Starting phenix.real_space_refine on Tue Aug 26 05:37:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7eeq_31080/08_2025/7eeq_31080.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eeq_31080/08_2025/7eeq_31080.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7eeq_31080/08_2025/7eeq_31080.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eeq_31080/08_2025/7eeq_31080.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7eeq_31080/08_2025/7eeq_31080.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eeq_31080/08_2025/7eeq_31080.map" } resolution = 3.96 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= 0.003 sd= 0.008 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 66 5.16 5 C 21726 2.51 5 N 5682 2.21 5 O 6786 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 90 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: 34260 Number of models: 1 Model: "" Number of chains: 2 Chain: "1" Number of atoms: 3430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3430 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 14, 'TRANS': 427} Chain: "A" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 760 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Restraints were copied for chains: 2, 3, 4, 5, 6, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R Time building chain proxies: 4.31, per 1000 atoms: 0.13 Number of scatterers: 34260 At special positions: 0 Unit cell: (181.327, 195.509, 107.378, 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 66 16.00 O 6786 8.00 N 5682 7.00 C 21726 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.66 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 476.8 nanoseconds 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8088 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 118 sheets defined 2.9% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain '1' and resid 378 through 381 Processing helix chain '2' and resid 378 through 381 Processing helix chain '3' and resid 378 through 381 Processing helix chain '4' and resid 378 through 381 Processing helix chain '5' and resid 378 through 381 Processing helix chain '6' and resid 378 through 381 Processing helix chain 'A' and resid 94 through 99 removed outlier: 3.925A pdb=" N LEU A 98 " --> pdb=" O ILE A 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 99 removed outlier: 3.926A pdb=" N LEU B 98 " --> pdb=" O ILE B 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 99 removed outlier: 3.925A pdb=" N LEU C 98 " --> pdb=" O ILE C 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 99 removed outlier: 3.925A pdb=" N LEU D 98 " --> pdb=" O ILE D 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 99 removed outlier: 3.926A pdb=" N LEU E 98 " --> pdb=" O ILE E 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 99 removed outlier: 3.925A pdb=" N LEU F 98 " --> pdb=" O ILE F 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 99 removed outlier: 3.926A pdb=" N LEU G 98 " --> pdb=" O ILE G 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 99 removed outlier: 3.926A pdb=" N LEU H 98 " --> pdb=" O ILE H 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 99 removed outlier: 3.925A pdb=" N LEU I 98 " --> pdb=" O ILE I 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 99 removed outlier: 3.926A pdb=" N LEU J 98 " --> pdb=" O ILE J 94 " (cutoff:3.500A) Processing helix chain 'K' and resid 94 through 99 removed outlier: 3.926A pdb=" N LEU K 98 " --> pdb=" O ILE K 94 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 99 removed outlier: 3.926A pdb=" N LEU L 98 " --> pdb=" O ILE L 94 " (cutoff:3.500A) Processing helix chain 'M' and resid 94 through 99 removed outlier: 3.925A pdb=" N LEU M 98 " --> pdb=" O ILE M 94 " (cutoff:3.500A) Processing helix chain 'N' and resid 94 through 99 removed outlier: 3.925A pdb=" N LEU N 98 " --> pdb=" O ILE N 94 " (cutoff:3.500A) Processing helix chain 'O' and resid 94 through 99 removed outlier: 3.926A pdb=" N LEU O 98 " --> pdb=" O ILE O 94 " (cutoff:3.500A) Processing helix chain 'P' and resid 94 through 99 removed outlier: 3.925A pdb=" N LEU P 98 " --> pdb=" O ILE P 94 " (cutoff:3.500A) Processing helix chain 'Q' and resid 94 through 99 removed outlier: 3.926A pdb=" N LEU Q 98 " --> pdb=" O ILE Q 94 " (cutoff:3.500A) Processing helix chain 'R' and resid 94 through 99 removed outlier: 3.926A pdb=" N LEU R 98 " --> pdb=" O ILE R 94 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '1' and resid 26 through 29 removed outlier: 10.143A pdb=" N VAL 1 35 " --> pdb=" O ASP 1 430 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ASP 1 430 " --> pdb=" O VAL 1 35 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N THR 1 353 " --> pdb=" O SER 1 429 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N VAL 1 431 " --> pdb=" O ARG 1 351 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ARG 1 351 " --> pdb=" O VAL 1 431 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N VAL 1 401 " --> pdb=" O LEU 1 352 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '1' and resid 47 through 48 Processing sheet with id=AA3, first strand: chain '1' and resid 69 through 72 Processing sheet with id=AA4, first strand: chain '1' and resid 93 through 96 removed outlier: 3.981A pdb=" N ARG 1 93 " --> pdb=" O ASN 1 104 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR 1 110 " --> pdb=" O VAL 1 103 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '1' and resid 138 through 140 removed outlier: 3.660A pdb=" N TRP 1 147 " --> pdb=" O ALA 1 164 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '1' and resid 173 through 178 removed outlier: 3.545A pdb=" N ASP 1 175 " --> pdb=" O PHE 1 186 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '1' and resid 222 through 223 Processing sheet with id=AA8, first strand: chain '1' and resid 239 through 240 Processing sheet with id=AA9, first strand: chain '1' and resid 264 through 270 Processing sheet with id=AB1, first strand: chain '1' and resid 332 through 338 removed outlier: 3.600A pdb=" N ALA 1 337 " --> pdb=" O PHE 1 416 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LEU 1 415 " --> pdb=" O SER 1 376 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N PHE 1 375 " --> pdb=" O ASP 1 385 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ASP 1 385 " --> pdb=" O PHE 1 375 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N TYR 1 377 " --> pdb=" O TRP 1 383 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N TRP 1 383 " --> pdb=" O TYR 1 377 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '1' and resid 345 through 347 removed outlier: 3.897A pdb=" N THR 1 345 " --> pdb=" O PHE 1 409 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE 1 409 " --> pdb=" O THR 1 345 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '2' and resid 26 through 29 removed outlier: 10.144A pdb=" N VAL 2 35 " --> pdb=" O ASP 2 430 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ASP 2 430 " --> pdb=" O VAL 2 35 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N THR 2 353 " --> pdb=" O SER 2 429 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N VAL 2 431 " --> pdb=" O ARG 2 351 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ARG 2 351 " --> pdb=" O VAL 2 431 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N VAL 2 401 " --> pdb=" O LEU 2 352 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '2' and resid 47 through 48 Processing sheet with id=AB5, first strand: chain '2' and resid 69 through 72 Processing sheet with id=AB6, first strand: chain '2' and resid 93 through 96 removed outlier: 3.982A pdb=" N ARG 2 93 " --> pdb=" O ASN 2 104 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR 2 110 " --> pdb=" O VAL 2 103 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '2' and resid 138 through 140 removed outlier: 3.661A pdb=" N TRP 2 147 " --> pdb=" O ALA 2 164 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '2' and resid 173 through 178 removed outlier: 3.545A pdb=" N ASP 2 175 " --> pdb=" O PHE 2 186 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain '2' and resid 222 through 223 Processing sheet with id=AC1, first strand: chain '2' and resid 239 through 240 Processing sheet with id=AC2, first strand: chain '2' and resid 264 through 270 Processing sheet with id=AC3, first strand: chain '2' and resid 332 through 338 removed outlier: 3.600A pdb=" N ALA 2 337 " --> pdb=" O PHE 2 416 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LEU 2 415 " --> pdb=" O SER 2 376 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N PHE 2 375 " --> pdb=" O ASP 2 385 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ASP 2 385 " --> pdb=" O PHE 2 375 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N TYR 2 377 " --> pdb=" O TRP 2 383 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N TRP 2 383 " --> pdb=" O TYR 2 377 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain '2' and resid 345 through 347 removed outlier: 3.897A pdb=" N THR 2 345 " --> pdb=" O PHE 2 409 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE 2 409 " --> pdb=" O THR 2 345 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain '3' and resid 26 through 29 removed outlier: 10.144A pdb=" N VAL 3 35 " --> pdb=" O ASP 3 430 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ASP 3 430 " --> pdb=" O VAL 3 35 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N THR 3 353 " --> pdb=" O SER 3 429 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N VAL 3 431 " --> pdb=" O ARG 3 351 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ARG 3 351 " --> pdb=" O VAL 3 431 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N VAL 3 401 " --> pdb=" O LEU 3 352 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain '3' and resid 47 through 48 Processing sheet with id=AC7, first strand: chain '3' and resid 69 through 72 Processing sheet with id=AC8, first strand: chain '3' and resid 93 through 96 removed outlier: 3.982A pdb=" N ARG 3 93 " --> pdb=" O ASN 3 104 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR 3 110 " --> pdb=" O VAL 3 103 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain '3' and resid 138 through 140 removed outlier: 3.662A pdb=" N TRP 3 147 " --> pdb=" O ALA 3 164 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain '3' and resid 173 through 178 removed outlier: 3.545A pdb=" N ASP 3 175 " --> pdb=" O PHE 3 186 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain '3' and resid 222 through 223 Processing sheet with id=AD3, first strand: chain '3' and resid 239 through 240 Processing sheet with id=AD4, first strand: chain '3' and resid 264 through 270 Processing sheet with id=AD5, first strand: chain '3' and resid 332 through 338 removed outlier: 3.601A pdb=" N ALA 3 337 " --> pdb=" O PHE 3 416 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LEU 3 415 " --> pdb=" O SER 3 376 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N PHE 3 375 " --> pdb=" O ASP 3 385 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ASP 3 385 " --> pdb=" O PHE 3 375 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N TYR 3 377 " --> pdb=" O TRP 3 383 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N TRP 3 383 " --> pdb=" O TYR 3 377 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain '3' and resid 345 through 347 removed outlier: 3.897A pdb=" N THR 3 345 " --> pdb=" O PHE 3 409 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE 3 409 " --> pdb=" O THR 3 345 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain '4' and resid 26 through 29 removed outlier: 10.144A pdb=" N VAL 4 35 " --> pdb=" O ASP 4 430 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ASP 4 430 " --> pdb=" O VAL 4 35 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N THR 4 353 " --> pdb=" O SER 4 429 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N VAL 4 431 " --> pdb=" O ARG 4 351 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ARG 4 351 " --> pdb=" O VAL 4 431 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N VAL 4 401 " --> pdb=" O LEU 4 352 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain '4' and resid 47 through 48 Processing sheet with id=AD9, first strand: chain '4' and resid 69 through 72 Processing sheet with id=AE1, first strand: chain '4' and resid 93 through 96 removed outlier: 3.981A pdb=" N ARG 4 93 " --> pdb=" O ASN 4 104 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR 4 110 " --> pdb=" O VAL 4 103 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain '4' and resid 138 through 140 removed outlier: 3.661A pdb=" N TRP 4 147 " --> pdb=" O ALA 4 164 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain '4' and resid 173 through 178 removed outlier: 3.545A pdb=" N ASP 4 175 " --> pdb=" O PHE 4 186 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain '4' and resid 222 through 223 Processing sheet with id=AE5, first strand: chain '4' and resid 239 through 240 Processing sheet with id=AE6, first strand: chain '4' and resid 264 through 270 Processing sheet with id=AE7, first strand: chain '4' and resid 332 through 338 removed outlier: 3.600A pdb=" N ALA 4 337 " --> pdb=" O PHE 4 416 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LEU 4 415 " --> pdb=" O SER 4 376 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N PHE 4 375 " --> pdb=" O ASP 4 385 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ASP 4 385 " --> pdb=" O PHE 4 375 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N TYR 4 377 " --> pdb=" O TRP 4 383 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N TRP 4 383 " --> pdb=" O TYR 4 377 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain '4' and resid 345 through 347 removed outlier: 3.897A pdb=" N THR 4 345 " --> pdb=" O PHE 4 409 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE 4 409 " --> pdb=" O THR 4 345 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain '5' and resid 26 through 29 removed outlier: 10.144A pdb=" N VAL 5 35 " --> pdb=" O ASP 5 430 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ASP 5 430 " --> pdb=" O VAL 5 35 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N THR 5 353 " --> pdb=" O SER 5 429 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N VAL 5 431 " --> pdb=" O ARG 5 351 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ARG 5 351 " --> pdb=" O VAL 5 431 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N VAL 5 401 " --> pdb=" O LEU 5 352 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain '5' and resid 47 through 48 Processing sheet with id=AF2, first strand: chain '5' and resid 69 through 72 Processing sheet with id=AF3, first strand: chain '5' and resid 93 through 96 removed outlier: 3.981A pdb=" N ARG 5 93 " --> pdb=" O ASN 5 104 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR 5 110 " --> pdb=" O VAL 5 103 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain '5' and resid 138 through 140 removed outlier: 3.662A pdb=" N TRP 5 147 " --> pdb=" O ALA 5 164 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain '5' and resid 173 through 178 removed outlier: 3.544A pdb=" N ASP 5 175 " --> pdb=" O PHE 5 186 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain '5' and resid 222 through 223 Processing sheet with id=AF7, first strand: chain '5' and resid 239 through 240 Processing sheet with id=AF8, first strand: chain '5' and resid 264 through 270 Processing sheet with id=AF9, first strand: chain '5' and resid 332 through 338 removed outlier: 3.600A pdb=" N ALA 5 337 " --> pdb=" O PHE 5 416 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LEU 5 415 " --> pdb=" O SER 5 376 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N PHE 5 375 " --> pdb=" O ASP 5 385 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ASP 5 385 " --> pdb=" O PHE 5 375 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N TYR 5 377 " --> pdb=" O TRP 5 383 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N TRP 5 383 " --> pdb=" O TYR 5 377 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain '5' and resid 345 through 347 removed outlier: 3.897A pdb=" N THR 5 345 " --> pdb=" O PHE 5 409 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE 5 409 " --> pdb=" O THR 5 345 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain '6' and resid 26 through 29 removed outlier: 10.143A pdb=" N VAL 6 35 " --> pdb=" O ASP 6 430 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ASP 6 430 " --> pdb=" O VAL 6 35 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N THR 6 353 " --> pdb=" O SER 6 429 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N VAL 6 431 " --> pdb=" O ARG 6 351 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ARG 6 351 " --> pdb=" O VAL 6 431 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N VAL 6 401 " --> pdb=" O LEU 6 352 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain '6' and resid 47 through 48 Processing sheet with id=AG4, first strand: chain '6' and resid 69 through 72 Processing sheet with id=AG5, first strand: chain '6' and resid 93 through 96 removed outlier: 3.981A pdb=" N ARG 6 93 " --> pdb=" O ASN 6 104 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR 6 110 " --> pdb=" O VAL 6 103 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain '6' and resid 138 through 140 removed outlier: 3.661A pdb=" N TRP 6 147 " --> pdb=" O ALA 6 164 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain '6' and resid 173 through 178 removed outlier: 3.545A pdb=" N ASP 6 175 " --> pdb=" O PHE 6 186 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain '6' and resid 222 through 223 Processing sheet with id=AG9, first strand: chain '6' and resid 239 through 240 Processing sheet with id=AH1, first strand: chain '6' and resid 264 through 270 Processing sheet with id=AH2, first strand: chain '6' and resid 332 through 338 removed outlier: 3.600A pdb=" N ALA 6 337 " --> pdb=" O PHE 6 416 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LEU 6 415 " --> pdb=" O SER 6 376 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N PHE 6 375 " --> pdb=" O ASP 6 385 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ASP 6 385 " --> pdb=" O PHE 6 375 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N TYR 6 377 " --> pdb=" O TRP 6 383 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N TRP 6 383 " --> pdb=" O TYR 6 377 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain '6' and resid 345 through 347 removed outlier: 3.897A pdb=" N THR 6 345 " --> pdb=" O PHE 6 409 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE 6 409 " --> pdb=" O THR 6 345 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'A' and resid 3 through 5 Processing sheet with id=AH5, first strand: chain 'A' and resid 24 through 28 removed outlier: 3.627A pdb=" N PHE A 26 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG A 72 " --> pdb=" O TYR A 28 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY A 73 " --> pdb=" O ILE A 87 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'A' and resid 38 through 39 removed outlier: 4.557A pdb=" N VAL A 38 " --> pdb=" O HIS A 48 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'A' and resid 64 through 66 removed outlier: 3.572A pdb=" N GLU C 4 " --> pdb=" O PHE A 65 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'B' and resid 3 through 5 removed outlier: 3.637A pdb=" N GLU B 4 " --> pdb=" O PHE C 65 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'B' and resid 24 through 28 removed outlier: 3.627A pdb=" N PHE B 26 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG B 72 " --> pdb=" O TYR B 28 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY B 73 " --> pdb=" O ILE B 87 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'B' and resid 38 through 39 removed outlier: 4.557A pdb=" N VAL B 38 " --> pdb=" O HIS B 48 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'C' and resid 24 through 28 removed outlier: 3.626A pdb=" N PHE C 26 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG C 72 " --> pdb=" O TYR C 28 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY C 73 " --> pdb=" O ILE C 87 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'C' and resid 38 through 39 removed outlier: 4.558A pdb=" N VAL C 38 " --> pdb=" O HIS C 48 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'D' and resid 3 through 5 Processing sheet with id=AI5, first strand: chain 'D' and resid 24 through 28 removed outlier: 3.626A pdb=" N PHE D 26 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG D 72 " --> pdb=" O TYR D 28 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY D 73 " --> pdb=" O ILE D 87 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'D' and resid 38 through 39 removed outlier: 4.557A pdb=" N VAL D 38 " --> pdb=" O HIS D 48 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'D' and resid 64 through 66 removed outlier: 3.659A pdb=" N GLU F 4 " --> pdb=" O PHE D 65 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'E' and resid 3 through 5 removed outlier: 3.590A pdb=" N GLU E 4 " --> pdb=" O PHE F 65 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'E' and resid 24 through 28 removed outlier: 3.627A pdb=" N PHE E 26 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG E 72 " --> pdb=" O TYR E 28 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY E 73 " --> pdb=" O ILE E 87 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'E' and resid 38 through 39 removed outlier: 4.557A pdb=" N VAL E 38 " --> pdb=" O HIS E 48 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'F' and resid 24 through 28 removed outlier: 3.626A pdb=" N PHE F 26 " --> pdb=" O VAL F 74 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG F 72 " --> pdb=" O TYR F 28 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY F 73 " --> pdb=" O ILE F 87 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'F' and resid 38 through 39 removed outlier: 4.557A pdb=" N VAL F 38 " --> pdb=" O HIS F 48 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'G' and resid 3 through 5 removed outlier: 3.573A pdb=" N GLU G 4 " --> pdb=" O PHE H 65 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'G' and resid 24 through 28 removed outlier: 3.627A pdb=" N PHE G 26 " --> pdb=" O VAL G 74 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG G 72 " --> pdb=" O TYR G 28 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY G 73 " --> pdb=" O ILE G 87 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'G' and resid 38 through 39 removed outlier: 4.557A pdb=" N VAL G 38 " --> pdb=" O HIS G 48 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'G' and resid 64 through 66 removed outlier: 3.538A pdb=" N GLU I 4 " --> pdb=" O PHE G 65 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.738A pdb=" N GLU H 4 " --> pdb=" O PHE I 65 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'H' and resid 24 through 28 removed outlier: 3.626A pdb=" N PHE H 26 " --> pdb=" O VAL H 74 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG H 72 " --> pdb=" O TYR H 28 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY H 73 " --> pdb=" O ILE H 87 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'H' and resid 38 through 39 removed outlier: 4.557A pdb=" N VAL H 38 " --> pdb=" O HIS H 48 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'I' and resid 24 through 28 removed outlier: 3.627A pdb=" N PHE I 26 " --> pdb=" O VAL I 74 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG I 72 " --> pdb=" O TYR I 28 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY I 73 " --> pdb=" O ILE I 87 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'I' and resid 38 through 39 removed outlier: 4.557A pdb=" N VAL I 38 " --> pdb=" O HIS I 48 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'J' and resid 3 through 5 removed outlier: 3.555A pdb=" N GLU J 4 " --> pdb=" O PHE K 65 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'J' and resid 24 through 28 removed outlier: 3.627A pdb=" N PHE J 26 " --> pdb=" O VAL J 74 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG J 72 " --> pdb=" O TYR J 28 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY J 73 " --> pdb=" O ILE J 87 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'J' and resid 38 through 39 removed outlier: 4.556A pdb=" N VAL J 38 " --> pdb=" O HIS J 48 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'J' and resid 64 through 66 removed outlier: 3.641A pdb=" N GLU L 4 " --> pdb=" O PHE J 65 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'K' and resid 3 through 5 removed outlier: 3.738A pdb=" N GLU K 4 " --> pdb=" O PHE L 65 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'K' and resid 24 through 28 removed outlier: 3.627A pdb=" N PHE K 26 " --> pdb=" O VAL K 74 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG K 72 " --> pdb=" O TYR K 28 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY K 73 " --> pdb=" O ILE K 87 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'K' and resid 38 through 39 removed outlier: 4.557A pdb=" N VAL K 38 " --> pdb=" O HIS K 48 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'L' and resid 24 through 28 removed outlier: 3.627A pdb=" N PHE L 26 " --> pdb=" O VAL L 74 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG L 72 " --> pdb=" O TYR L 28 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY L 73 " --> pdb=" O ILE L 87 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'L' and resid 38 through 39 removed outlier: 4.557A pdb=" N VAL L 38 " --> pdb=" O HIS L 48 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'M' and resid 24 through 28 removed outlier: 3.627A pdb=" N PHE M 26 " --> pdb=" O VAL M 74 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG M 72 " --> pdb=" O TYR M 28 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY M 73 " --> pdb=" O ILE M 87 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'M' and resid 38 through 39 removed outlier: 4.557A pdb=" N VAL M 38 " --> pdb=" O HIS M 48 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'M' and resid 64 through 66 removed outlier: 3.670A pdb=" N GLU O 4 " --> pdb=" O PHE M 65 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'N' and resid 24 through 28 removed outlier: 3.626A pdb=" N PHE N 26 " --> pdb=" O VAL N 74 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG N 72 " --> pdb=" O TYR N 28 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY N 73 " --> pdb=" O ILE N 87 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'N' and resid 38 through 39 removed outlier: 4.557A pdb=" N VAL N 38 " --> pdb=" O HIS N 48 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'O' and resid 24 through 28 removed outlier: 3.627A pdb=" N PHE O 26 " --> pdb=" O VAL O 74 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG O 72 " --> pdb=" O TYR O 28 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY O 73 " --> pdb=" O ILE O 87 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'O' and resid 38 through 39 removed outlier: 4.556A pdb=" N VAL O 38 " --> pdb=" O HIS O 48 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'P' and resid 3 through 5 removed outlier: 3.601A pdb=" N GLU P 4 " --> pdb=" O PHE Q 65 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'P' and resid 24 through 28 removed outlier: 3.627A pdb=" N PHE P 26 " --> pdb=" O VAL P 74 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG P 72 " --> pdb=" O TYR P 28 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY P 73 " --> pdb=" O ILE P 87 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'P' and resid 38 through 39 removed outlier: 4.557A pdb=" N VAL P 38 " --> pdb=" O HIS P 48 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'P' and resid 64 through 66 removed outlier: 3.547A pdb=" N GLU R 4 " --> pdb=" O PHE P 65 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'Q' and resid 3 through 5 removed outlier: 3.703A pdb=" N GLU Q 4 " --> pdb=" O PHE R 65 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'Q' and resid 24 through 28 removed outlier: 3.627A pdb=" N PHE Q 26 " --> pdb=" O VAL Q 74 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG Q 72 " --> pdb=" O TYR Q 28 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY Q 73 " --> pdb=" O ILE Q 87 " (cutoff:3.500A) Processing sheet with id=AM8, first strand: chain 'Q' and resid 38 through 39 removed outlier: 4.557A pdb=" N VAL Q 38 " --> pdb=" O HIS Q 48 " (cutoff:3.500A) Processing sheet with id=AM9, first strand: chain 'R' and resid 24 through 28 removed outlier: 3.627A pdb=" N PHE R 26 " --> pdb=" O VAL R 74 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG R 72 " --> pdb=" O TYR R 28 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY R 73 " --> pdb=" O ILE R 87 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'R' and resid 38 through 39 removed outlier: 4.557A pdb=" N VAL R 38 " --> pdb=" O HIS R 48 " (cutoff:3.500A) 522 hydrogen bonds defined for protein. 1296 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.36 Time building geometry restraints manager: 3.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11015 1.34 - 1.45: 6155 1.45 - 1.57: 17774 1.57 - 1.69: 0 1.69 - 1.81: 108 Bond restraints: 35052 Sorted by residual: bond pdb=" C ASP P 88 " pdb=" N PRO P 89 " ideal model delta sigma weight residual 1.334 1.381 -0.047 2.34e-02 1.83e+03 4.02e+00 bond pdb=" C ASP A 88 " pdb=" N PRO A 89 " ideal model delta sigma weight residual 1.334 1.380 -0.046 2.34e-02 1.83e+03 3.94e+00 bond pdb=" C ASP J 88 " pdb=" N PRO J 89 " ideal model delta sigma weight residual 1.334 1.380 -0.046 2.34e-02 1.83e+03 3.91e+00 bond pdb=" C ASP C 88 " pdb=" N PRO C 89 " ideal model delta sigma weight residual 1.334 1.380 -0.046 2.34e-02 1.83e+03 3.89e+00 bond pdb=" C ASP F 88 " pdb=" N PRO F 89 " ideal model delta sigma weight residual 1.334 1.380 -0.046 2.34e-02 1.83e+03 3.88e+00 ... (remaining 35047 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 46197 2.41 - 4.83: 1406 4.83 - 7.24: 125 7.24 - 9.65: 55 9.65 - 12.06: 7 Bond angle restraints: 47790 Sorted by residual: angle pdb=" C TYR 3 325 " pdb=" N ASP 3 326 " pdb=" CA ASP 3 326 " ideal model delta sigma weight residual 122.46 130.78 -8.32 1.41e+00 5.03e-01 3.49e+01 angle pdb=" C TYR 6 325 " pdb=" N ASP 6 326 " pdb=" CA ASP 6 326 " ideal model delta sigma weight residual 122.46 130.78 -8.32 1.41e+00 5.03e-01 3.48e+01 angle pdb=" C TYR 1 325 " pdb=" N ASP 1 326 " pdb=" CA ASP 1 326 " ideal model delta sigma weight residual 122.46 130.78 -8.32 1.41e+00 5.03e-01 3.48e+01 angle pdb=" C TYR 4 325 " pdb=" N ASP 4 326 " pdb=" CA ASP 4 326 " ideal model delta sigma weight residual 122.46 130.75 -8.29 1.41e+00 5.03e-01 3.46e+01 angle pdb=" C TYR 5 325 " pdb=" N ASP 5 326 " pdb=" CA ASP 5 326 " ideal model delta sigma weight residual 122.46 130.75 -8.29 1.41e+00 5.03e-01 3.46e+01 ... (remaining 47785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.90: 18864 14.90 - 29.79: 1056 29.79 - 44.69: 246 44.69 - 59.58: 6 59.58 - 74.48: 24 Dihedral angle restraints: 20196 sinusoidal: 7458 harmonic: 12738 Sorted by residual: dihedral pdb=" CA PHE 4 76 " pdb=" C PHE 4 76 " pdb=" N TYR 4 77 " pdb=" CA TYR 4 77 " ideal model delta harmonic sigma weight residual 180.00 152.99 27.01 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA PHE 5 76 " pdb=" C PHE 5 76 " pdb=" N TYR 5 77 " pdb=" CA TYR 5 77 " ideal model delta harmonic sigma weight residual 180.00 153.00 27.00 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA PHE 1 76 " pdb=" C PHE 1 76 " pdb=" N TYR 1 77 " pdb=" CA TYR 1 77 " ideal model delta harmonic sigma weight residual 180.00 153.01 26.99 0 5.00e+00 4.00e-02 2.91e+01 ... (remaining 20193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 3414 0.046 - 0.091: 1415 0.091 - 0.137: 409 0.137 - 0.182: 72 0.182 - 0.228: 54 Chirality restraints: 5364 Sorted by residual: chirality pdb=" CA ASP 5 326 " pdb=" N ASP 5 326 " pdb=" C ASP 5 326 " pdb=" CB ASP 5 326 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA ASP 2 326 " pdb=" N ASP 2 326 " pdb=" C ASP 2 326 " pdb=" CB ASP 2 326 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA ASP 4 326 " pdb=" N ASP 4 326 " pdb=" C ASP 4 326 " pdb=" CB ASP 4 326 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 5361 not shown) Planarity restraints: 6240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP 5 411 " 0.041 5.00e-02 4.00e+02 6.24e-02 6.22e+00 pdb=" N PRO 5 412 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO 5 412 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO 5 412 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP 3 411 " 0.041 5.00e-02 4.00e+02 6.24e-02 6.22e+00 pdb=" N PRO 3 412 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO 3 412 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO 3 412 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP 2 411 " -0.041 5.00e-02 4.00e+02 6.23e-02 6.22e+00 pdb=" N PRO 2 412 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO 2 412 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO 2 412 " -0.034 5.00e-02 4.00e+02 ... (remaining 6237 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 10973 2.83 - 3.35: 27640 3.35 - 3.87: 55008 3.87 - 4.38: 61203 4.38 - 4.90: 107921 Nonbonded interactions: 262745 Sorted by model distance: nonbonded pdb=" OG SER 6 30 " pdb=" O GLN 6 33 " model vdw 2.316 3.040 nonbonded pdb=" OG SER 2 30 " pdb=" O GLN 2 33 " model vdw 2.316 3.040 nonbonded pdb=" OG SER 5 30 " pdb=" O GLN 5 33 " model vdw 2.316 3.040 nonbonded pdb=" OG SER 1 30 " pdb=" O GLN 1 33 " model vdw 2.317 3.040 nonbonded pdb=" OG SER 4 30 " pdb=" O GLN 4 33 " model vdw 2.317 3.040 ... (remaining 262740 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: 0.09 Found NCS groups: ncs_group { reference = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' } 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' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 28.010 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 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 : 0.006 0.067 35052 Z= 0.253 Angle : 0.978 12.064 47790 Z= 0.540 Chirality : 0.056 0.228 5364 Planarity : 0.008 0.062 6240 Dihedral : 10.423 74.481 12108 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.03 % Favored : 87.97 % Rotamer: Outliers : 0.17 % Allowed : 3.53 % Favored : 96.30 % 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: -4.80 (0.09), residues: 4440 helix: -5.17 (0.07), residues: 168 sheet: -3.01 (0.15), residues: 852 loop : -3.43 (0.08), residues: 3420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG 3 400 TYR 0.017 0.003 TYR 3 239 PHE 0.035 0.003 PHE 1 76 TRP 0.023 0.004 TRP O 25 HIS 0.005 0.002 HIS 4 285 Details of bonding type rmsd covalent geometry : bond 0.00569 (35052) covalent geometry : angle 0.97834 (47790) hydrogen bonds : bond 0.32483 ( 522) hydrogen bonds : angle 10.26873 ( 1296) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 378 time to evaluate : 0.967 Fit side-chains REVERT: A 74 VAL cc_start: 0.7939 (m) cc_final: 0.7485 (p) REVERT: A 85 TYR cc_start: 0.6583 (m-80) cc_final: 0.6333 (m-80) REVERT: B 1 MET cc_start: 0.2909 (mtp) cc_final: 0.2640 (mtt) REVERT: B 97 VAL cc_start: 0.4316 (t) cc_final: 0.3944 (p) REVERT: C 38 VAL cc_start: 0.7896 (t) cc_final: 0.7694 (m) REVERT: D 74 VAL cc_start: 0.7937 (m) cc_final: 0.7510 (p) REVERT: E 1 MET cc_start: 0.3277 (mtp) cc_final: 0.2791 (mtt) REVERT: E 97 VAL cc_start: 0.3936 (t) cc_final: 0.3514 (p) REVERT: F 14 SER cc_start: 0.7518 (p) cc_final: 0.7305 (t) REVERT: F 86 ASP cc_start: 0.7784 (t0) cc_final: 0.7518 (t70) REVERT: G 74 VAL cc_start: 0.8109 (m) cc_final: 0.7737 (p) REVERT: H 1 MET cc_start: 0.2622 (mtp) cc_final: 0.2231 (mtt) REVERT: H 97 VAL cc_start: 0.4006 (t) cc_final: 0.3719 (p) REVERT: I 55 ASP cc_start: 0.7628 (m-30) cc_final: 0.7407 (m-30) REVERT: I 91 ASN cc_start: 0.6760 (t0) cc_final: 0.6481 (t0) REVERT: J 66 ASP cc_start: 0.6470 (t0) cc_final: 0.6214 (t0) REVERT: J 74 VAL cc_start: 0.8108 (m) cc_final: 0.7675 (p) REVERT: K 5 LEU cc_start: 0.8189 (tt) cc_final: 0.7823 (tp) REVERT: K 97 VAL cc_start: 0.4367 (t) cc_final: 0.4026 (p) REVERT: L 14 SER cc_start: 0.7824 (p) cc_final: 0.7571 (t) REVERT: L 86 ASP cc_start: 0.7720 (t0) cc_final: 0.7467 (t0) REVERT: M 74 VAL cc_start: 0.8105 (m) cc_final: 0.7710 (p) REVERT: N 1 MET cc_start: 0.3379 (mtp) cc_final: 0.2866 (mtt) REVERT: N 97 VAL cc_start: 0.3650 (t) cc_final: 0.3358 (p) REVERT: O 87 ILE cc_start: 0.8757 (mp) cc_final: 0.8441 (mt) REVERT: O 91 ASN cc_start: 0.6178 (t0) cc_final: 0.5785 (t0) REVERT: P 74 VAL cc_start: 0.8056 (m) cc_final: 0.7666 (p) REVERT: Q 1 MET cc_start: 0.2714 (mtp) cc_final: 0.2255 (mtt) REVERT: Q 97 VAL cc_start: 0.4117 (t) cc_final: 0.3839 (p) REVERT: R 86 ASP cc_start: 0.7758 (t0) cc_final: 0.6766 (p0) REVERT: R 91 ASN cc_start: 0.6574 (t0) cc_final: 0.6279 (t0) outliers start: 6 outliers final: 0 residues processed: 384 average time/residue: 0.1778 time to fit residues: 118.7221 Evaluate side-chains 174 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 432 optimal weight: 20.0000 chunk 197 optimal weight: 8.9990 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 7.9990 chunk 401 optimal weight: 6.9990 chunk 424 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 33 GLN 1 246 GLN 1 285 HIS 1 417 GLN 2 33 GLN 2 246 GLN 2 285 HIS ** 2 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 33 GLN 3 246 GLN 3 285 HIS ** 3 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 33 GLN ** 4 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 285 HIS ** 4 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 33 GLN 5 246 GLN 5 285 HIS 5 417 GLN 6 246 GLN 6 285 HIS ** 6 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 HIS C 36 GLN F 6 HIS F 19 ASN F 91 ASN I 6 HIS L 6 HIS L 19 ASN L 36 GLN O 6 HIS O 19 ASN R 6 HIS Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.061044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.053940 restraints weight = 179625.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.054789 restraints weight = 111822.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.055388 restraints weight = 77895.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.055821 restraints weight = 58806.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.056075 restraints weight = 46992.896| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 35052 Z= 0.225 Angle : 0.749 9.706 47790 Z= 0.389 Chirality : 0.048 0.162 5364 Planarity : 0.006 0.049 6240 Dihedral : 6.399 27.801 4842 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.38 % Favored : 89.62 % Rotamer: Outliers : 1.32 % Allowed : 8.32 % Favored : 90.36 % 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: -4.32 (0.10), residues: 4440 helix: -4.98 (0.09), residues: 150 sheet: -2.52 (0.14), residues: 954 loop : -3.13 (0.09), residues: 3336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG 6 224 TYR 0.018 0.002 TYR G 39 PHE 0.025 0.002 PHE 1 76 TRP 0.026 0.002 TRP 5 320 HIS 0.006 0.002 HIS H 6 Details of bonding type rmsd covalent geometry : bond 0.00540 (35052) covalent geometry : angle 0.74912 (47790) hydrogen bonds : bond 0.05092 ( 522) hydrogen bonds : angle 6.50347 ( 1296) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 193 time to evaluate : 1.287 Fit side-chains REVERT: A 85 TYR cc_start: 0.6737 (m-80) cc_final: 0.6443 (m-80) REVERT: B 1 MET cc_start: 0.2430 (mtp) cc_final: 0.2051 (mtm) REVERT: C 24 LYS cc_start: 0.8287 (mtmm) cc_final: 0.7822 (mppt) REVERT: C 66 ASP cc_start: 0.6701 (m-30) cc_final: 0.6432 (m-30) REVERT: C 86 ASP cc_start: 0.7799 (t0) cc_final: 0.6953 (p0) REVERT: E 1 MET cc_start: 0.2746 (mtp) cc_final: 0.2061 (mtt) REVERT: E 95 LEU cc_start: 0.6639 (mt) cc_final: 0.6423 (mp) REVERT: F 86 ASP cc_start: 0.7713 (t0) cc_final: 0.7145 (p0) REVERT: F 91 ASN cc_start: 0.6746 (OUTLIER) cc_final: 0.5907 (t0) REVERT: H 1 MET cc_start: 0.2205 (mtp) cc_final: 0.1546 (mtt) REVERT: H 95 LEU cc_start: 0.6822 (mt) cc_final: 0.6484 (mp) REVERT: I 86 ASP cc_start: 0.7732 (t0) cc_final: 0.6836 (p0) REVERT: I 91 ASN cc_start: 0.6999 (t0) cc_final: 0.6513 (t0) REVERT: L 14 SER cc_start: 0.7659 (p) cc_final: 0.7312 (t) REVERT: L 24 LYS cc_start: 0.8311 (mtmm) cc_final: 0.7884 (mppt) REVERT: L 66 ASP cc_start: 0.6849 (m-30) cc_final: 0.6597 (m-30) REVERT: L 86 ASP cc_start: 0.7780 (t0) cc_final: 0.7326 (p0) REVERT: N 1 MET cc_start: 0.3123 (mtp) cc_final: 0.2492 (mtt) REVERT: N 97 VAL cc_start: 0.4175 (t) cc_final: 0.3969 (p) REVERT: O 86 ASP cc_start: 0.7720 (t70) cc_final: 0.6698 (p0) REVERT: O 91 ASN cc_start: 0.6752 (t0) cc_final: 0.6400 (t0) REVERT: P 69 LEU cc_start: 0.6920 (OUTLIER) cc_final: 0.6697 (pp) REVERT: R 86 ASP cc_start: 0.7697 (t0) cc_final: 0.7392 (p0) REVERT: R 91 ASN cc_start: 0.6908 (t0) cc_final: 0.6391 (t0) outliers start: 47 outliers final: 17 residues processed: 231 average time/residue: 0.1814 time to fit residues: 75.5576 Evaluate side-chains 185 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 166 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 130 ILE Chi-restraints excluded: chain 1 residue 320 TRP Chi-restraints excluded: chain 2 residue 130 ILE Chi-restraints excluded: chain 2 residue 320 TRP Chi-restraints excluded: chain 3 residue 130 ILE Chi-restraints excluded: chain 3 residue 320 TRP Chi-restraints excluded: chain 4 residue 130 ILE Chi-restraints excluded: chain 4 residue 320 TRP Chi-restraints excluded: chain 5 residue 130 ILE Chi-restraints excluded: chain 5 residue 320 TRP Chi-restraints excluded: chain 6 residue 130 ILE Chi-restraints excluded: chain 6 residue 320 TRP Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain F residue 91 ASN Chi-restraints excluded: chain I residue 15 SER Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain P residue 69 LEU Chi-restraints excluded: chain R residue 15 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 79 optimal weight: 6.9990 chunk 295 optimal weight: 20.0000 chunk 363 optimal weight: 20.0000 chunk 282 optimal weight: 6.9990 chunk 440 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 250 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 168 optimal weight: 9.9990 chunk 391 optimal weight: 6.9990 chunk 146 optimal weight: 20.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 417 GLN 3 417 GLN ** 4 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 417 GLN 6 417 GLN C 19 ASN F 91 ASN P 36 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.061588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.054501 restraints weight = 178569.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.055334 restraints weight = 111174.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.055953 restraints weight = 77631.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.056393 restraints weight = 58460.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.056685 restraints weight = 46444.615| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 35052 Z= 0.134 Angle : 0.621 7.515 47790 Z= 0.323 Chirality : 0.045 0.246 5364 Planarity : 0.005 0.040 6240 Dihedral : 5.607 24.975 4842 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 1.76 % Allowed : 9.16 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.92 (0.11), residues: 4440 helix: -4.93 (0.09), residues: 150 sheet: -1.96 (0.15), residues: 966 loop : -2.92 (0.09), residues: 3324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 1 427 TYR 0.013 0.001 TYR Q 39 PHE 0.013 0.001 PHE I 65 TRP 0.020 0.002 TRP 1 320 HIS 0.004 0.001 HIS H 48 Details of bonding type rmsd covalent geometry : bond 0.00315 (35052) covalent geometry : angle 0.62052 (47790) hydrogen bonds : bond 0.04254 ( 522) hydrogen bonds : angle 6.13038 ( 1296) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 185 time to evaluate : 1.378 Fit side-chains REVERT: 2 336 MET cc_start: 0.7837 (mmt) cc_final: 0.7240 (mmt) REVERT: 3 373 MET cc_start: 0.8656 (ptm) cc_final: 0.8298 (tmm) REVERT: 3 442 ARG cc_start: 0.6330 (OUTLIER) cc_final: 0.6091 (ppp80) REVERT: 6 373 MET cc_start: 0.8675 (ptm) cc_final: 0.8333 (tmm) REVERT: 6 442 ARG cc_start: 0.6323 (OUTLIER) cc_final: 0.6055 (ppp80) REVERT: B 1 MET cc_start: 0.2367 (mtp) cc_final: 0.1829 (mtt) REVERT: B 69 LEU cc_start: 0.7219 (OUTLIER) cc_final: 0.7002 (pp) REVERT: B 95 LEU cc_start: 0.6992 (mm) cc_final: 0.6565 (mp) REVERT: C 24 LYS cc_start: 0.8316 (mtmm) cc_final: 0.8062 (mppt) REVERT: C 66 ASP cc_start: 0.6931 (m-30) cc_final: 0.6679 (m-30) REVERT: C 86 ASP cc_start: 0.7711 (t0) cc_final: 0.7027 (p0) REVERT: E 1 MET cc_start: 0.3121 (mtp) cc_final: 0.2365 (mtt) REVERT: E 95 LEU cc_start: 0.6751 (mt) cc_final: 0.6487 (mp) REVERT: F 86 ASP cc_start: 0.7744 (t0) cc_final: 0.7197 (p0) REVERT: G 75 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.6759 (tp) REVERT: H 95 LEU cc_start: 0.6798 (mt) cc_final: 0.6412 (mp) REVERT: I 86 ASP cc_start: 0.7658 (t0) cc_final: 0.6871 (p0) REVERT: J 75 LEU cc_start: 0.7429 (OUTLIER) cc_final: 0.6719 (tp) REVERT: K 95 LEU cc_start: 0.6404 (mt) cc_final: 0.6053 (mp) REVERT: L 24 LYS cc_start: 0.8398 (mtmm) cc_final: 0.8194 (mppt) REVERT: L 86 ASP cc_start: 0.7657 (t0) cc_final: 0.7336 (p0) REVERT: N 1 MET cc_start: 0.3172 (mtp) cc_final: 0.2474 (mtt) REVERT: N 95 LEU cc_start: 0.6154 (mt) cc_final: 0.5832 (mp) REVERT: O 86 ASP cc_start: 0.7697 (t70) cc_final: 0.6764 (p0) REVERT: O 91 ASN cc_start: 0.7013 (t0) cc_final: 0.6722 (t0) REVERT: P 75 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.6680 (tp) REVERT: Q 95 LEU cc_start: 0.6831 (mt) cc_final: 0.6414 (mp) REVERT: R 86 ASP cc_start: 0.7766 (t0) cc_final: 0.7417 (p0) REVERT: R 91 ASN cc_start: 0.7089 (t0) cc_final: 0.6523 (t0) outliers start: 63 outliers final: 24 residues processed: 238 average time/residue: 0.1884 time to fit residues: 79.0076 Evaluate side-chains 189 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 159 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 76 PHE Chi-restraints excluded: chain 1 residue 130 ILE Chi-restraints excluded: chain 1 residue 320 TRP Chi-restraints excluded: chain 2 residue 76 PHE Chi-restraints excluded: chain 2 residue 130 ILE Chi-restraints excluded: chain 2 residue 320 TRP Chi-restraints excluded: chain 3 residue 76 PHE Chi-restraints excluded: chain 3 residue 130 ILE Chi-restraints excluded: chain 3 residue 320 TRP Chi-restraints excluded: chain 3 residue 442 ARG Chi-restraints excluded: chain 4 residue 76 PHE Chi-restraints excluded: chain 4 residue 130 ILE Chi-restraints excluded: chain 4 residue 320 TRP Chi-restraints excluded: chain 5 residue 76 PHE Chi-restraints excluded: chain 5 residue 130 ILE Chi-restraints excluded: chain 5 residue 320 TRP Chi-restraints excluded: chain 6 residue 76 PHE Chi-restraints excluded: chain 6 residue 130 ILE Chi-restraints excluded: chain 6 residue 320 TRP Chi-restraints excluded: chain 6 residue 442 ARG Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain P residue 75 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 71 optimal weight: 5.9990 chunk 128 optimal weight: 10.0000 chunk 97 optimal weight: 20.0000 chunk 164 optimal weight: 8.9990 chunk 299 optimal weight: 6.9990 chunk 405 optimal weight: 40.0000 chunk 409 optimal weight: 10.0000 chunk 6 optimal weight: 0.5980 chunk 356 optimal weight: 0.8980 chunk 22 optimal weight: 8.9990 chunk 220 optimal weight: 20.0000 overall best weight: 4.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 246 GLN E 6 HIS H 6 HIS I 91 ASN N 6 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.061094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.054060 restraints weight = 178924.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.054881 restraints weight = 113152.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.055493 restraints weight = 79939.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.055890 restraints weight = 60399.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.056166 restraints weight = 48962.489| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 35052 Z= 0.157 Angle : 0.629 7.351 47790 Z= 0.328 Chirality : 0.045 0.202 5364 Planarity : 0.005 0.038 6240 Dihedral : 5.557 25.760 4842 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.07 % Favored : 89.93 % Rotamer: Outliers : 2.58 % Allowed : 10.06 % Favored : 87.37 % 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: -3.57 (0.11), residues: 4440 helix: -5.50 (0.13), residues: 42 sheet: -1.86 (0.15), residues: 996 loop : -2.71 (0.09), residues: 3402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 6 224 TYR 0.012 0.002 TYR H 28 PHE 0.016 0.002 PHE I 65 TRP 0.025 0.002 TRP 4 320 HIS 0.005 0.001 HIS B 6 Details of bonding type rmsd covalent geometry : bond 0.00373 (35052) covalent geometry : angle 0.62919 (47790) hydrogen bonds : bond 0.03847 ( 522) hydrogen bonds : angle 5.84084 ( 1296) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 171 time to evaluate : 1.393 Fit side-chains REVERT: 2 422 ASP cc_start: 0.7955 (OUTLIER) cc_final: 0.7428 (m-30) REVERT: 2 442 ARG cc_start: 0.6299 (OUTLIER) cc_final: 0.6072 (ppp80) REVERT: 3 442 ARG cc_start: 0.6329 (OUTLIER) cc_final: 0.6049 (ppp80) REVERT: 5 422 ASP cc_start: 0.8013 (OUTLIER) cc_final: 0.7484 (m-30) REVERT: 5 442 ARG cc_start: 0.6296 (OUTLIER) cc_final: 0.6069 (ppp80) REVERT: 6 442 ARG cc_start: 0.6303 (OUTLIER) cc_final: 0.5989 (ppp80) REVERT: B 69 LEU cc_start: 0.7261 (OUTLIER) cc_final: 0.7046 (pp) REVERT: B 95 LEU cc_start: 0.7231 (mm) cc_final: 0.6773 (mp) REVERT: C 66 ASP cc_start: 0.7024 (m-30) cc_final: 0.6767 (m-30) REVERT: C 86 ASP cc_start: 0.7707 (t0) cc_final: 0.7243 (p0) REVERT: E 1 MET cc_start: 0.2841 (mtp) cc_final: 0.2176 (mtt) REVERT: E 69 LEU cc_start: 0.6934 (OUTLIER) cc_final: 0.6715 (pp) REVERT: E 95 LEU cc_start: 0.6587 (mt) cc_final: 0.6266 (tp) REVERT: F 86 ASP cc_start: 0.7715 (t0) cc_final: 0.7379 (p0) REVERT: G 75 LEU cc_start: 0.7424 (OUTLIER) cc_final: 0.6634 (tp) REVERT: H 69 LEU cc_start: 0.6735 (OUTLIER) cc_final: 0.6510 (pp) REVERT: H 95 LEU cc_start: 0.6680 (mt) cc_final: 0.6369 (tp) REVERT: I 86 ASP cc_start: 0.7650 (t0) cc_final: 0.7027 (p0) REVERT: I 91 ASN cc_start: 0.6868 (OUTLIER) cc_final: 0.6166 (t0) REVERT: J 75 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.6666 (tp) REVERT: K 95 LEU cc_start: 0.6749 (mt) cc_final: 0.6313 (mp) REVERT: L 86 ASP cc_start: 0.7626 (t0) cc_final: 0.7361 (p0) REVERT: N 1 MET cc_start: 0.2868 (mtp) cc_final: 0.2119 (mtt) REVERT: N 69 LEU cc_start: 0.7003 (OUTLIER) cc_final: 0.6788 (pp) REVERT: N 95 LEU cc_start: 0.6459 (mt) cc_final: 0.6131 (tp) REVERT: O 86 ASP cc_start: 0.7748 (t70) cc_final: 0.6921 (p0) REVERT: O 91 ASN cc_start: 0.7203 (t0) cc_final: 0.6957 (t0) REVERT: P 69 LEU cc_start: 0.6690 (OUTLIER) cc_final: 0.6479 (pp) REVERT: P 75 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.6591 (tp) REVERT: Q 95 LEU cc_start: 0.6917 (mt) cc_final: 0.6495 (mp) REVERT: R 86 ASP cc_start: 0.7782 (t0) cc_final: 0.7543 (p0) outliers start: 92 outliers final: 51 residues processed: 251 average time/residue: 0.1884 time to fit residues: 83.8866 Evaluate side-chains 222 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 156 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 76 PHE Chi-restraints excluded: chain 1 residue 83 LEU Chi-restraints excluded: chain 1 residue 129 THR Chi-restraints excluded: chain 1 residue 130 ILE Chi-restraints excluded: chain 1 residue 320 TRP Chi-restraints excluded: chain 2 residue 76 PHE Chi-restraints excluded: chain 2 residue 83 LEU Chi-restraints excluded: chain 2 residue 129 THR Chi-restraints excluded: chain 2 residue 130 ILE Chi-restraints excluded: chain 2 residue 320 TRP Chi-restraints excluded: chain 2 residue 422 ASP Chi-restraints excluded: chain 2 residue 442 ARG Chi-restraints excluded: chain 3 residue 76 PHE Chi-restraints excluded: chain 3 residue 83 LEU Chi-restraints excluded: chain 3 residue 129 THR Chi-restraints excluded: chain 3 residue 130 ILE Chi-restraints excluded: chain 3 residue 320 TRP Chi-restraints excluded: chain 3 residue 442 ARG Chi-restraints excluded: chain 4 residue 76 PHE Chi-restraints excluded: chain 4 residue 83 LEU Chi-restraints excluded: chain 4 residue 129 THR Chi-restraints excluded: chain 4 residue 130 ILE Chi-restraints excluded: chain 4 residue 320 TRP Chi-restraints excluded: chain 5 residue 76 PHE Chi-restraints excluded: chain 5 residue 83 LEU Chi-restraints excluded: chain 5 residue 130 ILE Chi-restraints excluded: chain 5 residue 320 TRP Chi-restraints excluded: chain 5 residue 422 ASP Chi-restraints excluded: chain 5 residue 442 ARG Chi-restraints excluded: chain 6 residue 76 PHE Chi-restraints excluded: chain 6 residue 83 LEU Chi-restraints excluded: chain 6 residue 129 THR Chi-restraints excluded: chain 6 residue 130 ILE Chi-restraints excluded: chain 6 residue 171 ASP Chi-restraints excluded: chain 6 residue 320 TRP Chi-restraints excluded: chain 6 residue 442 ARG Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 91 ASN Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain L residue 18 LEU Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 52 VAL Chi-restraints excluded: chain O residue 69 LEU Chi-restraints excluded: chain P residue 69 LEU Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 97 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 255 optimal weight: 10.0000 chunk 190 optimal weight: 20.0000 chunk 375 optimal weight: 10.0000 chunk 379 optimal weight: 0.9990 chunk 67 optimal weight: 9.9990 chunk 380 optimal weight: 0.4980 chunk 176 optimal weight: 20.0000 chunk 203 optimal weight: 7.9990 chunk 302 optimal weight: 9.9990 chunk 343 optimal weight: 30.0000 chunk 97 optimal weight: 20.0000 overall best weight: 5.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 19 ASN C 91 ASN K 91 ASN L 91 ASN Q 6 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.063879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.057238 restraints weight = 167265.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.057914 restraints weight = 121979.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.058533 restraints weight = 85254.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.058472 restraints weight = 68863.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.058603 restraints weight = 62208.707| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 35052 Z= 0.178 Angle : 0.653 7.631 47790 Z= 0.340 Chirality : 0.046 0.169 5364 Planarity : 0.005 0.041 6240 Dihedral : 5.667 27.535 4842 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.37 % Favored : 90.63 % Rotamer: Outliers : 2.75 % Allowed : 11.37 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.43 (0.11), residues: 4440 helix: -5.49 (0.13), residues: 42 sheet: -1.71 (0.15), residues: 1032 loop : -2.64 (0.10), residues: 3366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG 6 224 TYR 0.013 0.002 TYR N 39 PHE 0.013 0.002 PHE 2 76 TRP 0.025 0.002 TRP 6 320 HIS 0.006 0.001 HIS H 48 Details of bonding type rmsd covalent geometry : bond 0.00428 (35052) covalent geometry : angle 0.65339 (47790) hydrogen bonds : bond 0.03900 ( 522) hydrogen bonds : angle 5.80051 ( 1296) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 169 time to evaluate : 1.354 Fit side-chains REVERT: 1 422 ASP cc_start: 0.8023 (OUTLIER) cc_final: 0.7773 (m-30) REVERT: 2 442 ARG cc_start: 0.6273 (OUTLIER) cc_final: 0.6053 (ppp80) REVERT: 3 442 ARG cc_start: 0.6511 (OUTLIER) cc_final: 0.6242 (ppp80) REVERT: 4 422 ASP cc_start: 0.8061 (OUTLIER) cc_final: 0.7796 (m-30) REVERT: 5 422 ASP cc_start: 0.8081 (OUTLIER) cc_final: 0.7477 (m-30) REVERT: 5 442 ARG cc_start: 0.6215 (OUTLIER) cc_final: 0.5991 (ppp80) REVERT: 6 442 ARG cc_start: 0.6561 (OUTLIER) cc_final: 0.6271 (ppp80) REVERT: B 69 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.7196 (pp) REVERT: C 55 ASP cc_start: 0.7250 (m-30) cc_final: 0.6929 (m-30) REVERT: C 66 ASP cc_start: 0.6997 (m-30) cc_final: 0.6792 (m-30) REVERT: C 86 ASP cc_start: 0.7514 (t70) cc_final: 0.7155 (p0) REVERT: E 1 MET cc_start: 0.2885 (mtp) cc_final: 0.2087 (mtt) REVERT: E 69 LEU cc_start: 0.6962 (OUTLIER) cc_final: 0.6750 (pp) REVERT: E 95 LEU cc_start: 0.6687 (mt) cc_final: 0.6305 (tp) REVERT: F 70 GLU cc_start: 0.6948 (mm-30) cc_final: 0.6643 (tp30) REVERT: F 86 ASP cc_start: 0.7938 (t0) cc_final: 0.7602 (p0) REVERT: G 75 LEU cc_start: 0.7379 (OUTLIER) cc_final: 0.6739 (tp) REVERT: H 69 LEU cc_start: 0.7066 (OUTLIER) cc_final: 0.6826 (pp) REVERT: H 95 LEU cc_start: 0.6200 (mt) cc_final: 0.5874 (tt) REVERT: I 86 ASP cc_start: 0.7709 (t70) cc_final: 0.7157 (p0) REVERT: J 75 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.6813 (tp) REVERT: K 95 LEU cc_start: 0.6455 (mt) cc_final: 0.6121 (tp) REVERT: L 55 ASP cc_start: 0.7234 (m-30) cc_final: 0.6878 (m-30) REVERT: N 1 MET cc_start: 0.2973 (mtp) cc_final: 0.2264 (mtt) REVERT: N 69 LEU cc_start: 0.7120 (OUTLIER) cc_final: 0.6920 (pp) REVERT: N 95 LEU cc_start: 0.6414 (mt) cc_final: 0.6112 (tp) REVERT: O 86 ASP cc_start: 0.7768 (t70) cc_final: 0.7048 (p0) REVERT: O 91 ASN cc_start: 0.7260 (t0) cc_final: 0.7036 (t0) REVERT: P 69 LEU cc_start: 0.6620 (OUTLIER) cc_final: 0.6413 (pp) REVERT: P 75 LEU cc_start: 0.7233 (OUTLIER) cc_final: 0.6598 (tp) REVERT: Q 95 LEU cc_start: 0.6258 (mt) cc_final: 0.5895 (tt) outliers start: 98 outliers final: 56 residues processed: 260 average time/residue: 0.1905 time to fit residues: 87.0203 Evaluate side-chains 224 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 153 time to evaluate : 1.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 76 PHE Chi-restraints excluded: chain 1 residue 83 LEU Chi-restraints excluded: chain 1 residue 129 THR Chi-restraints excluded: chain 1 residue 130 ILE Chi-restraints excluded: chain 1 residue 320 TRP Chi-restraints excluded: chain 1 residue 371 LEU Chi-restraints excluded: chain 1 residue 422 ASP Chi-restraints excluded: chain 1 residue 442 ARG Chi-restraints excluded: chain 2 residue 76 PHE Chi-restraints excluded: chain 2 residue 83 LEU Chi-restraints excluded: chain 2 residue 129 THR Chi-restraints excluded: chain 2 residue 130 ILE Chi-restraints excluded: chain 2 residue 320 TRP Chi-restraints excluded: chain 2 residue 442 ARG Chi-restraints excluded: chain 3 residue 76 PHE Chi-restraints excluded: chain 3 residue 82 LEU Chi-restraints excluded: chain 3 residue 83 LEU Chi-restraints excluded: chain 3 residue 129 THR Chi-restraints excluded: chain 3 residue 130 ILE Chi-restraints excluded: chain 3 residue 320 TRP Chi-restraints excluded: chain 3 residue 431 VAL Chi-restraints excluded: chain 3 residue 442 ARG Chi-restraints excluded: chain 4 residue 76 PHE Chi-restraints excluded: chain 4 residue 83 LEU Chi-restraints excluded: chain 4 residue 129 THR Chi-restraints excluded: chain 4 residue 130 ILE Chi-restraints excluded: chain 4 residue 320 TRP Chi-restraints excluded: chain 4 residue 371 LEU Chi-restraints excluded: chain 4 residue 422 ASP Chi-restraints excluded: chain 4 residue 442 ARG Chi-restraints excluded: chain 5 residue 76 PHE Chi-restraints excluded: chain 5 residue 83 LEU Chi-restraints excluded: chain 5 residue 129 THR Chi-restraints excluded: chain 5 residue 130 ILE Chi-restraints excluded: chain 5 residue 320 TRP Chi-restraints excluded: chain 5 residue 422 ASP Chi-restraints excluded: chain 5 residue 442 ARG Chi-restraints excluded: chain 6 residue 76 PHE Chi-restraints excluded: chain 6 residue 82 LEU Chi-restraints excluded: chain 6 residue 83 LEU Chi-restraints excluded: chain 6 residue 129 THR Chi-restraints excluded: chain 6 residue 130 ILE Chi-restraints excluded: chain 6 residue 320 TRP Chi-restraints excluded: chain 6 residue 431 VAL Chi-restraints excluded: chain 6 residue 442 ARG Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain H residue 59 LYS Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain K residue 91 ASN Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain O residue 52 VAL Chi-restraints excluded: chain O residue 69 LEU Chi-restraints excluded: chain P residue 69 LEU Chi-restraints excluded: chain P residue 75 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 396 optimal weight: 3.9990 chunk 213 optimal weight: 9.9990 chunk 134 optimal weight: 5.9990 chunk 21 optimal weight: 20.0000 chunk 179 optimal weight: 9.9990 chunk 439 optimal weight: 8.9990 chunk 333 optimal weight: 20.0000 chunk 178 optimal weight: 9.9990 chunk 228 optimal weight: 30.0000 chunk 196 optimal weight: 6.9990 chunk 357 optimal weight: 6.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 ASN R 91 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.061357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.054222 restraints weight = 176337.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.054957 restraints weight = 125984.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.055273 restraints weight = 89639.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.055523 restraints weight = 78635.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.055639 restraints weight = 72805.820| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 35052 Z= 0.193 Angle : 0.665 7.298 47790 Z= 0.347 Chirality : 0.046 0.171 5364 Planarity : 0.005 0.039 6240 Dihedral : 5.759 28.567 4842 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.50 % Favored : 89.50 % Rotamer: Outliers : 3.39 % Allowed : 12.07 % Favored : 84.54 % 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: -3.42 (0.11), residues: 4440 helix: -5.49 (0.13), residues: 42 sheet: -1.71 (0.15), residues: 1044 loop : -2.63 (0.10), residues: 3354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG 3 224 TYR 0.013 0.002 TYR K 39 PHE 0.014 0.002 PHE 5 76 TRP 0.026 0.002 TRP 1 320 HIS 0.006 0.001 HIS H 48 Details of bonding type rmsd covalent geometry : bond 0.00464 (35052) covalent geometry : angle 0.66520 (47790) hydrogen bonds : bond 0.03913 ( 522) hydrogen bonds : angle 5.80021 ( 1296) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 159 time to evaluate : 1.102 Fit side-chains REVERT: 1 124 GLU cc_start: 0.6856 (OUTLIER) cc_final: 0.5851 (pp20) REVERT: 1 422 ASP cc_start: 0.8130 (OUTLIER) cc_final: 0.7805 (m-30) REVERT: 2 59 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7745 (pp30) REVERT: 2 422 ASP cc_start: 0.8147 (OUTLIER) cc_final: 0.7489 (m-30) REVERT: 2 442 ARG cc_start: 0.6303 (OUTLIER) cc_final: 0.6079 (ppp80) REVERT: 3 59 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.8115 (pp30) REVERT: 3 371 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7508 (pt) REVERT: 3 442 ARG cc_start: 0.6494 (OUTLIER) cc_final: 0.6198 (ppp80) REVERT: 4 124 GLU cc_start: 0.6849 (OUTLIER) cc_final: 0.5914 (pp20) REVERT: 4 422 ASP cc_start: 0.8179 (OUTLIER) cc_final: 0.7833 (m-30) REVERT: 5 59 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7768 (pp30) REVERT: 5 422 ASP cc_start: 0.8171 (OUTLIER) cc_final: 0.7529 (m-30) REVERT: 5 442 ARG cc_start: 0.6370 (OUTLIER) cc_final: 0.6137 (ppp80) REVERT: 6 59 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.8049 (pp30) REVERT: 6 371 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7502 (pt) REVERT: 6 442 ARG cc_start: 0.6509 (OUTLIER) cc_final: 0.6206 (ppp80) REVERT: B 69 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.7214 (pp) REVERT: C 66 ASP cc_start: 0.7050 (m-30) cc_final: 0.6818 (m-30) REVERT: C 70 GLU cc_start: 0.6911 (mm-30) cc_final: 0.6559 (tp30) REVERT: C 86 ASP cc_start: 0.7476 (t70) cc_final: 0.7205 (p0) REVERT: E 1 MET cc_start: 0.2993 (mtp) cc_final: 0.2162 (mtt) REVERT: E 69 LEU cc_start: 0.7140 (OUTLIER) cc_final: 0.6925 (pp) REVERT: E 95 LEU cc_start: 0.6849 (mt) cc_final: 0.6471 (tp) REVERT: F 70 GLU cc_start: 0.6947 (mm-30) cc_final: 0.6721 (tp30) REVERT: F 86 ASP cc_start: 0.7827 (t0) cc_final: 0.7540 (p0) REVERT: G 75 LEU cc_start: 0.7124 (OUTLIER) cc_final: 0.6502 (tp) REVERT: H 69 LEU cc_start: 0.7076 (OUTLIER) cc_final: 0.6826 (pp) REVERT: H 95 LEU cc_start: 0.6710 (mt) cc_final: 0.6213 (tt) REVERT: I 86 ASP cc_start: 0.7708 (t70) cc_final: 0.7233 (p0) REVERT: J 75 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.6775 (tp) REVERT: K 95 LEU cc_start: 0.6858 (mt) cc_final: 0.6424 (tp) REVERT: L 70 GLU cc_start: 0.6925 (mm-30) cc_final: 0.6518 (tp30) REVERT: N 1 MET cc_start: 0.3174 (mtp) cc_final: 0.2659 (mtp) REVERT: N 69 LEU cc_start: 0.7243 (OUTLIER) cc_final: 0.7039 (pp) REVERT: N 95 LEU cc_start: 0.6691 (mt) cc_final: 0.6136 (tt) REVERT: O 86 ASP cc_start: 0.7753 (t70) cc_final: 0.7146 (p0) REVERT: P 75 LEU cc_start: 0.7088 (OUTLIER) cc_final: 0.6422 (tp) REVERT: Q 95 LEU cc_start: 0.6546 (mt) cc_final: 0.6150 (tt) REVERT: R 91 ASN cc_start: 0.7097 (OUTLIER) cc_final: 0.6292 (t0) outliers start: 121 outliers final: 79 residues processed: 270 average time/residue: 0.1931 time to fit residues: 91.1752 Evaluate side-chains 254 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 151 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 59 GLN Chi-restraints excluded: chain 1 residue 76 PHE Chi-restraints excluded: chain 1 residue 83 LEU Chi-restraints excluded: chain 1 residue 108 LEU Chi-restraints excluded: chain 1 residue 124 GLU Chi-restraints excluded: chain 1 residue 129 THR Chi-restraints excluded: chain 1 residue 130 ILE Chi-restraints excluded: chain 1 residue 320 TRP Chi-restraints excluded: chain 1 residue 371 LEU Chi-restraints excluded: chain 1 residue 422 ASP Chi-restraints excluded: chain 1 residue 431 VAL Chi-restraints excluded: chain 1 residue 442 ARG Chi-restraints excluded: chain 2 residue 59 GLN Chi-restraints excluded: chain 2 residue 76 PHE Chi-restraints excluded: chain 2 residue 82 LEU Chi-restraints excluded: chain 2 residue 83 LEU Chi-restraints excluded: chain 2 residue 129 THR Chi-restraints excluded: chain 2 residue 130 ILE Chi-restraints excluded: chain 2 residue 171 ASP Chi-restraints excluded: chain 2 residue 289 VAL Chi-restraints excluded: chain 2 residue 320 TRP Chi-restraints excluded: chain 2 residue 422 ASP Chi-restraints excluded: chain 2 residue 442 ARG Chi-restraints excluded: chain 3 residue 59 GLN Chi-restraints excluded: chain 3 residue 76 PHE Chi-restraints excluded: chain 3 residue 82 LEU Chi-restraints excluded: chain 3 residue 83 LEU Chi-restraints excluded: chain 3 residue 108 LEU Chi-restraints excluded: chain 3 residue 129 THR Chi-restraints excluded: chain 3 residue 130 ILE Chi-restraints excluded: chain 3 residue 320 TRP Chi-restraints excluded: chain 3 residue 371 LEU Chi-restraints excluded: chain 3 residue 442 ARG Chi-restraints excluded: chain 4 residue 59 GLN Chi-restraints excluded: chain 4 residue 76 PHE Chi-restraints excluded: chain 4 residue 83 LEU Chi-restraints excluded: chain 4 residue 108 LEU Chi-restraints excluded: chain 4 residue 124 GLU Chi-restraints excluded: chain 4 residue 129 THR Chi-restraints excluded: chain 4 residue 130 ILE Chi-restraints excluded: chain 4 residue 320 TRP Chi-restraints excluded: chain 4 residue 371 LEU Chi-restraints excluded: chain 4 residue 422 ASP Chi-restraints excluded: chain 4 residue 431 VAL Chi-restraints excluded: chain 4 residue 442 ARG Chi-restraints excluded: chain 5 residue 59 GLN Chi-restraints excluded: chain 5 residue 76 PHE Chi-restraints excluded: chain 5 residue 83 LEU Chi-restraints excluded: chain 5 residue 129 THR Chi-restraints excluded: chain 5 residue 130 ILE Chi-restraints excluded: chain 5 residue 289 VAL Chi-restraints excluded: chain 5 residue 320 TRP Chi-restraints excluded: chain 5 residue 422 ASP Chi-restraints excluded: chain 5 residue 442 ARG Chi-restraints excluded: chain 6 residue 59 GLN Chi-restraints excluded: chain 6 residue 76 PHE Chi-restraints excluded: chain 6 residue 82 LEU Chi-restraints excluded: chain 6 residue 83 LEU Chi-restraints excluded: chain 6 residue 108 LEU Chi-restraints excluded: chain 6 residue 129 THR Chi-restraints excluded: chain 6 residue 130 ILE Chi-restraints excluded: chain 6 residue 320 TRP Chi-restraints excluded: chain 6 residue 371 LEU Chi-restraints excluded: chain 6 residue 442 ARG Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 91 ASN Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain F residue 37 SER Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain O residue 52 VAL Chi-restraints excluded: chain O residue 69 LEU Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 74 VAL Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 90 ILE Chi-restraints excluded: chain R residue 91 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 178 optimal weight: 9.9990 chunk 405 optimal weight: 7.9990 chunk 150 optimal weight: 0.9990 chunk 202 optimal weight: 8.9990 chunk 321 optimal weight: 30.0000 chunk 132 optimal weight: 20.0000 chunk 145 optimal weight: 20.0000 chunk 344 optimal weight: 9.9990 chunk 168 optimal weight: 4.9990 chunk 96 optimal weight: 20.0000 chunk 264 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 91 ASN N 91 ASN P 36 GLN R 91 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.060121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.053418 restraints weight = 181508.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.054218 restraints weight = 117609.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.054822 restraints weight = 85008.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.055218 restraints weight = 65393.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.055559 restraints weight = 53446.290| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 35052 Z= 0.193 Angle : 0.665 7.288 47790 Z= 0.348 Chirality : 0.046 0.170 5364 Planarity : 0.005 0.039 6240 Dihedral : 5.781 29.573 4842 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer: Outliers : 3.87 % Allowed : 11.93 % Favored : 84.20 % 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: -3.36 (0.11), residues: 4440 helix: -5.48 (0.13), residues: 42 sheet: -1.67 (0.15), residues: 1044 loop : -2.59 (0.10), residues: 3354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG 6 427 TYR 0.013 0.002 TYR B 39 PHE 0.012 0.002 PHE 2 76 TRP 0.026 0.002 TRP 1 320 HIS 0.006 0.001 HIS H 48 Details of bonding type rmsd covalent geometry : bond 0.00464 (35052) covalent geometry : angle 0.66509 (47790) hydrogen bonds : bond 0.03890 ( 522) hydrogen bonds : angle 5.82543 ( 1296) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 156 time to evaluate : 1.398 Fit side-chains REVERT: 1 422 ASP cc_start: 0.8122 (OUTLIER) cc_final: 0.7797 (m-30) REVERT: 2 59 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7750 (pp30) REVERT: 2 422 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7485 (m-30) REVERT: 2 442 ARG cc_start: 0.6365 (OUTLIER) cc_final: 0.6152 (ppp80) REVERT: 3 59 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.8099 (pp30) REVERT: 3 371 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7470 (pt) REVERT: 3 373 MET cc_start: 0.8700 (ptm) cc_final: 0.8333 (tmm) REVERT: 3 442 ARG cc_start: 0.6531 (OUTLIER) cc_final: 0.6233 (ppp80) REVERT: 4 124 GLU cc_start: 0.6885 (OUTLIER) cc_final: 0.5877 (pp20) REVERT: 4 422 ASP cc_start: 0.8169 (OUTLIER) cc_final: 0.7837 (m-30) REVERT: 5 59 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7769 (pp30) REVERT: 5 422 ASP cc_start: 0.8129 (OUTLIER) cc_final: 0.7479 (m-30) REVERT: 5 442 ARG cc_start: 0.6476 (OUTLIER) cc_final: 0.6258 (ppp80) REVERT: 6 59 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.8027 (pp30) REVERT: 6 371 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7470 (pt) REVERT: 6 373 MET cc_start: 0.8709 (ptm) cc_final: 0.8386 (tmm) REVERT: 6 442 ARG cc_start: 0.6531 (OUTLIER) cc_final: 0.6213 (ppp80) REVERT: B 69 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7290 (pp) REVERT: C 66 ASP cc_start: 0.6910 (m-30) cc_final: 0.6640 (m-30) REVERT: C 70 GLU cc_start: 0.6825 (mm-30) cc_final: 0.6560 (tp30) REVERT: C 86 ASP cc_start: 0.7375 (t70) cc_final: 0.7170 (p0) REVERT: E 1 MET cc_start: 0.3157 (mtp) cc_final: 0.2510 (mtp) REVERT: E 69 LEU cc_start: 0.7166 (OUTLIER) cc_final: 0.6944 (pp) REVERT: G 75 LEU cc_start: 0.7266 (OUTLIER) cc_final: 0.6674 (tp) REVERT: H 69 LEU cc_start: 0.7062 (OUTLIER) cc_final: 0.6798 (pp) REVERT: H 95 LEU cc_start: 0.6825 (mt) cc_final: 0.6314 (tt) REVERT: I 86 ASP cc_start: 0.7687 (t70) cc_final: 0.7284 (p0) REVERT: J 75 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.6889 (tp) REVERT: K 59 LYS cc_start: 0.7600 (mtpt) cc_final: 0.7323 (ttpt) REVERT: K 95 LEU cc_start: 0.6566 (mt) cc_final: 0.6313 (tp) REVERT: L 70 GLU cc_start: 0.6849 (mm-30) cc_final: 0.6579 (tp30) REVERT: N 1 MET cc_start: 0.3245 (mtp) cc_final: 0.2723 (mtp) REVERT: N 95 LEU cc_start: 0.6609 (mt) cc_final: 0.6066 (tt) REVERT: O 86 ASP cc_start: 0.7600 (t70) cc_final: 0.7053 (p0) REVERT: P 75 LEU cc_start: 0.7224 (OUTLIER) cc_final: 0.6608 (tp) outliers start: 138 outliers final: 89 residues processed: 284 average time/residue: 0.1903 time to fit residues: 94.7034 Evaluate side-chains 261 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 151 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 59 GLN Chi-restraints excluded: chain 1 residue 76 PHE Chi-restraints excluded: chain 1 residue 83 LEU Chi-restraints excluded: chain 1 residue 108 LEU Chi-restraints excluded: chain 1 residue 129 THR Chi-restraints excluded: chain 1 residue 130 ILE Chi-restraints excluded: chain 1 residue 320 TRP Chi-restraints excluded: chain 1 residue 371 LEU Chi-restraints excluded: chain 1 residue 422 ASP Chi-restraints excluded: chain 1 residue 431 VAL Chi-restraints excluded: chain 1 residue 442 ARG Chi-restraints excluded: chain 2 residue 59 GLN Chi-restraints excluded: chain 2 residue 76 PHE Chi-restraints excluded: chain 2 residue 83 LEU Chi-restraints excluded: chain 2 residue 129 THR Chi-restraints excluded: chain 2 residue 130 ILE Chi-restraints excluded: chain 2 residue 289 VAL Chi-restraints excluded: chain 2 residue 320 TRP Chi-restraints excluded: chain 2 residue 422 ASP Chi-restraints excluded: chain 2 residue 431 VAL Chi-restraints excluded: chain 2 residue 442 ARG Chi-restraints excluded: chain 3 residue 59 GLN Chi-restraints excluded: chain 3 residue 76 PHE Chi-restraints excluded: chain 3 residue 82 LEU Chi-restraints excluded: chain 3 residue 83 LEU Chi-restraints excluded: chain 3 residue 108 LEU Chi-restraints excluded: chain 3 residue 129 THR Chi-restraints excluded: chain 3 residue 130 ILE Chi-restraints excluded: chain 3 residue 320 TRP Chi-restraints excluded: chain 3 residue 371 LEU Chi-restraints excluded: chain 3 residue 431 VAL Chi-restraints excluded: chain 3 residue 442 ARG Chi-restraints excluded: chain 4 residue 59 GLN Chi-restraints excluded: chain 4 residue 76 PHE Chi-restraints excluded: chain 4 residue 83 LEU Chi-restraints excluded: chain 4 residue 108 LEU Chi-restraints excluded: chain 4 residue 124 GLU Chi-restraints excluded: chain 4 residue 129 THR Chi-restraints excluded: chain 4 residue 130 ILE Chi-restraints excluded: chain 4 residue 171 ASP Chi-restraints excluded: chain 4 residue 320 TRP Chi-restraints excluded: chain 4 residue 371 LEU Chi-restraints excluded: chain 4 residue 422 ASP Chi-restraints excluded: chain 4 residue 431 VAL Chi-restraints excluded: chain 4 residue 442 ARG Chi-restraints excluded: chain 5 residue 59 GLN Chi-restraints excluded: chain 5 residue 76 PHE Chi-restraints excluded: chain 5 residue 82 LEU Chi-restraints excluded: chain 5 residue 83 LEU Chi-restraints excluded: chain 5 residue 129 THR Chi-restraints excluded: chain 5 residue 130 ILE Chi-restraints excluded: chain 5 residue 289 VAL Chi-restraints excluded: chain 5 residue 320 TRP Chi-restraints excluded: chain 5 residue 422 ASP Chi-restraints excluded: chain 5 residue 431 VAL Chi-restraints excluded: chain 5 residue 442 ARG Chi-restraints excluded: chain 6 residue 59 GLN Chi-restraints excluded: chain 6 residue 76 PHE Chi-restraints excluded: chain 6 residue 82 LEU Chi-restraints excluded: chain 6 residue 83 LEU Chi-restraints excluded: chain 6 residue 129 THR Chi-restraints excluded: chain 6 residue 130 ILE Chi-restraints excluded: chain 6 residue 320 TRP Chi-restraints excluded: chain 6 residue 371 LEU Chi-restraints excluded: chain 6 residue 431 VAL Chi-restraints excluded: chain 6 residue 442 ARG Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain F residue 37 SER Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 59 LYS Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 90 ILE Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain O residue 52 VAL Chi-restraints excluded: chain O residue 69 LEU Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain R residue 90 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 227 optimal weight: 7.9990 chunk 32 optimal weight: 9.9990 chunk 50 optimal weight: 20.0000 chunk 65 optimal weight: 5.9990 chunk 421 optimal weight: 6.9990 chunk 79 optimal weight: 10.0000 chunk 293 optimal weight: 20.0000 chunk 40 optimal weight: 0.8980 chunk 64 optimal weight: 8.9990 chunk 360 optimal weight: 0.0980 chunk 413 optimal weight: 10.0000 overall best weight: 4.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.060538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.053780 restraints weight = 180483.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.054588 restraints weight = 118102.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.055195 restraints weight = 85494.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.055593 restraints weight = 65725.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.055935 restraints weight = 53778.654| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 35052 Z= 0.145 Angle : 0.617 7.121 47790 Z= 0.322 Chirality : 0.045 0.207 5364 Planarity : 0.004 0.040 6240 Dihedral : 5.467 26.583 4842 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 3.19 % Allowed : 13.17 % Favored : 83.64 % 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: -3.22 (0.11), residues: 4440 helix: -5.48 (0.13), residues: 42 sheet: -1.54 (0.15), residues: 1032 loop : -2.50 (0.10), residues: 3366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 6 427 TYR 0.011 0.001 TYR K 39 PHE 0.011 0.001 PHE 1 76 TRP 0.024 0.002 TRP 4 320 HIS 0.005 0.001 HIS H 48 Details of bonding type rmsd covalent geometry : bond 0.00343 (35052) covalent geometry : angle 0.61683 (47790) hydrogen bonds : bond 0.03493 ( 522) hydrogen bonds : angle 5.76635 ( 1296) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 157 time to evaluate : 1.728 Fit side-chains REVERT: 1 124 GLU cc_start: 0.6938 (OUTLIER) cc_final: 0.5815 (pp20) REVERT: 1 422 ASP cc_start: 0.8178 (OUTLIER) cc_final: 0.7811 (m-30) REVERT: 2 59 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7690 (pp30) REVERT: 2 422 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7492 (m-30) REVERT: 2 442 ARG cc_start: 0.6355 (OUTLIER) cc_final: 0.6144 (ppp80) REVERT: 3 59 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.8053 (pp30) REVERT: 3 371 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7423 (pt) REVERT: 3 373 MET cc_start: 0.8663 (ptm) cc_final: 0.8376 (tmm) REVERT: 4 124 GLU cc_start: 0.6946 (OUTLIER) cc_final: 0.5806 (pp20) REVERT: 4 422 ASP cc_start: 0.8207 (OUTLIER) cc_final: 0.7844 (m-30) REVERT: 5 422 ASP cc_start: 0.8076 (OUTLIER) cc_final: 0.7473 (m-30) REVERT: 5 442 ARG cc_start: 0.6386 (OUTLIER) cc_final: 0.6171 (ppp80) REVERT: 6 371 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7436 (pt) REVERT: 6 373 MET cc_start: 0.8662 (ptm) cc_final: 0.8440 (tmm) REVERT: C 66 ASP cc_start: 0.6828 (m-30) cc_final: 0.6559 (m-30) REVERT: C 70 GLU cc_start: 0.6854 (mm-30) cc_final: 0.6581 (tp30) REVERT: E 1 MET cc_start: 0.3070 (mtp) cc_final: 0.2165 (mtt) REVERT: E 69 LEU cc_start: 0.7183 (OUTLIER) cc_final: 0.6950 (pp) REVERT: E 95 LEU cc_start: 0.7353 (mt) cc_final: 0.6657 (tp) REVERT: G 75 LEU cc_start: 0.7095 (OUTLIER) cc_final: 0.6532 (tp) REVERT: H 69 LEU cc_start: 0.6993 (OUTLIER) cc_final: 0.6756 (pp) REVERT: I 86 ASP cc_start: 0.7742 (t70) cc_final: 0.7303 (p0) REVERT: J 75 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.6863 (tp) REVERT: K 4 GLU cc_start: 0.7524 (tp30) cc_final: 0.7307 (tm-30) REVERT: K 59 LYS cc_start: 0.7564 (mtpt) cc_final: 0.7268 (ttpt) REVERT: K 95 LEU cc_start: 0.6515 (mt) cc_final: 0.6312 (tp) REVERT: L 59 LYS cc_start: 0.7525 (OUTLIER) cc_final: 0.7308 (ttpt) REVERT: L 70 GLU cc_start: 0.6914 (mm-30) cc_final: 0.6557 (tp30) REVERT: N 1 MET cc_start: 0.3202 (mtp) cc_final: 0.2653 (mtp) REVERT: N 95 LEU cc_start: 0.6556 (mt) cc_final: 0.5981 (tt) REVERT: O 86 ASP cc_start: 0.7596 (t70) cc_final: 0.7058 (p0) REVERT: P 75 LEU cc_start: 0.7057 (OUTLIER) cc_final: 0.6457 (tp) REVERT: Q 95 LEU cc_start: 0.7241 (mt) cc_final: 0.6425 (tt) outliers start: 114 outliers final: 75 residues processed: 264 average time/residue: 0.1892 time to fit residues: 88.1937 Evaluate side-chains 247 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 154 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 59 GLN Chi-restraints excluded: chain 1 residue 76 PHE Chi-restraints excluded: chain 1 residue 83 LEU Chi-restraints excluded: chain 1 residue 124 GLU Chi-restraints excluded: chain 1 residue 129 THR Chi-restraints excluded: chain 1 residue 130 ILE Chi-restraints excluded: chain 1 residue 171 ASP Chi-restraints excluded: chain 1 residue 320 TRP Chi-restraints excluded: chain 1 residue 422 ASP Chi-restraints excluded: chain 1 residue 442 ARG Chi-restraints excluded: chain 2 residue 59 GLN Chi-restraints excluded: chain 2 residue 76 PHE Chi-restraints excluded: chain 2 residue 83 LEU Chi-restraints excluded: chain 2 residue 129 THR Chi-restraints excluded: chain 2 residue 130 ILE Chi-restraints excluded: chain 2 residue 289 VAL Chi-restraints excluded: chain 2 residue 320 TRP Chi-restraints excluded: chain 2 residue 422 ASP Chi-restraints excluded: chain 2 residue 442 ARG Chi-restraints excluded: chain 3 residue 59 GLN Chi-restraints excluded: chain 3 residue 76 PHE Chi-restraints excluded: chain 3 residue 82 LEU Chi-restraints excluded: chain 3 residue 83 LEU Chi-restraints excluded: chain 3 residue 129 THR Chi-restraints excluded: chain 3 residue 130 ILE Chi-restraints excluded: chain 3 residue 320 TRP Chi-restraints excluded: chain 3 residue 371 LEU Chi-restraints excluded: chain 3 residue 431 VAL Chi-restraints excluded: chain 4 residue 76 PHE Chi-restraints excluded: chain 4 residue 83 LEU Chi-restraints excluded: chain 4 residue 124 GLU Chi-restraints excluded: chain 4 residue 129 THR Chi-restraints excluded: chain 4 residue 130 ILE Chi-restraints excluded: chain 4 residue 320 TRP Chi-restraints excluded: chain 4 residue 422 ASP Chi-restraints excluded: chain 4 residue 442 ARG Chi-restraints excluded: chain 5 residue 76 PHE Chi-restraints excluded: chain 5 residue 83 LEU Chi-restraints excluded: chain 5 residue 129 THR Chi-restraints excluded: chain 5 residue 130 ILE Chi-restraints excluded: chain 5 residue 289 VAL Chi-restraints excluded: chain 5 residue 320 TRP Chi-restraints excluded: chain 5 residue 422 ASP Chi-restraints excluded: chain 5 residue 442 ARG Chi-restraints excluded: chain 6 residue 76 PHE Chi-restraints excluded: chain 6 residue 82 LEU Chi-restraints excluded: chain 6 residue 83 LEU Chi-restraints excluded: chain 6 residue 129 THR Chi-restraints excluded: chain 6 residue 130 ILE Chi-restraints excluded: chain 6 residue 320 TRP Chi-restraints excluded: chain 6 residue 371 LEU Chi-restraints excluded: chain 6 residue 431 VAL Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain F residue 37 SER Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 69 LEU Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 59 LYS Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain O residue 52 VAL Chi-restraints excluded: chain O residue 69 LEU Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain R residue 90 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 411 optimal weight: 30.0000 chunk 435 optimal weight: 40.0000 chunk 37 optimal weight: 10.0000 chunk 266 optimal weight: 20.0000 chunk 426 optimal weight: 20.0000 chunk 366 optimal weight: 20.0000 chunk 399 optimal weight: 20.0000 chunk 351 optimal weight: 20.0000 chunk 376 optimal weight: 8.9990 chunk 325 optimal weight: 8.9990 chunk 75 optimal weight: 9.9990 overall best weight: 11.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 ASN E 91 ASN ** O 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.081244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.063830 restraints weight = 155484.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.064990 restraints weight = 112016.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.065981 restraints weight = 88804.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.066666 restraints weight = 74505.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.066966 restraints weight = 65781.337| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 35052 Z= 0.308 Angle : 0.820 8.581 47790 Z= 0.430 Chirality : 0.051 0.194 5364 Planarity : 0.006 0.068 6240 Dihedral : 6.585 32.597 4842 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.59 % Favored : 87.41 % Rotamer: Outliers : 3.31 % Allowed : 13.64 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.45 % 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: -3.48 (0.11), residues: 4440 helix: -4.88 (0.26), residues: 48 sheet: -1.80 (0.15), residues: 1080 loop : -2.66 (0.10), residues: 3312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG 6 224 TYR 0.017 0.002 TYR 1 230 PHE 0.017 0.002 PHE 5 426 TRP 0.028 0.003 TRP 5 320 HIS 0.011 0.002 HIS B 48 Details of bonding type rmsd covalent geometry : bond 0.00739 (35052) covalent geometry : angle 0.82035 (47790) hydrogen bonds : bond 0.04735 ( 522) hydrogen bonds : angle 6.09791 ( 1296) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 153 time to evaluate : 1.313 Fit side-chains REVERT: 1 75 GLU cc_start: 0.7936 (pt0) cc_final: 0.7710 (pt0) REVERT: 1 422 ASP cc_start: 0.8006 (OUTLIER) cc_final: 0.7703 (t0) REVERT: 2 59 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.7709 (pp30) REVERT: 2 422 ASP cc_start: 0.8025 (OUTLIER) cc_final: 0.7526 (m-30) REVERT: 2 442 ARG cc_start: 0.6493 (OUTLIER) cc_final: 0.6270 (ppp80) REVERT: 3 59 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.8048 (pp30) REVERT: 3 371 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7617 (pt) REVERT: 3 442 ARG cc_start: 0.6473 (OUTLIER) cc_final: 0.6168 (ppp80) REVERT: 4 75 GLU cc_start: 0.7953 (pt0) cc_final: 0.7714 (pt0) REVERT: 4 422 ASP cc_start: 0.8013 (OUTLIER) cc_final: 0.7722 (t0) REVERT: 5 59 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.7781 (pp30) REVERT: 5 422 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7533 (m-30) REVERT: 5 442 ARG cc_start: 0.6556 (OUTLIER) cc_final: 0.6338 (ppp80) REVERT: 6 59 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.8042 (pp30) REVERT: 6 371 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7636 (pt) REVERT: 6 442 ARG cc_start: 0.6438 (OUTLIER) cc_final: 0.6139 (ppp80) REVERT: C 70 GLU cc_start: 0.6356 (mm-30) cc_final: 0.5942 (tp30) REVERT: E 1 MET cc_start: 0.1645 (mtp) cc_final: 0.1396 (mtp) REVERT: G 75 LEU cc_start: 0.6751 (OUTLIER) cc_final: 0.6252 (tp) REVERT: H 95 LEU cc_start: 0.6975 (mp) cc_final: 0.6686 (tp) REVERT: I 70 GLU cc_start: 0.6680 (mt-10) cc_final: 0.6437 (tp30) REVERT: I 86 ASP cc_start: 0.7981 (t70) cc_final: 0.7712 (p0) REVERT: J 75 LEU cc_start: 0.6601 (OUTLIER) cc_final: 0.6184 (tp) REVERT: K 4 GLU cc_start: 0.5395 (tp30) cc_final: 0.5129 (tm-30) REVERT: K 95 LEU cc_start: 0.7228 (mt) cc_final: 0.6955 (tp) REVERT: L 70 GLU cc_start: 0.6412 (mm-30) cc_final: 0.5939 (tp30) REVERT: N 1 MET cc_start: 0.1808 (mtp) cc_final: 0.1505 (mtp) REVERT: N 95 LEU cc_start: 0.6784 (mt) cc_final: 0.6337 (tt) REVERT: O 86 ASP cc_start: 0.7701 (t70) cc_final: 0.7314 (p0) REVERT: P 75 LEU cc_start: 0.6802 (OUTLIER) cc_final: 0.6321 (tp) outliers start: 118 outliers final: 85 residues processed: 266 average time/residue: 0.1924 time to fit residues: 89.5513 Evaluate side-chains 251 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 149 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 59 GLN Chi-restraints excluded: chain 1 residue 76 PHE Chi-restraints excluded: chain 1 residue 83 LEU Chi-restraints excluded: chain 1 residue 108 LEU Chi-restraints excluded: chain 1 residue 129 THR Chi-restraints excluded: chain 1 residue 171 ASP Chi-restraints excluded: chain 1 residue 289 VAL Chi-restraints excluded: chain 1 residue 320 TRP Chi-restraints excluded: chain 1 residue 371 LEU Chi-restraints excluded: chain 1 residue 422 ASP Chi-restraints excluded: chain 1 residue 431 VAL Chi-restraints excluded: chain 1 residue 442 ARG Chi-restraints excluded: chain 2 residue 59 GLN Chi-restraints excluded: chain 2 residue 76 PHE Chi-restraints excluded: chain 2 residue 83 LEU Chi-restraints excluded: chain 2 residue 129 THR Chi-restraints excluded: chain 2 residue 289 VAL Chi-restraints excluded: chain 2 residue 320 TRP Chi-restraints excluded: chain 2 residue 422 ASP Chi-restraints excluded: chain 2 residue 431 VAL Chi-restraints excluded: chain 2 residue 442 ARG Chi-restraints excluded: chain 3 residue 59 GLN Chi-restraints excluded: chain 3 residue 76 PHE Chi-restraints excluded: chain 3 residue 82 LEU Chi-restraints excluded: chain 3 residue 83 LEU Chi-restraints excluded: chain 3 residue 108 LEU Chi-restraints excluded: chain 3 residue 129 THR Chi-restraints excluded: chain 3 residue 289 VAL Chi-restraints excluded: chain 3 residue 320 TRP Chi-restraints excluded: chain 3 residue 371 LEU Chi-restraints excluded: chain 3 residue 431 VAL Chi-restraints excluded: chain 3 residue 442 ARG Chi-restraints excluded: chain 4 residue 59 GLN Chi-restraints excluded: chain 4 residue 76 PHE Chi-restraints excluded: chain 4 residue 83 LEU Chi-restraints excluded: chain 4 residue 108 LEU Chi-restraints excluded: chain 4 residue 129 THR Chi-restraints excluded: chain 4 residue 171 ASP Chi-restraints excluded: chain 4 residue 289 VAL Chi-restraints excluded: chain 4 residue 320 TRP Chi-restraints excluded: chain 4 residue 371 LEU Chi-restraints excluded: chain 4 residue 422 ASP Chi-restraints excluded: chain 4 residue 431 VAL Chi-restraints excluded: chain 4 residue 442 ARG Chi-restraints excluded: chain 5 residue 59 GLN Chi-restraints excluded: chain 5 residue 76 PHE Chi-restraints excluded: chain 5 residue 83 LEU Chi-restraints excluded: chain 5 residue 129 THR Chi-restraints excluded: chain 5 residue 289 VAL Chi-restraints excluded: chain 5 residue 320 TRP Chi-restraints excluded: chain 5 residue 422 ASP Chi-restraints excluded: chain 5 residue 431 VAL Chi-restraints excluded: chain 5 residue 442 ARG Chi-restraints excluded: chain 6 residue 59 GLN Chi-restraints excluded: chain 6 residue 76 PHE Chi-restraints excluded: chain 6 residue 82 LEU Chi-restraints excluded: chain 6 residue 83 LEU Chi-restraints excluded: chain 6 residue 129 THR Chi-restraints excluded: chain 6 residue 289 VAL Chi-restraints excluded: chain 6 residue 320 TRP Chi-restraints excluded: chain 6 residue 371 LEU Chi-restraints excluded: chain 6 residue 431 VAL Chi-restraints excluded: chain 6 residue 442 ARG Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 16 ASN Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain F residue 37 SER Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain H residue 59 LYS Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain M residue 13 THR Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 74 VAL Chi-restraints excluded: chain O residue 37 SER Chi-restraints excluded: chain O residue 52 VAL Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain R residue 90 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 366 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 213 optimal weight: 6.9990 chunk 233 optimal weight: 2.9990 chunk 221 optimal weight: 7.9990 chunk 379 optimal weight: 30.0000 chunk 393 optimal weight: 0.5980 chunk 285 optimal weight: 30.0000 chunk 83 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 36 GLN K 6 HIS O 19 ASN ** O 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.060191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.053570 restraints weight = 181413.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.054362 restraints weight = 116826.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.054941 restraints weight = 84245.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.055337 restraints weight = 65837.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.055563 restraints weight = 53670.765| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 35052 Z= 0.146 Angle : 0.636 6.999 47790 Z= 0.333 Chirality : 0.045 0.174 5364 Planarity : 0.004 0.045 6240 Dihedral : 5.694 27.355 4842 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 2.55 % Allowed : 14.48 % 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: -3.25 (0.11), residues: 4440 helix: -5.46 (0.13), residues: 42 sheet: -1.50 (0.16), residues: 1002 loop : -2.53 (0.10), residues: 3396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 1 427 TYR 0.011 0.001 TYR E 39 PHE 0.011 0.001 PHE L 65 TRP 0.025 0.002 TRP 1 320 HIS 0.005 0.001 HIS H 48 Details of bonding type rmsd covalent geometry : bond 0.00345 (35052) covalent geometry : angle 0.63559 (47790) hydrogen bonds : bond 0.03577 ( 522) hydrogen bonds : angle 5.94364 ( 1296) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 157 time to evaluate : 1.377 Fit side-chains REVERT: 1 124 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.5841 (pp20) REVERT: 1 422 ASP cc_start: 0.8208 (OUTLIER) cc_final: 0.7806 (m-30) REVERT: 2 422 ASP cc_start: 0.8030 (OUTLIER) cc_final: 0.7506 (m-30) REVERT: 2 442 ARG cc_start: 0.6347 (OUTLIER) cc_final: 0.6140 (ppp80) REVERT: 3 371 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7327 (pt) REVERT: 3 373 MET cc_start: 0.8658 (ptm) cc_final: 0.8374 (tmm) REVERT: 3 442 ARG cc_start: 0.6339 (OUTLIER) cc_final: 0.6041 (ppp80) REVERT: 4 422 ASP cc_start: 0.8240 (OUTLIER) cc_final: 0.7836 (m-30) REVERT: 5 59 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7761 (pp30) REVERT: 5 422 ASP cc_start: 0.8081 (OUTLIER) cc_final: 0.7500 (m-30) REVERT: 5 442 ARG cc_start: 0.6323 (OUTLIER) cc_final: 0.6114 (ppp80) REVERT: 6 371 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7341 (pt) REVERT: 6 373 MET cc_start: 0.8636 (ptm) cc_final: 0.8412 (tmm) REVERT: 6 442 ARG cc_start: 0.6314 (OUTLIER) cc_final: 0.5999 (ppp80) REVERT: B 1 MET cc_start: 0.3080 (mtp) cc_final: 0.2110 (mtp) REVERT: C 66 ASP cc_start: 0.7155 (m-30) cc_final: 0.6876 (t0) REVERT: C 70 GLU cc_start: 0.6978 (mm-30) cc_final: 0.6630 (tp30) REVERT: E 1 MET cc_start: 0.2923 (mtp) cc_final: 0.2538 (mtp) REVERT: G 75 LEU cc_start: 0.7137 (OUTLIER) cc_final: 0.6630 (tp) REVERT: H 4 GLU cc_start: 0.6899 (tp30) cc_final: 0.6532 (tp30) REVERT: I 86 ASP cc_start: 0.7697 (t70) cc_final: 0.7304 (p0) REVERT: J 75 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.6828 (tp) REVERT: K 55 ASP cc_start: 0.6564 (m-30) cc_final: 0.6252 (m-30) REVERT: L 66 ASP cc_start: 0.7488 (m-30) cc_final: 0.7112 (t0) REVERT: L 70 GLU cc_start: 0.7001 (mm-30) cc_final: 0.6622 (tp30) REVERT: M 21 ASP cc_start: 0.6588 (p0) cc_final: 0.6303 (p0) REVERT: N 1 MET cc_start: 0.2761 (mtp) cc_final: 0.2390 (mtp) REVERT: N 95 LEU cc_start: 0.6406 (mt) cc_final: 0.6077 (tt) REVERT: O 86 ASP cc_start: 0.7554 (t70) cc_final: 0.7095 (p0) REVERT: P 75 LEU cc_start: 0.7056 (OUTLIER) cc_final: 0.6517 (tp) REVERT: Q 4 GLU cc_start: 0.6920 (tp30) cc_final: 0.6545 (tp30) REVERT: R 70 GLU cc_start: 0.6517 (tp30) cc_final: 0.6236 (tm-30) outliers start: 91 outliers final: 66 residues processed: 243 average time/residue: 0.1977 time to fit residues: 83.4239 Evaluate side-chains 233 residues out of total 3570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 152 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 76 PHE Chi-restraints excluded: chain 1 residue 83 LEU Chi-restraints excluded: chain 1 residue 108 LEU Chi-restraints excluded: chain 1 residue 124 GLU Chi-restraints excluded: chain 1 residue 129 THR Chi-restraints excluded: chain 1 residue 171 ASP Chi-restraints excluded: chain 1 residue 320 TRP Chi-restraints excluded: chain 1 residue 422 ASP Chi-restraints excluded: chain 1 residue 442 ARG Chi-restraints excluded: chain 2 residue 76 PHE Chi-restraints excluded: chain 2 residue 83 LEU Chi-restraints excluded: chain 2 residue 129 THR Chi-restraints excluded: chain 2 residue 289 VAL Chi-restraints excluded: chain 2 residue 320 TRP Chi-restraints excluded: chain 2 residue 422 ASP Chi-restraints excluded: chain 2 residue 442 ARG Chi-restraints excluded: chain 3 residue 76 PHE Chi-restraints excluded: chain 3 residue 83 LEU Chi-restraints excluded: chain 3 residue 108 LEU Chi-restraints excluded: chain 3 residue 129 THR Chi-restraints excluded: chain 3 residue 289 VAL Chi-restraints excluded: chain 3 residue 320 TRP Chi-restraints excluded: chain 3 residue 371 LEU Chi-restraints excluded: chain 3 residue 431 VAL Chi-restraints excluded: chain 3 residue 442 ARG Chi-restraints excluded: chain 4 residue 59 GLN Chi-restraints excluded: chain 4 residue 76 PHE Chi-restraints excluded: chain 4 residue 83 LEU Chi-restraints excluded: chain 4 residue 108 LEU Chi-restraints excluded: chain 4 residue 129 THR Chi-restraints excluded: chain 4 residue 171 ASP Chi-restraints excluded: chain 4 residue 320 TRP Chi-restraints excluded: chain 4 residue 422 ASP Chi-restraints excluded: chain 4 residue 442 ARG Chi-restraints excluded: chain 5 residue 59 GLN Chi-restraints excluded: chain 5 residue 76 PHE Chi-restraints excluded: chain 5 residue 83 LEU Chi-restraints excluded: chain 5 residue 129 THR Chi-restraints excluded: chain 5 residue 289 VAL Chi-restraints excluded: chain 5 residue 320 TRP Chi-restraints excluded: chain 5 residue 422 ASP Chi-restraints excluded: chain 5 residue 431 VAL Chi-restraints excluded: chain 5 residue 442 ARG Chi-restraints excluded: chain 6 residue 76 PHE Chi-restraints excluded: chain 6 residue 82 LEU Chi-restraints excluded: chain 6 residue 83 LEU Chi-restraints excluded: chain 6 residue 129 THR Chi-restraints excluded: chain 6 residue 289 VAL Chi-restraints excluded: chain 6 residue 320 TRP Chi-restraints excluded: chain 6 residue 371 LEU Chi-restraints excluded: chain 6 residue 431 VAL Chi-restraints excluded: chain 6 residue 442 ARG Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 69 LEU Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain O residue 37 SER Chi-restraints excluded: chain O residue 52 VAL Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 69 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 269 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 359 optimal weight: 10.0000 chunk 70 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 221 optimal weight: 0.5980 chunk 431 optimal weight: 8.9990 chunk 126 optimal weight: 1.9990 chunk 311 optimal weight: 6.9990 chunk 119 optimal weight: 6.9990 chunk 169 optimal weight: 10.0000 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 36 GLN O 91 ASN Q 36 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.057960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.051025 restraints weight = 180296.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.051858 restraints weight = 112923.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.052486 restraints weight = 79971.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.052900 restraints weight = 60353.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.053256 restraints weight = 48730.921| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 35052 Z= 0.139 Angle : 0.613 7.155 47790 Z= 0.321 Chirality : 0.045 0.188 5364 Planarity : 0.004 0.044 6240 Dihedral : 5.437 26.630 4842 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 2.44 % Allowed : 14.62 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.15 (0.12), residues: 4440 helix: -5.47 (0.13), residues: 42 sheet: -1.48 (0.16), residues: 1032 loop : -2.45 (0.10), residues: 3366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 4 374 TYR 0.010 0.001 TYR B 39 PHE 0.012 0.001 PHE E 65 TRP 0.024 0.002 TRP 4 320 HIS 0.005 0.001 HIS B 48 Details of bonding type rmsd covalent geometry : bond 0.00327 (35052) covalent geometry : angle 0.61301 (47790) hydrogen bonds : bond 0.03479 ( 522) hydrogen bonds : angle 5.78407 ( 1296) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4396.48 seconds wall clock time: 77 minutes 52.49 seconds (4672.49 seconds total)