F residue 255 THR Chi-restraints excluded: chain F residue 436 THR Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain H residue 140 ARG Chi-restraints excluded: chain I residue 255 THR Chi-restraints excluded: chain I residue 436 THR Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain K residue 255 THR Chi-restraints excluded: chain K residue 436 THR Chi-restraints excluded: chain L residue 140 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 377 optimal weight: 5.9990 chunk 396 optimal weight: 7.9990 chunk 53 optimal weight: 8.9990 chunk 474 optimal weight: 1.9990 chunk 192 optimal weight: 0.9980 chunk 368 optimal weight: 0.5980 chunk 483 optimal weight: 8.9990 chunk 172 optimal weight: 10.0000 chunk 395 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 383 optimal weight: 7.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 318 ASN ** D 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 318 ASN ** G 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 318 ASN ** J 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 318 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.090209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.068115 restraints weight = 88715.775| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 3.41 r_work: 0.2848 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.4602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 41628 Z= 0.211 Angle : 0.623 10.785 56304 Z= 0.301 Chirality : 0.044 0.163 6132 Planarity : 0.005 0.061 7452 Dihedral : 4.153 19.331 5628 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.01 % Allowed : 16.11 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.12), residues: 5172 helix: 2.43 (0.12), residues: 1812 sheet: 0.31 (0.15), residues: 1260 loop : -0.35 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 21 TYR 0.030 0.002 TYR J 288 PHE 0.013 0.001 PHE H 398 TRP 0.006 0.001 TRP H 58 HIS 0.003 0.001 HIS G 210 Details of bonding type rmsd covalent geometry : bond 0.00487 (41628) covalent geometry : angle 0.62300 (56304) hydrogen bonds : bond 0.03397 ( 1548) hydrogen bonds : angle 4.07733 ( 4464) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 516 time to evaluate : 1.048 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: A 30 GLN cc_start: 0.8845 (mm-40) cc_final: 0.8457 (mp10) REVERT: A 208 GLU cc_start: 0.8328 (pt0) cc_final: 0.7811 (tm-30) REVERT: A 353 LYS cc_start: 0.9284 (mptt) cc_final: 0.9023 (tppt) REVERT: B 30 GLN cc_start: 0.8593 (mp10) cc_final: 0.8287 (mp10) REVERT: B 208 GLU cc_start: 0.8383 (pt0) cc_final: 0.7952 (tm-30) REVERT: B 332 MET cc_start: 0.8672 (mmt) cc_final: 0.8446 (mmt) REVERT: B 441 ASP cc_start: 0.8843 (m-30) cc_final: 0.8446 (m-30) REVERT: C 30 GLN cc_start: 0.8755 (mm-40) cc_final: 0.8137 (mp10) REVERT: C 208 GLU cc_start: 0.8447 (pt0) cc_final: 0.7957 (tm-30) REVERT: C 421 GLU cc_start: 0.8793 (mm-30) cc_final: 0.8485 (mm-30) REVERT: C 441 ASP cc_start: 0.8867 (m-30) cc_final: 0.8421 (m-30) REVERT: D 30 GLN cc_start: 0.8841 (mm-40) cc_final: 0.8455 (mp10) REVERT: D 208 GLU cc_start: 0.8461 (pt0) cc_final: 0.7929 (tm-30) REVERT: D 353 LYS cc_start: 0.9295 (mptt) cc_final: 0.9035 (tppt) REVERT: E 30 GLN cc_start: 0.8599 (mp10) cc_final: 0.8292 (mp10) REVERT: E 208 GLU cc_start: 0.8410 (pt0) cc_final: 0.7920 (tm-30) REVERT: E 332 MET cc_start: 0.8671 (mmt) cc_final: 0.8412 (mmt) REVERT: E 441 ASP cc_start: 0.8840 (m-30) cc_final: 0.8446 (m-30) REVERT: F 30 GLN cc_start: 0.8739 (mm-40) cc_final: 0.8118 (mp10) REVERT: F 208 GLU cc_start: 0.8457 (pt0) cc_final: 0.7970 (tm-30) REVERT: F 421 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8484 (mm-30) REVERT: F 441 ASP cc_start: 0.8874 (m-30) cc_final: 0.8436 (m-30) REVERT: G 30 GLN cc_start: 0.8840 (mm-40) cc_final: 0.8451 (mp10) REVERT: G 208 GLU cc_start: 0.8340 (pt0) cc_final: 0.7806 (tm-30) REVERT: G 353 LYS cc_start: 0.9296 (mptt) cc_final: 0.9030 (tppt) REVERT: H 30 GLN cc_start: 0.8621 (mp10) cc_final: 0.8282 (mp10) REVERT: H 208 GLU cc_start: 0.8405 (pt0) cc_final: 0.7974 (tm-30) REVERT: H 332 MET cc_start: 0.8686 (mmt) cc_final: 0.8460 (mmt) REVERT: H 441 ASP cc_start: 0.8846 (m-30) cc_final: 0.8449 (m-30) REVERT: I 30 GLN cc_start: 0.8739 (mm-40) cc_final: 0.8119 (mp10) REVERT: I 208 GLU cc_start: 0.8450 (pt0) cc_final: 0.7967 (tm-30) REVERT: I 421 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8480 (mm-30) REVERT: I 441 ASP cc_start: 0.8865 (m-30) cc_final: 0.8417 (m-30) REVERT: J 30 GLN cc_start: 0.8844 (mm-40) cc_final: 0.8446 (mp10) REVERT: J 208 GLU cc_start: 0.8414 (pt0) cc_final: 0.7919 (tm-30) REVERT: J 353 LYS cc_start: 0.9290 (mptt) cc_final: 0.9031 (tppt) REVERT: K 28 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8310 (mtpp) REVERT: K 30 GLN cc_start: 0.8524 (mm110) cc_final: 0.8003 (mp10) REVERT: K 208 GLU cc_start: 0.8418 (pt0) cc_final: 0.7957 (tm-30) REVERT: K 421 GLU cc_start: 0.8760 (mm-30) cc_final: 0.8453 (mm-30) REVERT: K 441 ASP cc_start: 0.8873 (m-30) cc_final: 0.8429 (m-30) REVERT: L 30 GLN cc_start: 0.8622 (mp10) cc_final: 0.8279 (mp10) REVERT: L 208 GLU cc_start: 0.8421 (pt0) cc_final: 0.7936 (tm-30) REVERT: L 332 MET cc_start: 0.8655 (mmt) cc_final: 0.8399 (mmt) REVERT: L 441 ASP cc_start: 0.8847 (m-30) cc_final: 0.8454 (m-30) outliers start: 44 outliers final: 24 residues processed: 554 average time/residue: 0.2139 time to fit residues: 201.4820 Evaluate side-chains 518 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 493 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain E residue 140 ARG Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 255 THR Chi-restraints excluded: chain F residue 436 THR Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 255 THR Chi-restraints excluded: chain H residue 140 ARG Chi-restraints excluded: chain I residue 205 LEU Chi-restraints excluded: chain I residue 255 THR Chi-restraints excluded: chain I residue 436 THR Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 255 THR Chi-restraints excluded: chain K residue 28 LYS Chi-restraints excluded: chain K residue 205 LEU Chi-restraints excluded: chain K residue 255 THR Chi-restraints excluded: chain K residue 436 THR Chi-restraints excluded: chain L residue 140 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 76 optimal weight: 4.9990 chunk 250 optimal weight: 5.9990 chunk 215 optimal weight: 10.0000 chunk 302 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 484 optimal weight: 0.8980 chunk 86 optimal weight: 10.0000 chunk 413 optimal weight: 3.9990 chunk 382 optimal weight: 6.9990 chunk 410 optimal weight: 10.0000 chunk 294 optimal weight: 4.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN ** A 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 GLN ** D 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 318 ASN ** F 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 219 GLN ** G 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 219 GLN ** J 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 318 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.087395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.065556 restraints weight = 90267.995| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 3.38 r_work: 0.2795 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.4639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.047 41628 Z= 0.333 Angle : 0.734 13.009 56304 Z= 0.357 Chirality : 0.047 0.184 6132 Planarity : 0.005 0.062 7452 Dihedral : 4.692 22.219 5628 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.69 % Allowed : 16.34 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.12), residues: 5172 helix: 1.93 (0.12), residues: 1884 sheet: 0.36 (0.15), residues: 1200 loop : -0.43 (0.14), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 21 TYR 0.030 0.002 TYR D 288 PHE 0.016 0.002 PHE B 398 TRP 0.007 0.001 TRP H 58 HIS 0.004 0.001 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00760 (41628) covalent geometry : angle 0.73382 (56304) hydrogen bonds : bond 0.04017 ( 1548) hydrogen bonds : angle 4.48106 ( 4464) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 498 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLN cc_start: 0.8926 (mm-40) cc_final: 0.8486 (mp10) REVERT: B 30 GLN cc_start: 0.8651 (mp10) cc_final: 0.8256 (mp10) REVERT: B 208 GLU cc_start: 0.8431 (pt0) cc_final: 0.8047 (tm-30) REVERT: B 441 ASP cc_start: 0.8846 (m-30) cc_final: 0.8419 (m-30) REVERT: C 208 GLU cc_start: 0.8517 (pt0) cc_final: 0.8082 (tm-30) REVERT: C 421 GLU cc_start: 0.8803 (mm-30) cc_final: 0.8572 (mm-30) REVERT: C 441 ASP cc_start: 0.8923 (m-30) cc_final: 0.8499 (m-30) REVERT: D 30 GLN cc_start: 0.8932 (mm-40) cc_final: 0.8493 (mp10) REVERT: D 208 GLU cc_start: 0.8538 (pt0) cc_final: 0.8042 (tm-30) REVERT: E 30 GLN cc_start: 0.8660 (mp10) cc_final: 0.8272 (mp10) REVERT: E 208 GLU cc_start: 0.8394 (pt0) cc_final: 0.7983 (tm-30) REVERT: E 441 ASP cc_start: 0.8839 (m-30) cc_final: 0.8415 (m-30) REVERT: F 208 GLU cc_start: 0.8534 (pt0) cc_final: 0.8083 (tm-30) REVERT: F 235 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8504 (tt0) REVERT: F 421 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8567 (mm-30) REVERT: F 441 ASP cc_start: 0.8931 (m-30) cc_final: 0.8512 (m-30) REVERT: G 30 GLN cc_start: 0.8928 (mm-40) cc_final: 0.8485 (mp10) REVERT: G 353 LYS cc_start: 0.9292 (mptt) cc_final: 0.9091 (tptt) REVERT: H 30 GLN cc_start: 0.8694 (mp10) cc_final: 0.8266 (mp10) REVERT: H 208 GLU cc_start: 0.8460 (pt0) cc_final: 0.8076 (tm-30) REVERT: H 441 ASP cc_start: 0.8840 (m-30) cc_final: 0.8409 (m-30) REVERT: I 208 GLU cc_start: 0.8520 (pt0) cc_final: 0.8086 (tm-30) REVERT: I 421 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8558 (mm-30) REVERT: I 441 ASP cc_start: 0.8906 (m-30) cc_final: 0.8492 (m-30) REVERT: J 30 GLN cc_start: 0.8927 (mm-40) cc_final: 0.8483 (mp10) REVERT: J 208 GLU cc_start: 0.8506 (pt0) cc_final: 0.8030 (tm-30) REVERT: K 69 MET cc_start: 0.8973 (tpt) cc_final: 0.8488 (tpt) REVERT: K 208 GLU cc_start: 0.8509 (pt0) cc_final: 0.8077 (tm-30) REVERT: K 235 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8537 (tt0) REVERT: K 421 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8543 (mm-30) REVERT: K 441 ASP cc_start: 0.8924 (m-30) cc_final: 0.8512 (m-30) REVERT: L 30 GLN cc_start: 0.8681 (mp10) cc_final: 0.8248 (mp10) REVERT: L 208 GLU cc_start: 0.8404 (pt0) cc_final: 0.7988 (tm-30) REVERT: L 441 ASP cc_start: 0.8851 (m-30) cc_final: 0.8426 (m-30) outliers start: 30 outliers final: 22 residues processed: 526 average time/residue: 0.2122 time to fit residues: 192.0067 Evaluate side-chains 495 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 473 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain E residue 140 ARG Chi-restraints excluded: chain F residue 255 THR Chi-restraints excluded: chain F residue 436 THR Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 255 THR Chi-restraints excluded: chain H residue 140 ARG Chi-restraints excluded: chain I residue 205 LEU Chi-restraints excluded: chain I residue 255 THR Chi-restraints excluded: chain I residue 436 THR Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 255 THR Chi-restraints excluded: chain K residue 255 THR Chi-restraints excluded: chain K residue 436 THR Chi-restraints excluded: chain L residue 140 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 441 optimal weight: 0.9990 chunk 480 optimal weight: 6.9990 chunk 489 optimal weight: 0.8980 chunk 342 optimal weight: 4.9990 chunk 511 optimal weight: 4.9990 chunk 141 optimal weight: 7.9990 chunk 355 optimal weight: 0.9990 chunk 399 optimal weight: 7.9990 chunk 118 optimal weight: 0.7980 chunk 154 optimal weight: 4.9990 chunk 507 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 GLN ** C 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 GLN E 219 GLN E 318 ASN ** F 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 219 GLN ** I 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 202 GLN L 219 GLN L 318 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.090089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.068288 restraints weight = 88772.277| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 3.42 r_work: 0.2854 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.4730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 41628 Z= 0.150 Angle : 0.618 11.354 56304 Z= 0.299 Chirality : 0.043 0.143 6132 Planarity : 0.005 0.060 7452 Dihedral : 4.319 18.816 5628 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.62 % Allowed : 16.55 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.12), residues: 5172 helix: 2.30 (0.12), residues: 1812 sheet: 0.18 (0.15), residues: 1260 loop : -0.29 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 21 TYR 0.026 0.002 TYR D 288 PHE 0.014 0.001 PHE F 398 TRP 0.004 0.001 TRP D 58 HIS 0.003 0.001 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00351 (41628) covalent geometry : angle 0.61793 (56304) hydrogen bonds : bond 0.03347 ( 1548) hydrogen bonds : angle 4.16072 ( 4464) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 491 time to evaluate : 1.678 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLN cc_start: 0.8825 (mm-40) cc_final: 0.8452 (mp10) REVERT: A 50 PHE cc_start: 0.8257 (t80) cc_final: 0.8047 (t80) REVERT: B 30 GLN cc_start: 0.8571 (mp10) cc_final: 0.8202 (mp10) REVERT: B 208 GLU cc_start: 0.8350 (pt0) cc_final: 0.7887 (tm-30) REVERT: B 408 ILE cc_start: 0.8028 (mm) cc_final: 0.7690 (tp) REVERT: B 441 ASP cc_start: 0.8819 (m-30) cc_final: 0.8381 (m-30) REVERT: C 30 GLN cc_start: 0.8656 (mp10) cc_final: 0.7978 (mp10) REVERT: C 208 GLU cc_start: 0.8432 (pt0) cc_final: 0.7944 (tm-30) REVERT: C 235 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8557 (tt0) REVERT: C 421 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8535 (mm-30) REVERT: C 441 ASP cc_start: 0.8871 (m-30) cc_final: 0.8435 (m-30) REVERT: D 30 GLN cc_start: 0.8834 (mm-40) cc_final: 0.8465 (mp10) REVERT: D 50 PHE cc_start: 0.8265 (t80) cc_final: 0.8054 (t80) REVERT: D 208 GLU cc_start: 0.8418 (pt0) cc_final: 0.7885 (tm-30) REVERT: E 30 GLN cc_start: 0.8580 (mp10) cc_final: 0.8217 (mp10) REVERT: E 208 GLU cc_start: 0.8349 (pt0) cc_final: 0.7932 (tm-30) REVERT: E 332 MET cc_start: 0.8666 (mmt) cc_final: 0.8310 (mmt) REVERT: E 408 ILE cc_start: 0.8018 (mm) cc_final: 0.7660 (tp) REVERT: E 441 ASP cc_start: 0.8815 (m-30) cc_final: 0.8402 (m-30) REVERT: F 30 GLN cc_start: 0.8659 (mp10) cc_final: 0.7982 (mp10) REVERT: F 208 GLU cc_start: 0.8445 (pt0) cc_final: 0.7944 (tm-30) REVERT: F 235 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8531 (tt0) REVERT: F 421 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8523 (mm-30) REVERT: F 441 ASP cc_start: 0.8873 (m-30) cc_final: 0.8443 (m-30) REVERT: G 30 GLN cc_start: 0.8825 (mm-40) cc_final: 0.8449 (mp10) REVERT: G 50 PHE cc_start: 0.8265 (t80) cc_final: 0.8056 (t80) REVERT: G 353 LYS cc_start: 0.9246 (mptt) cc_final: 0.8994 (tppt) REVERT: H 30 GLN cc_start: 0.8597 (mp10) cc_final: 0.8219 (mp10) REVERT: H 208 GLU cc_start: 0.8362 (pt0) cc_final: 0.7929 (tm-30) REVERT: H 408 ILE cc_start: 0.8027 (mm) cc_final: 0.7684 (tp) REVERT: H 441 ASP cc_start: 0.8820 (m-30) cc_final: 0.8384 (m-30) REVERT: I 30 GLN cc_start: 0.8655 (mp10) cc_final: 0.7975 (mp10) REVERT: I 208 GLU cc_start: 0.8435 (pt0) cc_final: 0.7955 (tm-30) REVERT: I 235 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8554 (tt0) REVERT: I 421 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8526 (mm-30) REVERT: I 441 ASP cc_start: 0.8862 (m-30) cc_final: 0.8434 (m-30) REVERT: J 30 GLN cc_start: 0.8847 (mm-40) cc_final: 0.8452 (mp10) REVERT: J 50 PHE cc_start: 0.8262 (t80) cc_final: 0.8046 (t80) REVERT: J 208 GLU cc_start: 0.8387 (pt0) cc_final: 0.7879 (tm-30) REVERT: K 30 GLN cc_start: 0.8598 (mp10) cc_final: 0.7904 (mp10) REVERT: K 208 GLU cc_start: 0.8394 (pt0) cc_final: 0.7933 (tm-30) REVERT: K 235 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8544 (tt0) REVERT: K 421 GLU cc_start: 0.8748 (mm-30) cc_final: 0.8512 (mm-30) REVERT: K 441 ASP cc_start: 0.8872 (m-30) cc_final: 0.8443 (m-30) REVERT: L 30 GLN cc_start: 0.8591 (mp10) cc_final: 0.8209 (mp10) REVERT: L 208 GLU cc_start: 0.8355 (pt0) cc_final: 0.7933 (tm-30) REVERT: L 332 MET cc_start: 0.8653 (mmt) cc_final: 0.8297 (mmt) REVERT: L 408 ILE cc_start: 0.8017 (mm) cc_final: 0.7659 (tp) REVERT: L 441 ASP cc_start: 0.8824 (m-30) cc_final: 0.8410 (m-30) outliers start: 27 outliers final: 24 residues processed: 514 average time/residue: 0.2393 time to fit residues: 210.0766 Evaluate side-chains 506 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 482 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain B residue 327 TYR Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 327 TYR Chi-restraints excluded: chain E residue 140 ARG Chi-restraints excluded: chain F residue 255 THR Chi-restraints excluded: chain F residue 436 THR Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 255 THR Chi-restraints excluded: chain H residue 140 ARG Chi-restraints excluded: chain H residue 327 TYR Chi-restraints excluded: chain I residue 255 THR Chi-restraints excluded: chain I residue 436 THR Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 255 THR Chi-restraints excluded: chain J residue 327 TYR Chi-restraints excluded: chain K residue 255 THR Chi-restraints excluded: chain K residue 436 THR Chi-restraints excluded: chain L residue 140 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 473 optimal weight: 10.0000 chunk 5 optimal weight: 0.0170 chunk 27 optimal weight: 0.9990 chunk 50 optimal weight: 6.9990 chunk 169 optimal weight: 0.7980 chunk 442 optimal weight: 0.9990 chunk 471 optimal weight: 5.9990 chunk 510 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 377 optimal weight: 1.9990 overall best weight: 0.7422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 ASN C 310 ASN C 318 ASN D 310 ASN E 202 GLN F 310 ASN F 318 ASN G 310 ASN I 310 ASN I 318 ASN J 310 ASN K 310 ASN L 202 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.092638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.070872 restraints weight = 88379.672| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 3.43 r_work: 0.2913 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.4932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 41628 Z= 0.107 Angle : 0.586 10.999 56304 Z= 0.281 Chirality : 0.042 0.149 6132 Planarity : 0.004 0.061 7452 Dihedral : 3.969 17.664 5628 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.60 % Allowed : 16.76 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.12), residues: 5172 helix: 2.29 (0.12), residues: 1812 sheet: 0.30 (0.15), residues: 1212 loop : -0.35 (0.13), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 193 TYR 0.024 0.002 TYR D 288 PHE 0.014 0.001 PHE I 398 TRP 0.003 0.001 TRP E 58 HIS 0.003 0.001 HIS L 5 Details of bonding type rmsd covalent geometry : bond 0.00256 (41628) covalent geometry : angle 0.58621 (56304) hydrogen bonds : bond 0.02904 ( 1548) hydrogen bonds : angle 3.95247 ( 4464) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8021.53 seconds wall clock time: 138 minutes 56.91 seconds (8336.91 seconds total)