Starting phenix.real_space_refine on Tue Aug 26 22:27:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xb5_38211/08_2025/8xb5_38211.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xb5_38211/08_2025/8xb5_38211.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xb5_38211/08_2025/8xb5_38211.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xb5_38211/08_2025/8xb5_38211.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xb5_38211/08_2025/8xb5_38211.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xb5_38211/08_2025/8xb5_38211.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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 204 5.16 5 C 26988 2.51 5 N 7428 2.21 5 O 8376 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.04s 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: 42996 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3583 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 17, 'TRANS': 432} Chain breaks: 1 Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L Time building chain proxies: 4.40, per 1000 atoms: 0.10 Number of scatterers: 42996 At special positions: 0 Unit cell: (175.56, 175.56, 121.44, 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 204 16.00 O 8376 8.00 N 7428 7.00 C 26988 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.36 Conformation dependent library (CDL) restraints added in 1.8 seconds Enol-peptide restraints added in 1.2 microseconds 10704 Ramachandran restraints generated. 5352 Oldfield, 0 Emsley, 5352 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10104 Finding SS restraints... Secondary structure from input PDB file: 204 helices and 36 sheets defined 49.1% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 11 through 30 removed outlier: 4.156A pdb=" N LYS A 19 " --> pdb=" O LYS A 15 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU A 20 " --> pdb=" O LYS A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 37 removed outlier: 3.621A pdb=" N ILE A 34 " --> pdb=" O GLY A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 42 removed outlier: 3.735A pdb=" N PHE A 41 " --> pdb=" O ASN A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 52 through 65 Processing helix chain 'A' and resid 70 through 84 removed outlier: 3.693A pdb=" N ASN A 74 " --> pdb=" O GLY A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 96 No H-bonds generated for 'chain 'A' and resid 94 through 96' Processing helix chain 'A' and resid 97 through 103 Processing helix chain 'A' and resid 110 through 125 Processing helix chain 'A' and resid 262 through 287 Processing helix chain 'A' and resid 297 through 304 Processing helix chain 'A' and resid 334 through 350 Processing helix chain 'A' and resid 366 through 375 removed outlier: 3.916A pdb=" N GLU A 370 " --> pdb=" O GLU A 366 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ALA A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ALA A 373 " --> pdb=" O MET A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 401 Processing helix chain 'A' and resid 420 through 433 Processing helix chain 'A' and resid 437 through 448 Processing helix chain 'A' and resid 454 through 464 removed outlier: 4.197A pdb=" N GLN A 464 " --> pdb=" O ASN A 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 30 removed outlier: 4.155A pdb=" N LYS B 19 " --> pdb=" O LYS B 15 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU B 20 " --> pdb=" O LYS B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 37 removed outlier: 3.621A pdb=" N ILE B 34 " --> pdb=" O GLY B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 42 removed outlier: 3.735A pdb=" N PHE B 41 " --> pdb=" O ASN B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 52 Processing helix chain 'B' and resid 52 through 65 Processing helix chain 'B' and resid 70 through 84 removed outlier: 3.694A pdb=" N ASN B 74 " --> pdb=" O GLY B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 96 No H-bonds generated for 'chain 'B' and resid 94 through 96' Processing helix chain 'B' and resid 97 through 103 Processing helix chain 'B' and resid 110 through 125 Processing helix chain 'B' and resid 262 through 287 Processing helix chain 'B' and resid 297 through 304 Processing helix chain 'B' and resid 334 through 350 Processing helix chain 'B' and resid 366 through 375 removed outlier: 3.916A pdb=" N GLU B 370 " --> pdb=" O GLU B 366 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ALA B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ALA B 373 " --> pdb=" O MET B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 401 Processing helix chain 'B' and resid 420 through 433 Processing helix chain 'B' and resid 437 through 448 Processing helix chain 'B' and resid 454 through 464 removed outlier: 4.197A pdb=" N GLN B 464 " --> pdb=" O ASN B 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 30 removed outlier: 4.156A pdb=" N LYS C 19 " --> pdb=" O LYS C 15 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU C 20 " --> pdb=" O LYS C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 37 removed outlier: 3.621A pdb=" N ILE C 34 " --> pdb=" O GLY C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 42 removed outlier: 3.735A pdb=" N PHE C 41 " --> pdb=" O ASN C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 52 Processing helix chain 'C' and resid 52 through 65 Processing helix chain 'C' and resid 70 through 84 removed outlier: 3.694A pdb=" N ASN C 74 " --> pdb=" O GLY C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 96 No H-bonds generated for 'chain 'C' and resid 94 through 96' Processing helix chain 'C' and resid 97 through 103 Processing helix chain 'C' and resid 110 through 125 Processing helix chain 'C' and resid 262 through 287 Processing helix chain 'C' and resid 297 through 304 Processing helix chain 'C' and resid 334 through 350 Processing helix chain 'C' and resid 366 through 375 removed outlier: 3.917A pdb=" N GLU C 370 " --> pdb=" O GLU C 366 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ALA C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ALA C 373 " --> pdb=" O MET C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 401 Processing helix chain 'C' and resid 420 through 433 Processing helix chain 'C' and resid 437 through 448 Processing helix chain 'C' and resid 454 through 464 removed outlier: 4.196A pdb=" N GLN C 464 " --> pdb=" O ASN C 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 30 removed outlier: 4.156A pdb=" N LYS D 19 " --> pdb=" O LYS D 15 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU D 20 " --> pdb=" O LYS D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 37 removed outlier: 3.622A pdb=" N ILE D 34 " --> pdb=" O GLY D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 42 removed outlier: 3.735A pdb=" N PHE D 41 " --> pdb=" O ASN D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 52 Processing helix chain 'D' and resid 52 through 65 Processing helix chain 'D' and resid 70 through 84 removed outlier: 3.693A pdb=" N ASN D 74 " --> pdb=" O GLY D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 96 No H-bonds generated for 'chain 'D' and resid 94 through 96' Processing helix chain 'D' and resid 97 through 103 Processing helix chain 'D' and resid 110 through 125 Processing helix chain 'D' and resid 262 through 287 Processing helix chain 'D' and resid 297 through 304 Processing helix chain 'D' and resid 334 through 350 Processing helix chain 'D' and resid 366 through 375 removed outlier: 3.916A pdb=" N GLU D 370 " --> pdb=" O GLU D 366 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ALA D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ALA D 373 " --> pdb=" O MET D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 401 Processing helix chain 'D' and resid 420 through 433 Processing helix chain 'D' and resid 437 through 448 Processing helix chain 'D' and resid 454 through 464 removed outlier: 4.196A pdb=" N GLN D 464 " --> pdb=" O ASN D 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 30 removed outlier: 4.156A pdb=" N LYS E 19 " --> pdb=" O LYS E 15 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU E 20 " --> pdb=" O LYS E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 37 removed outlier: 3.621A pdb=" N ILE E 34 " --> pdb=" O GLY E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 42 removed outlier: 3.735A pdb=" N PHE E 41 " --> pdb=" O ASN E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 52 Processing helix chain 'E' and resid 52 through 65 Processing helix chain 'E' and resid 70 through 84 removed outlier: 3.693A pdb=" N ASN E 74 " --> pdb=" O GLY E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 96 No H-bonds generated for 'chain 'E' and resid 94 through 96' Processing helix chain 'E' and resid 97 through 103 Processing helix chain 'E' and resid 110 through 125 Processing helix chain 'E' and resid 262 through 287 Processing helix chain 'E' and resid 297 through 304 Processing helix chain 'E' and resid 334 through 350 Processing helix chain 'E' and resid 366 through 375 removed outlier: 3.916A pdb=" N GLU E 370 " --> pdb=" O GLU E 366 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ALA E 372 " --> pdb=" O SER E 368 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ALA E 373 " --> pdb=" O MET E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 375 through 401 Processing helix chain 'E' and resid 420 through 433 Processing helix chain 'E' and resid 437 through 448 Processing helix chain 'E' and resid 454 through 464 removed outlier: 4.197A pdb=" N GLN E 464 " --> pdb=" O ASN E 460 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 30 removed outlier: 4.157A pdb=" N LYS F 19 " --> pdb=" O LYS F 15 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU F 20 " --> pdb=" O LYS F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 37 removed outlier: 3.621A pdb=" N ILE F 34 " --> pdb=" O GLY F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 42 removed outlier: 3.735A pdb=" N PHE F 41 " --> pdb=" O ASN F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 52 Processing helix chain 'F' and resid 52 through 65 Processing helix chain 'F' and resid 70 through 84 removed outlier: 3.693A pdb=" N ASN F 74 " --> pdb=" O GLY F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 96 No H-bonds generated for 'chain 'F' and resid 94 through 96' Processing helix chain 'F' and resid 97 through 103 Processing helix chain 'F' and resid 110 through 125 Processing helix chain 'F' and resid 262 through 287 Processing helix chain 'F' and resid 297 through 304 Processing helix chain 'F' and resid 334 through 350 Processing helix chain 'F' and resid 366 through 375 removed outlier: 3.916A pdb=" N GLU F 370 " --> pdb=" O GLU F 366 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ALA F 372 " --> pdb=" O SER F 368 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ALA F 373 " --> pdb=" O MET F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 375 through 401 Processing helix chain 'F' and resid 420 through 433 Processing helix chain 'F' and resid 437 through 448 Processing helix chain 'F' and resid 454 through 464 removed outlier: 4.197A pdb=" N GLN F 464 " --> pdb=" O ASN F 460 " (cutoff:3.500A) Processing helix chain 'G' and resid 11 through 30 removed outlier: 4.155A pdb=" N LYS G 19 " --> pdb=" O LYS G 15 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU G 20 " --> pdb=" O LYS G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 37 removed outlier: 3.621A pdb=" N ILE G 34 " --> pdb=" O GLY G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 42 removed outlier: 3.735A pdb=" N PHE G 41 " --> pdb=" O ASN G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 52 Processing helix chain 'G' and resid 52 through 65 Processing helix chain 'G' and resid 70 through 84 removed outlier: 3.694A pdb=" N ASN G 74 " --> pdb=" O GLY G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 96 No H-bonds generated for 'chain 'G' and resid 94 through 96' Processing helix chain 'G' and resid 97 through 103 Processing helix chain 'G' and resid 110 through 125 Processing helix chain 'G' and resid 262 through 287 Processing helix chain 'G' and resid 297 through 304 Processing helix chain 'G' and resid 334 through 350 Processing helix chain 'G' and resid 366 through 375 removed outlier: 3.916A pdb=" N GLU G 370 " --> pdb=" O GLU G 366 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ALA G 372 " --> pdb=" O SER G 368 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ALA G 373 " --> pdb=" O MET G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 375 through 401 Processing helix chain 'G' and resid 420 through 433 Processing helix chain 'G' and resid 437 through 448 Processing helix chain 'G' and resid 454 through 464 removed outlier: 4.197A pdb=" N GLN G 464 " --> pdb=" O ASN G 460 " (cutoff:3.500A) Processing helix chain 'H' and resid 11 through 30 removed outlier: 4.156A pdb=" N LYS H 19 " --> pdb=" O LYS H 15 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU H 20 " --> pdb=" O LYS H 16 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 37 removed outlier: 3.620A pdb=" N ILE H 34 " --> pdb=" O GLY H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 42 removed outlier: 3.735A pdb=" N PHE H 41 " --> pdb=" O ASN H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 52 Processing helix chain 'H' and resid 52 through 65 Processing helix chain 'H' and resid 70 through 84 removed outlier: 3.693A pdb=" N ASN H 74 " --> pdb=" O GLY H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 96 No H-bonds generated for 'chain 'H' and resid 94 through 96' Processing helix chain 'H' and resid 97 through 103 Processing helix chain 'H' and resid 110 through 125 Processing helix chain 'H' and resid 262 through 287 Processing helix chain 'H' and resid 297 through 304 Processing helix chain 'H' and resid 334 through 350 Processing helix chain 'H' and resid 366 through 375 removed outlier: 3.916A pdb=" N GLU H 370 " --> pdb=" O GLU H 366 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ALA H 372 " --> pdb=" O SER H 368 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ALA H 373 " --> pdb=" O MET H 369 " (cutoff:3.500A) Processing helix chain 'H' and resid 375 through 401 Processing helix chain 'H' and resid 420 through 433 Processing helix chain 'H' and resid 437 through 448 Processing helix chain 'H' and resid 454 through 464 removed outlier: 4.197A pdb=" N GLN H 464 " --> pdb=" O ASN H 460 " (cutoff:3.500A) Processing helix chain 'I' and resid 11 through 30 removed outlier: 4.156A pdb=" N LYS I 19 " --> pdb=" O LYS I 15 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU I 20 " --> pdb=" O LYS I 16 " (cutoff:3.500A) Processing helix chain 'I' and resid 30 through 37 removed outlier: 3.621A pdb=" N ILE I 34 " --> pdb=" O GLY I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 42 removed outlier: 3.735A pdb=" N PHE I 41 " --> pdb=" O ASN I 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 52 Processing helix chain 'I' and resid 52 through 65 Processing helix chain 'I' and resid 70 through 84 removed outlier: 3.693A pdb=" N ASN I 74 " --> pdb=" O GLY I 70 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 96 No H-bonds generated for 'chain 'I' and resid 94 through 96' Processing helix chain 'I' and resid 97 through 103 Processing helix chain 'I' and resid 110 through 125 Processing helix chain 'I' and resid 262 through 287 Processing helix chain 'I' and resid 297 through 304 Processing helix chain 'I' and resid 334 through 350 Processing helix chain 'I' and resid 366 through 375 removed outlier: 3.916A pdb=" N GLU I 370 " --> pdb=" O GLU I 366 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ALA I 372 " --> pdb=" O SER I 368 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ALA I 373 " --> pdb=" O MET I 369 " (cutoff:3.500A) Processing helix chain 'I' and resid 375 through 401 Processing helix chain 'I' and resid 420 through 433 Processing helix chain 'I' and resid 437 through 448 Processing helix chain 'I' and resid 454 through 464 removed outlier: 4.196A pdb=" N GLN I 464 " --> pdb=" O ASN I 460 " (cutoff:3.500A) Processing helix chain 'J' and resid 11 through 30 removed outlier: 4.156A pdb=" N LYS J 19 " --> pdb=" O LYS J 15 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LEU J 20 " --> pdb=" O LYS J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 37 removed outlier: 3.621A pdb=" N ILE J 34 " --> pdb=" O GLY J 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 42 removed outlier: 3.736A pdb=" N PHE J 41 " --> pdb=" O ASN J 37 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 52 Processing helix chain 'J' and resid 52 through 65 Processing helix chain 'J' and resid 70 through 84 removed outlier: 3.693A pdb=" N ASN J 74 " --> pdb=" O GLY J 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 96 No H-bonds generated for 'chain 'J' and resid 94 through 96' Processing helix chain 'J' and resid 97 through 103 Processing helix chain 'J' and resid 110 through 125 Processing helix chain 'J' and resid 262 through 287 Processing helix chain 'J' and resid 297 through 304 Processing helix chain 'J' and resid 334 through 350 Processing helix chain 'J' and resid 366 through 375 removed outlier: 3.916A pdb=" N GLU J 370 " --> pdb=" O GLU J 366 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ALA J 372 " --> pdb=" O SER J 368 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ALA J 373 " --> pdb=" O MET J 369 " (cutoff:3.500A) Processing helix chain 'J' and resid 375 through 401 Processing helix chain 'J' and resid 420 through 433 Processing helix chain 'J' and resid 437 through 448 Processing helix chain 'J' and resid 454 through 464 removed outlier: 4.197A pdb=" N GLN J 464 " --> pdb=" O ASN J 460 " (cutoff:3.500A) Processing helix chain 'K' and resid 11 through 30 removed outlier: 4.156A pdb=" N LYS K 19 " --> pdb=" O LYS K 15 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU K 20 " --> pdb=" O LYS K 16 " (cutoff:3.500A) Processing helix chain 'K' and resid 30 through 37 removed outlier: 3.621A pdb=" N ILE K 34 " --> pdb=" O GLY K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 42 removed outlier: 3.736A pdb=" N PHE K 41 " --> pdb=" O ASN K 37 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 52 Processing helix chain 'K' and resid 52 through 65 Processing helix chain 'K' and resid 70 through 84 removed outlier: 3.694A pdb=" N ASN K 74 " --> pdb=" O GLY K 70 " (cutoff:3.500A) Processing helix chain 'K' and resid 94 through 96 No H-bonds generated for 'chain 'K' and resid 94 through 96' Processing helix chain 'K' and resid 97 through 103 Processing helix chain 'K' and resid 110 through 125 Processing helix chain 'K' and resid 262 through 287 Processing helix chain 'K' and resid 297 through 304 Processing helix chain 'K' and resid 334 through 350 Processing helix chain 'K' and resid 366 through 375 removed outlier: 3.916A pdb=" N GLU K 370 " --> pdb=" O GLU K 366 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ALA K 372 " --> pdb=" O SER K 368 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ALA K 373 " --> pdb=" O MET K 369 " (cutoff:3.500A) Processing helix chain 'K' and resid 375 through 401 Processing helix chain 'K' and resid 420 through 433 Processing helix chain 'K' and resid 437 through 448 Processing helix chain 'K' and resid 454 through 464 removed outlier: 4.197A pdb=" N GLN K 464 " --> pdb=" O ASN K 460 " (cutoff:3.500A) Processing helix chain 'L' and resid 11 through 30 removed outlier: 4.157A pdb=" N LYS L 19 " --> pdb=" O LYS L 15 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LEU L 20 " --> pdb=" O LYS L 16 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 37 removed outlier: 3.621A pdb=" N ILE L 34 " --> pdb=" O GLY L 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 42 removed outlier: 3.735A pdb=" N PHE L 41 " --> pdb=" O ASN L 37 " (cutoff:3.500A) Processing helix chain 'L' and resid 46 through 52 Processing helix chain 'L' and resid 52 through 65 Processing helix chain 'L' and resid 70 through 84 removed outlier: 3.693A pdb=" N ASN L 74 " --> pdb=" O GLY L 70 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 96 No H-bonds generated for 'chain 'L' and resid 94 through 96' Processing helix chain 'L' and resid 97 through 103 Processing helix chain 'L' and resid 110 through 125 Processing helix chain 'L' and resid 262 through 287 Processing helix chain 'L' and resid 297 through 304 Processing helix chain 'L' and resid 334 through 350 Processing helix chain 'L' and resid 366 through 375 removed outlier: 3.916A pdb=" N GLU L 370 " --> pdb=" O GLU L 366 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ALA L 372 " --> pdb=" O SER L 368 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ALA L 373 " --> pdb=" O MET L 369 " (cutoff:3.500A) Processing helix chain 'L' and resid 375 through 401 Processing helix chain 'L' and resid 420 through 433 Processing helix chain 'L' and resid 437 through 448 Processing helix chain 'L' and resid 454 through 464 removed outlier: 4.198A pdb=" N GLN L 464 " --> pdb=" O ASN L 460 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 89 through 91 Processing sheet with id=AA2, first strand: chain 'A' and resid 154 through 156 Processing sheet with id=AA3, first strand: chain 'A' and resid 164 through 169 removed outlier: 5.639A pdb=" N ILE A 164 " --> pdb=" O ARG A 184 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ARG A 184 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU A 180 " --> pdb=" O ARG A 168 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N THR A 179 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N GLU A 200 " --> pdb=" O GLU A 219 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU A 219 " --> pdb=" O GLU A 200 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 89 through 91 Processing sheet with id=AA5, first strand: chain 'B' and resid 154 through 156 Processing sheet with id=AA6, first strand: chain 'B' and resid 164 through 169 removed outlier: 5.639A pdb=" N ILE B 164 " --> pdb=" O ARG B 184 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ARG B 184 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU B 180 " --> pdb=" O ARG B 168 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N THR B 179 " --> pdb=" O LEU B 207 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N GLU B 200 " --> pdb=" O GLU B 219 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU B 219 " --> pdb=" O GLU B 200 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 89 through 91 Processing sheet with id=AA8, first strand: chain 'C' and resid 154 through 156 Processing sheet with id=AA9, first strand: chain 'C' and resid 164 through 169 removed outlier: 5.639A pdb=" N ILE C 164 " --> pdb=" O ARG C 184 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ARG C 184 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU C 180 " --> pdb=" O ARG C 168 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N THR C 179 " --> pdb=" O LEU C 207 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N GLU C 200 " --> pdb=" O GLU C 219 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU C 219 " --> pdb=" O GLU C 200 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 89 through 91 Processing sheet with id=AB2, first strand: chain 'D' and resid 154 through 156 Processing sheet with id=AB3, first strand: chain 'D' and resid 164 through 169 removed outlier: 5.639A pdb=" N ILE D 164 " --> pdb=" O ARG D 184 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ARG D 184 " --> pdb=" O ILE D 164 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU D 180 " --> pdb=" O ARG D 168 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N THR D 179 " --> pdb=" O LEU D 207 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N GLU D 200 " --> pdb=" O GLU D 219 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU D 219 " --> pdb=" O GLU D 200 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 89 through 91 Processing sheet with id=AB5, first strand: chain 'E' and resid 154 through 156 Processing sheet with id=AB6, first strand: chain 'E' and resid 164 through 169 removed outlier: 5.639A pdb=" N ILE E 164 " --> pdb=" O ARG E 184 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ARG E 184 " --> pdb=" O ILE E 164 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU E 180 " --> pdb=" O ARG E 168 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N THR E 179 " --> pdb=" O LEU E 207 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N GLU E 200 " --> pdb=" O GLU E 219 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU E 219 " --> pdb=" O GLU E 200 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 89 through 91 Processing sheet with id=AB8, first strand: chain 'F' and resid 154 through 156 Processing sheet with id=AB9, first strand: chain 'F' and resid 164 through 169 removed outlier: 5.638A pdb=" N ILE F 164 " --> pdb=" O ARG F 184 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ARG F 184 " --> pdb=" O ILE F 164 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU F 180 " --> pdb=" O ARG F 168 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N THR F 179 " --> pdb=" O LEU F 207 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N GLU F 200 " --> pdb=" O GLU F 219 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU F 219 " --> pdb=" O GLU F 200 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 89 through 91 Processing sheet with id=AC2, first strand: chain 'G' and resid 154 through 156 Processing sheet with id=AC3, first strand: chain 'G' and resid 164 through 169 removed outlier: 5.640A pdb=" N ILE G 164 " --> pdb=" O ARG G 184 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ARG G 184 " --> pdb=" O ILE G 164 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU G 180 " --> pdb=" O ARG G 168 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N THR G 179 " --> pdb=" O LEU G 207 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N GLU G 200 " --> pdb=" O GLU G 219 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU G 219 " --> pdb=" O GLU G 200 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 89 through 91 Processing sheet with id=AC5, first strand: chain 'H' and resid 154 through 156 Processing sheet with id=AC6, first strand: chain 'H' and resid 164 through 169 removed outlier: 5.640A pdb=" N ILE H 164 " --> pdb=" O ARG H 184 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ARG H 184 " --> pdb=" O ILE H 164 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU H 180 " --> pdb=" O ARG H 168 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N THR H 179 " --> pdb=" O LEU H 207 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N GLU H 200 " --> pdb=" O GLU H 219 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU H 219 " --> pdb=" O GLU H 200 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 89 through 91 Processing sheet with id=AC8, first strand: chain 'I' and resid 154 through 156 Processing sheet with id=AC9, first strand: chain 'I' and resid 164 through 169 removed outlier: 5.639A pdb=" N ILE I 164 " --> pdb=" O ARG I 184 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ARG I 184 " --> pdb=" O ILE I 164 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU I 180 " --> pdb=" O ARG I 168 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N THR I 179 " --> pdb=" O LEU I 207 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N GLU I 200 " --> pdb=" O GLU I 219 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU I 219 " --> pdb=" O GLU I 200 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 89 through 91 Processing sheet with id=AD2, first strand: chain 'J' and resid 154 through 156 Processing sheet with id=AD3, first strand: chain 'J' and resid 164 through 169 removed outlier: 5.638A pdb=" N ILE J 164 " --> pdb=" O ARG J 184 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ARG J 184 " --> pdb=" O ILE J 164 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU J 180 " --> pdb=" O ARG J 168 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N THR J 179 " --> pdb=" O LEU J 207 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N GLU J 200 " --> pdb=" O GLU J 219 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU J 219 " --> pdb=" O GLU J 200 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 89 through 91 Processing sheet with id=AD5, first strand: chain 'K' and resid 154 through 156 Processing sheet with id=AD6, first strand: chain 'K' and resid 164 through 169 removed outlier: 5.639A pdb=" N ILE K 164 " --> pdb=" O ARG K 184 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ARG K 184 " --> pdb=" O ILE K 164 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU K 180 " --> pdb=" O ARG K 168 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N THR K 179 " --> pdb=" O LEU K 207 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N GLU K 200 " --> pdb=" O GLU K 219 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU K 219 " --> pdb=" O GLU K 200 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 89 through 91 Processing sheet with id=AD8, first strand: chain 'L' and resid 154 through 156 Processing sheet with id=AD9, first strand: chain 'L' and resid 164 through 169 removed outlier: 5.639A pdb=" N ILE L 164 " --> pdb=" O ARG L 184 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ARG L 184 " --> pdb=" O ILE L 164 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU L 180 " --> pdb=" O ARG L 168 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N THR L 179 " --> pdb=" O LEU L 207 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N GLU L 200 " --> pdb=" O GLU L 219 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU L 219 " --> pdb=" O GLU L 200 " (cutoff:3.500A) 2124 hydrogen bonds defined for protein. 6156 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: 8.43 Time building geometry restraints manager: 4.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 14616 1.34 - 1.46: 8622 1.46 - 1.58: 20286 1.58 - 1.69: 0 1.69 - 1.81: 384 Bond restraints: 43908 Sorted by residual: bond pdb=" N ARG H 153 " pdb=" CA ARG H 153 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.41e-02 5.03e+03 6.12e+00 bond pdb=" N ARG G 153 " pdb=" CA ARG G 153 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.41e-02 5.03e+03 6.11e+00 bond pdb=" N ARG L 153 " pdb=" CA ARG L 153 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.41e-02 5.03e+03 6.03e+00 bond pdb=" N ARG B 153 " pdb=" CA ARG B 153 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.41e-02 5.03e+03 5.96e+00 bond pdb=" N ARG C 153 " pdb=" CA ARG C 153 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.41e-02 5.03e+03 5.92e+00 ... (remaining 43903 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 58523 1.65 - 3.30: 748 3.30 - 4.95: 93 4.95 - 6.61: 12 6.61 - 8.26: 12 Bond angle restraints: 59388 Sorted by residual: angle pdb=" CA LEU C 354 " pdb=" CB LEU C 354 " pdb=" CG LEU C 354 " ideal model delta sigma weight residual 116.30 124.56 -8.26 3.50e+00 8.16e-02 5.57e+00 angle pdb=" CA LEU B 354 " pdb=" CB LEU B 354 " pdb=" CG LEU B 354 " ideal model delta sigma weight residual 116.30 124.55 -8.25 3.50e+00 8.16e-02 5.55e+00 angle pdb=" CA LEU L 354 " pdb=" CB LEU L 354 " pdb=" CG LEU L 354 " ideal model delta sigma weight residual 116.30 124.54 -8.24 3.50e+00 8.16e-02 5.54e+00 angle pdb=" CA LEU J 354 " pdb=" CB LEU J 354 " pdb=" CG LEU J 354 " ideal model delta sigma weight residual 116.30 124.52 -8.22 3.50e+00 8.16e-02 5.52e+00 angle pdb=" CA LEU E 354 " pdb=" CB LEU E 354 " pdb=" CG LEU E 354 " ideal model delta sigma weight residual 116.30 124.52 -8.22 3.50e+00 8.16e-02 5.52e+00 ... (remaining 59383 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 22338 17.95 - 35.89: 3102 35.89 - 53.84: 828 53.84 - 71.79: 108 71.79 - 89.74: 48 Dihedral angle restraints: 26424 sinusoidal: 10776 harmonic: 15648 Sorted by residual: dihedral pdb=" CB GLU D 40 " pdb=" CG GLU D 40 " pdb=" CD GLU D 40 " pdb=" OE1 GLU D 40 " ideal model delta sinusoidal sigma weight residual 0.00 89.74 -89.74 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU L 40 " pdb=" CG GLU L 40 " pdb=" CD GLU L 40 " pdb=" OE1 GLU L 40 " ideal model delta sinusoidal sigma weight residual 0.00 89.72 -89.72 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU I 40 " pdb=" CG GLU I 40 " pdb=" CD GLU I 40 " pdb=" OE1 GLU I 40 " ideal model delta sinusoidal sigma weight residual 0.00 89.70 -89.70 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 26421 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 4865 0.040 - 0.081: 993 0.081 - 0.121: 358 0.121 - 0.162: 12 0.162 - 0.202: 24 Chirality restraints: 6252 Sorted by residual: chirality pdb=" CB ILE L 355 " pdb=" CA ILE L 355 " pdb=" CG1 ILE L 355 " pdb=" CG2 ILE L 355 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CB ILE C 355 " pdb=" CA ILE C 355 " pdb=" CG1 ILE C 355 " pdb=" CG2 ILE C 355 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CB ILE B 355 " pdb=" CA ILE B 355 " pdb=" CG1 ILE B 355 " pdb=" CG2 ILE B 355 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.91e-01 ... (remaining 6249 not shown) Planarity restraints: 7860 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER G 420 " 0.026 5.00e-02 4.00e+02 3.92e-02 2.46e+00 pdb=" N PRO G 421 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO G 421 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO G 421 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 420 " -0.026 5.00e-02 4.00e+02 3.92e-02 2.45e+00 pdb=" N PRO A 421 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 421 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 421 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER F 420 " 0.026 5.00e-02 4.00e+02 3.91e-02 2.45e+00 pdb=" N PRO F 421 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO F 421 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO F 421 " 0.022 5.00e-02 4.00e+02 ... (remaining 7857 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 4422 2.75 - 3.28: 43182 3.28 - 3.82: 73631 3.82 - 4.36: 87772 4.36 - 4.90: 149219 Nonbonded interactions: 358226 Sorted by model distance: nonbonded pdb=" OH TYR L 62 " pdb=" OD1 ASP L 278 " model vdw 2.206 3.040 nonbonded pdb=" OH TYR H 62 " pdb=" OD1 ASP H 278 " model vdw 2.207 3.040 nonbonded pdb=" OH TYR K 62 " pdb=" OD1 ASP K 278 " model vdw 2.207 3.040 nonbonded pdb=" OH TYR G 62 " pdb=" OD1 ASP G 278 " model vdw 2.207 3.040 nonbonded pdb=" OH TYR B 62 " pdb=" OD1 ASP B 278 " model vdw 2.207 3.040 ... (remaining 358221 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.15 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 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: 0.030 Extract box with map and model: 0.570 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 31.460 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 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 : 0.003 0.035 43908 Z= 0.130 Angle : 0.476 8.257 59388 Z= 0.251 Chirality : 0.039 0.202 6252 Planarity : 0.004 0.039 7860 Dihedral : 17.359 89.737 16320 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.60 % Allowed : 25.88 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.12), residues: 5352 helix: 1.87 (0.11), residues: 2424 sheet: 0.82 (0.19), residues: 708 loop : -0.32 (0.14), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 184 TYR 0.005 0.001 TYR E 62 PHE 0.010 0.001 PHE G 84 TRP 0.013 0.001 TRP H 171 HIS 0.003 0.001 HIS K 299 Details of bonding type rmsd covalent geometry : bond 0.00265 (43908) covalent geometry : angle 0.47649 (59388) hydrogen bonds : bond 0.16649 ( 2124) hydrogen bonds : angle 5.99360 ( 6156) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10704 Ramachandran restraints generated. 5352 Oldfield, 0 Emsley, 5352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10704 Ramachandran restraints generated. 5352 Oldfield, 0 Emsley, 5352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 900 residues out of total 4524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 873 time to evaluate : 1.415 Fit side-chains REVERT: A 176 LYS cc_start: 0.8281 (mmtp) cc_final: 0.8065 (mmtt) REVERT: A 415 ASP cc_start: 0.7381 (m-30) cc_final: 0.7118 (m-30) REVERT: B 103 ASP cc_start: 0.7513 (p0) cc_final: 0.7290 (p0) REVERT: B 217 TRP cc_start: 0.8269 (m100) cc_final: 0.8060 (m100) REVERT: B 370 GLU cc_start: 0.7673 (mp0) cc_final: 0.7457 (mp0) REVERT: B 398 MET cc_start: 0.8469 (mtt) cc_final: 0.8097 (mtm) REVERT: B 455 ASP cc_start: 0.7299 (p0) cc_final: 0.7013 (m-30) REVERT: C 369 MET cc_start: 0.6745 (mmp) cc_final: 0.6456 (mmp) REVERT: C 398 MET cc_start: 0.8567 (mtt) cc_final: 0.8282 (mtt) REVERT: D 103 ASP cc_start: 0.7548 (p0) cc_final: 0.7233 (p0) REVERT: D 134 TYR cc_start: 0.8393 (t80) cc_final: 0.8113 (t80) REVERT: D 171 TRP cc_start: 0.6615 (m100) cc_final: 0.6194 (m100) REVERT: D 415 ASP cc_start: 0.6956 (m-30) cc_final: 0.6697 (m-30) REVERT: E 398 MET cc_start: 0.8450 (mtt) cc_final: 0.8048 (mtm) REVERT: E 455 ASP cc_start: 0.7371 (p0) cc_final: 0.6990 (m-30) REVERT: F 369 MET cc_start: 0.6327 (mmp) cc_final: 0.6049 (mmp) REVERT: G 415 ASP cc_start: 0.7105 (m-30) cc_final: 0.6817 (m-30) REVERT: H 383 LYS cc_start: 0.8324 (mmtp) cc_final: 0.8082 (mmtt) REVERT: H 398 MET cc_start: 0.8428 (mtt) cc_final: 0.7995 (mtm) REVERT: H 455 ASP cc_start: 0.7400 (p0) cc_final: 0.7068 (m-30) REVERT: I 176 LYS cc_start: 0.8046 (mmtp) cc_final: 0.7842 (mmtt) REVERT: J 176 LYS cc_start: 0.8187 (mmtp) cc_final: 0.7962 (mmtt) REVERT: K 398 MET cc_start: 0.8356 (mtt) cc_final: 0.7931 (mtm) REVERT: K 455 ASP cc_start: 0.7199 (p0) cc_final: 0.6942 (m-30) REVERT: L 177 ARG cc_start: 0.8292 (mmm-85) cc_final: 0.7996 (mmm-85) REVERT: L 369 MET cc_start: 0.6347 (mmp) cc_final: 0.6049 (mmp) outliers start: 27 outliers final: 25 residues processed: 884 average time/residue: 0.2313 time to fit residues: 337.4946 Evaluate side-chains 834 residues out of total 4524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 809 time to evaluate : 1.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain F residue 241 ASP Chi-restraints excluded: chain F residue 436 ILE Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 241 ASP Chi-restraints excluded: chain G residue 436 ILE Chi-restraints excluded: chain H residue 241 ASP Chi-restraints excluded: chain H residue 436 ILE Chi-restraints excluded: chain I residue 241 ASP Chi-restraints excluded: chain I residue 436 ILE Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 241 ASP Chi-restraints excluded: chain J residue 436 ILE Chi-restraints excluded: chain K residue 241 ASP Chi-restraints excluded: chain K residue 436 ILE Chi-restraints excluded: chain L residue 241 ASP Chi-restraints excluded: chain L residue 436 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 394 optimal weight: 20.0000 chunk 430 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 265 optimal weight: 1.9990 chunk 523 optimal weight: 3.9990 chunk 497 optimal weight: 1.9990 chunk 414 optimal weight: 0.0980 chunk 310 optimal weight: 0.9980 chunk 488 optimal weight: 3.9990 chunk 366 optimal weight: 4.9990 chunk 223 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN A 444 GLN B 195 GLN B 444 GLN C 195 GLN C 444 GLN D 195 GLN D 444 GLN E 195 GLN E 444 GLN F 195 GLN F 444 GLN G 195 GLN G 444 GLN H 195 GLN H 444 GLN I 195 GLN I 444 GLN J 195 GLN J 444 GLN K 195 GLN K 444 GLN L 195 GLN L 444 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.152186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.127973 restraints weight = 59156.058| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.22 r_work: 0.3171 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 43908 Z= 0.110 Angle : 0.481 6.718 59388 Z= 0.258 Chirality : 0.039 0.144 6252 Planarity : 0.004 0.041 7860 Dihedral : 3.774 43.062 5918 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.59 % Allowed : 26.79 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.12), residues: 5352 helix: 2.12 (0.10), residues: 2436 sheet: 0.12 (0.18), residues: 816 loop : -0.28 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 184 TYR 0.013 0.001 TYR H 389 PHE 0.009 0.001 PHE B 158 TRP 0.012 0.001 TRP F 171 HIS 0.002 0.000 HIS D 299 Details of bonding type rmsd covalent geometry : bond 0.00238 (43908) covalent geometry : angle 0.48055 (59388) hydrogen bonds : bond 0.03927 ( 2124) hydrogen bonds : angle 4.69540 ( 6156) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10704 Ramachandran restraints generated. 5352 Oldfield, 0 Emsley, 5352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10704 Ramachandran restraints generated. 5352 Oldfield, 0 Emsley, 5352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 950 residues out of total 4524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 878 time to evaluate : 1.546 Fit side-chains REVERT: A 103 ASP cc_start: 0.8014 (p0) cc_final: 0.7616 (p0) REVERT: A 415 ASP cc_start: 0.7580 (m-30) cc_final: 0.7216 (m-30) REVERT: B 103 ASP cc_start: 0.7488 (p0) cc_final: 0.7151 (p0) REVERT: B 184 ARG cc_start: 0.8717 (tmm-80) cc_final: 0.8384 (ttm-80) REVERT: B 185 GLU cc_start: 0.8455 (tm-30) cc_final: 0.8208 (tm-30) REVERT: B 200 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8246 (mt-10) REVERT: B 398 MET cc_start: 0.8380 (mtt) cc_final: 0.7961 (mtm) REVERT: B 455 ASP cc_start: 0.7218 (p0) cc_final: 0.6950 (m-30) REVERT: C 65 ARG cc_start: 0.8460 (mmm160) cc_final: 0.8199 (tpt170) REVERT: C 84 PHE cc_start: 0.8898 (m-80) cc_final: 0.8625 (m-80) REVERT: C 199 GLU cc_start: 0.8188 (pp20) cc_final: 0.7976 (pp20) REVERT: C 369 MET cc_start: 0.6793 (mmp) cc_final: 0.6425 (mmp) REVERT: D 103 ASP cc_start: 0.7823 (p0) cc_final: 0.7431 (p0) REVERT: D 415 ASP cc_start: 0.7371 (m-30) cc_final: 0.7055 (m-30) REVERT: E 98 ASP cc_start: 0.8402 (t0) cc_final: 0.8133 (t0) REVERT: E 184 ARG cc_start: 0.8735 (tmm-80) cc_final: 0.8475 (ttm-80) REVERT: E 251 LYS cc_start: 0.9204 (tttt) cc_final: 0.8931 (tttp) REVERT: E 398 MET cc_start: 0.8372 (mtt) cc_final: 0.7937 (mtm) REVERT: E 455 ASP cc_start: 0.7257 (p0) cc_final: 0.6924 (m-30) REVERT: F 65 ARG cc_start: 0.8491 (mmm160) cc_final: 0.8241 (tpt170) REVERT: F 84 PHE cc_start: 0.8970 (m-80) cc_final: 0.8691 (m-80) REVERT: F 103 ASP cc_start: 0.7629 (p0) cc_final: 0.7312 (p0) REVERT: F 176 LYS cc_start: 0.7930 (mmtt) cc_final: 0.7706 (mmtt) REVERT: F 199 GLU cc_start: 0.8188 (pp20) cc_final: 0.7966 (pp20) REVERT: F 217 TRP cc_start: 0.8714 (m100) cc_final: 0.8047 (m100) REVERT: F 369 MET cc_start: 0.6789 (mmp) cc_final: 0.6413 (mmp) REVERT: G 103 ASP cc_start: 0.8030 (p0) cc_final: 0.7614 (p0) REVERT: G 415 ASP cc_start: 0.7434 (m-30) cc_final: 0.7092 (m-30) REVERT: H 98 ASP cc_start: 0.8372 (t0) cc_final: 0.8080 (t0) REVERT: H 103 ASP cc_start: 0.7751 (p0) cc_final: 0.7275 (p0) REVERT: H 398 MET cc_start: 0.8431 (mtt) cc_final: 0.7997 (mtm) REVERT: H 455 ASP cc_start: 0.7443 (p0) cc_final: 0.7136 (m-30) REVERT: I 65 ARG cc_start: 0.8500 (mmm160) cc_final: 0.8208 (tpt170) REVERT: I 103 ASP cc_start: 0.7581 (p0) cc_final: 0.7365 (p0) REVERT: I 217 TRP cc_start: 0.8686 (m100) cc_final: 0.8096 (m100) REVERT: I 369 MET cc_start: 0.6644 (mmp) cc_final: 0.6380 (mmp) REVERT: J 103 ASP cc_start: 0.8060 (p0) cc_final: 0.7630 (p0) REVERT: K 103 ASP cc_start: 0.7766 (p0) cc_final: 0.7352 (p0) REVERT: K 398 MET cc_start: 0.8334 (mtt) cc_final: 0.7904 (mtm) REVERT: K 455 ASP cc_start: 0.7275 (p0) cc_final: 0.7020 (m-30) REVERT: L 65 ARG cc_start: 0.8474 (mmm160) cc_final: 0.8200 (tpt170) REVERT: L 98 ASP cc_start: 0.8124 (t0) cc_final: 0.7882 (t0) REVERT: L 217 TRP cc_start: 0.8644 (m100) cc_final: 0.8123 (m100) REVERT: L 329 GLN cc_start: 0.9029 (OUTLIER) cc_final: 0.8758 (pm20) REVERT: L 369 MET cc_start: 0.6346 (mmp) cc_final: 0.5964 (mmp) outliers start: 72 outliers final: 45 residues processed: 924 average time/residue: 0.2264 time to fit residues: 350.4408 Evaluate side-chains 890 residues out of total 4524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 844 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 416 ILE Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 186 GLU Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 416 ILE Chi-restraints excluded: chain G residue 246 VAL Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain G residue 416 ILE Chi-restraints excluded: chain G residue 419 MET Chi-restraints excluded: chain H residue 216 THR Chi-restraints excluded: chain H residue 290 THR Chi-restraints excluded: chain H residue 310 VAL Chi-restraints excluded: chain H residue 317 VAL Chi-restraints excluded: chain H residue 416 ILE Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 186 GLU Chi-restraints excluded: chain I residue 317 VAL Chi-restraints excluded: chain J residue 246 VAL Chi-restraints excluded: chain J residue 317 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain K residue 216 THR Chi-restraints excluded: chain K residue 310 VAL Chi-restraints excluded: chain K residue 317 VAL Chi-restraints excluded: chain K residue 416 ILE Chi-restraints excluded: chain L residue 186 GLU Chi-restraints excluded: chain L residue 317 VAL Chi-restraints excluded: chain L residue 329 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 339 optimal weight: 0.7980 chunk 484 optimal weight: 9.9990 chunk 229 optimal weight: 0.4980 chunk 217 optimal weight: 8.9990 chunk 525 optimal weight: 4.9990 chunk 213 optimal weight: 10.0000 chunk 408 optimal weight: 0.5980 chunk 506 optimal weight: 6.9990 chunk 389 optimal weight: 10.0000 chunk 93 optimal weight: 0.1980 chunk 374 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 444 GLN F 444 GLN I 444 GLN L 444 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.152319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.127530 restraints weight = 59112.838| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.27 r_work: 0.3289 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 43908 Z= 0.090 Angle : 0.432 5.517 59388 Z= 0.233 Chirality : 0.038 0.140 6252 Planarity : 0.003 0.042 7860 Dihedral : 3.371 22.092 5870 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 4.13 % Allowed : 24.65 % Favored : 71.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.12), residues: 5352 helix: 2.27 (0.10), residues: 2436 sheet: 0.45 (0.19), residues: 720 loop : -0.28 (0.14), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 184 TYR 0.014 0.001 TYR J 389 PHE 0.011 0.001 PHE B 158 TRP 0.012 0.001 TRP I 171 HIS 0.001 0.000 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00193 (43908) covalent geometry : angle 0.43238 (59388) hydrogen bonds : bond 0.03376 ( 2124) hydrogen bonds : angle 4.27664 ( 6156) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10704 Ramachandran restraints generated. 5352 Oldfield, 0 Emsley, 5352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10704 Ramachandran restraints generated. 5352 Oldfield, 0 Emsley, 5352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1102 residues out of total 4524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 915 time to evaluate : 1.497 Fit side-chains REVERT: A 103 ASP cc_start: 0.7983 (p0) cc_final: 0.7577 (p0) REVERT: A 171 TRP cc_start: 0.6525 (m100) cc_final: 0.5807 (m100) REVERT: A 329 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.8045 (pm20) REVERT: A 369 MET cc_start: 0.6209 (mmp) cc_final: 0.5862 (mmp) REVERT: A 415 ASP cc_start: 0.7549 (m-30) cc_final: 0.7186 (m-30) REVERT: B 103 ASP cc_start: 0.7590 (p0) cc_final: 0.7190 (p0) REVERT: B 165 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8687 (pp) REVERT: B 185 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8357 (tt0) REVERT: B 251 LYS cc_start: 0.9223 (tttt) cc_final: 0.8869 (tttp) REVERT: B 329 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.7954 (pm20) REVERT: B 398 MET cc_start: 0.8312 (mtt) cc_final: 0.7898 (mtm) REVERT: C 28 MET cc_start: 0.8738 (mmp) cc_final: 0.8486 (mmp) REVERT: C 84 PHE cc_start: 0.8844 (m-80) cc_final: 0.8568 (m-80) REVERT: C 120 GLU cc_start: 0.8451 (tt0) cc_final: 0.8202 (tt0) REVERT: C 329 GLN cc_start: 0.8938 (OUTLIER) cc_final: 0.8728 (pm20) REVERT: C 369 MET cc_start: 0.6722 (mmp) cc_final: 0.6329 (mmp) REVERT: C 405 LYS cc_start: 0.8495 (mmtp) cc_final: 0.8136 (pttm) REVERT: D 103 ASP cc_start: 0.7788 (p0) cc_final: 0.7436 (p0) REVERT: D 171 TRP cc_start: 0.6416 (m100) cc_final: 0.5747 (m100) REVERT: D 225 TYR cc_start: 0.5242 (m-10) cc_final: 0.4911 (m-80) REVERT: D 415 ASP cc_start: 0.7345 (m-30) cc_final: 0.7023 (m-30) REVERT: E 98 ASP cc_start: 0.8280 (t0) cc_final: 0.7600 (m-30) REVERT: E 165 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8600 (pp) REVERT: E 200 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7982 (mt-10) REVERT: E 225 TYR cc_start: 0.4984 (m-80) cc_final: 0.4688 (m-10) REVERT: E 329 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.7922 (pm20) REVERT: E 398 MET cc_start: 0.8376 (mtt) cc_final: 0.7929 (mtm) REVERT: E 455 ASP cc_start: 0.7395 (p0) cc_final: 0.7088 (m-30) REVERT: F 84 PHE cc_start: 0.8890 (m-80) cc_final: 0.8596 (m-80) REVERT: F 217 TRP cc_start: 0.8681 (m100) cc_final: 0.8057 (m100) REVERT: F 329 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.8750 (pm20) REVERT: F 369 MET cc_start: 0.6738 (mmp) cc_final: 0.6377 (mmp) REVERT: F 444 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.8341 (mm-40) REVERT: G 103 ASP cc_start: 0.8040 (p0) cc_final: 0.7641 (p0) REVERT: G 329 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.8091 (pm20) REVERT: G 415 ASP cc_start: 0.7388 (m-30) cc_final: 0.7035 (m-30) REVERT: H 98 ASP cc_start: 0.8267 (t0) cc_final: 0.7573 (m-30) REVERT: H 103 ASP cc_start: 0.7748 (p0) cc_final: 0.7313 (p0) REVERT: H 165 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8545 (pp) REVERT: H 223 GLN cc_start: 0.2525 (OUTLIER) cc_final: 0.2319 (tp40) REVERT: H 225 TYR cc_start: 0.4968 (m-80) cc_final: 0.4539 (m-10) REVERT: H 251 LYS cc_start: 0.9278 (tttt) cc_final: 0.8974 (tttp) REVERT: H 329 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.7770 (pm20) REVERT: H 398 MET cc_start: 0.8352 (mtt) cc_final: 0.7884 (mtm) REVERT: I 84 PHE cc_start: 0.8887 (m-80) cc_final: 0.8607 (m-80) REVERT: I 120 GLU cc_start: 0.8441 (tt0) cc_final: 0.8178 (tt0) REVERT: I 165 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8774 (pp) REVERT: I 217 TRP cc_start: 0.8629 (m100) cc_final: 0.8116 (m100) REVERT: I 241 ASP cc_start: 0.8079 (p0) cc_final: 0.7745 (p0) REVERT: I 329 GLN cc_start: 0.8969 (OUTLIER) cc_final: 0.8748 (pm20) REVERT: J 171 TRP cc_start: 0.6751 (m100) cc_final: 0.6371 (m100) REVERT: J 185 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7898 (tt0) REVERT: J 329 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8067 (pm20) REVERT: K 103 ASP cc_start: 0.7756 (p0) cc_final: 0.7333 (p0) REVERT: K 165 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8521 (pp) REVERT: K 184 ARG cc_start: 0.8779 (tmm-80) cc_final: 0.8534 (ttp80) REVERT: K 199 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7275 (pt0) REVERT: K 217 TRP cc_start: 0.8633 (m100) cc_final: 0.8346 (m-10) REVERT: K 223 GLN cc_start: 0.2359 (OUTLIER) cc_final: 0.2116 (tp40) REVERT: K 329 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.7784 (pm20) REVERT: K 398 MET cc_start: 0.8376 (mtt) cc_final: 0.7935 (mtm) REVERT: K 455 ASP cc_start: 0.7361 (p0) cc_final: 0.7040 (m-30) REVERT: L 84 PHE cc_start: 0.8846 (m-80) cc_final: 0.8551 (m-80) REVERT: L 98 ASP cc_start: 0.7962 (t0) cc_final: 0.7708 (t70) REVERT: L 165 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8832 (pp) REVERT: L 185 GLU cc_start: 0.8286 (tt0) cc_final: 0.8026 (tt0) REVERT: L 217 TRP cc_start: 0.8624 (m100) cc_final: 0.8156 (m100) REVERT: L 241 ASP cc_start: 0.8127 (p0) cc_final: 0.7795 (p0) REVERT: L 369 MET cc_start: 0.6517 (mmp) cc_final: 0.6106 (mmp) REVERT: L 383 LYS cc_start: 0.8582 (ttmt) cc_final: 0.8173 (mmtp) outliers start: 187 outliers final: 92 residues processed: 1049 average time/residue: 0.2302 time to fit residues: 398.4733 Evaluate side-chains 975 residues out of total 4524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 862 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 329 GLN Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 409 GLU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 329 GLN Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain D residue 278 ASP Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 357 SER Chi-restraints excluded: chain D residue 409 GLU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 329 GLN Chi-restraints excluded: chain E residue 357 SER Chi-restraints excluded: chain E residue 376 SER Chi-restraints excluded: chain E residue 409 GLU Chi-restraints excluded: chain E residue 416 ILE Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 329 GLN Chi-restraints excluded: chain F residue 357 SER Chi-restraints excluded: chain F residue 409 GLU Chi-restraints excluded: chain F residue 416 ILE Chi-restraints excluded: chain F residue 436 ILE Chi-restraints excluded: chain F residue 444 GLN Chi-restraints excluded: chain G residue 278 ASP Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain G residue 329 GLN Chi-restraints excluded: chain G residue 357 SER Chi-restraints excluded: chain G residue 409 GLU Chi-restraints excluded: chain G residue 416 ILE Chi-restraints excluded: chain G residue 436 ILE Chi-restraints excluded: chain H residue 165 LEU Chi-restraints excluded: chain H residue 223 GLN Chi-restraints excluded: chain H residue 310 VAL Chi-restraints excluded: chain H residue 317 VAL Chi-restraints excluded: chain H residue 329 GLN Chi-restraints excluded: chain H residue 357 SER Chi-restraints excluded: chain H residue 376 SER Chi-restraints excluded: chain H residue 409 GLU Chi-restraints excluded: chain H residue 416 ILE Chi-restraints excluded: chain H residue 436 ILE Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 246 VAL Chi-restraints excluded: chain I residue 278 ASP Chi-restraints excluded: chain I residue 317 VAL Chi-restraints excluded: chain I residue 329 GLN Chi-restraints excluded: chain I residue 357 SER Chi-restraints excluded: chain I residue 409 GLU Chi-restraints excluded: chain I residue 416 ILE Chi-restraints excluded: chain I residue 436 ILE Chi-restraints excluded: chain J residue 185 GLU Chi-restraints excluded: chain J residue 216 THR Chi-restraints excluded: chain J residue 278 ASP Chi-restraints excluded: chain J residue 317 VAL Chi-restraints excluded: chain J residue 329 GLN Chi-restraints excluded: chain J residue 357 SER Chi-restraints excluded: chain J residue 409 GLU Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 419 MET Chi-restraints excluded: chain J residue 436 ILE Chi-restraints excluded: chain K residue 165 LEU Chi-restraints excluded: chain K residue 199 GLU Chi-restraints excluded: chain K residue 223 GLN Chi-restraints excluded: chain K residue 310 VAL Chi-restraints excluded: chain K residue 317 VAL Chi-restraints excluded: chain K residue 329 GLN Chi-restraints excluded: chain K residue 357 SER Chi-restraints excluded: chain K residue 376 SER Chi-restraints excluded: chain K residue 409 GLU Chi-restraints excluded: chain K residue 436 ILE Chi-restraints excluded: chain L residue 19 LYS Chi-restraints excluded: chain L residue 165 LEU Chi-restraints excluded: chain L residue 180 LEU Chi-restraints excluded: chain L residue 246 VAL Chi-restraints excluded: chain L residue 278 ASP Chi-restraints excluded: chain L residue 317 VAL Chi-restraints excluded: chain L residue 357 SER Chi-restraints excluded: chain L residue 409 GLU Chi-restraints excluded: chain L residue 416 ILE Chi-restraints excluded: chain L residue 436 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 400 optimal weight: 0.6980 chunk 340 optimal weight: 0.9980 chunk 505 optimal weight: 9.9990 chunk 358 optimal weight: 7.9990 chunk 417 optimal weight: 9.9990 chunk 507 optimal weight: 6.9990 chunk 366 optimal weight: 3.9990 chunk 500 optimal weight: 7.9990 chunk 200 optimal weight: 20.0000 chunk 217 optimal weight: 5.9990 chunk 377 optimal weight: 5.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 ASN A 18 HIS A 299 HIS ** B 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 HIS ** C 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 299 HIS ** E 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 18 HIS G 6 ASN G 18 HIS G 299 HIS ** H 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 44 HIS ** I 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 299 HIS K 299 HIS L 299 HIS ** L 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.142144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.116931 restraints weight = 59296.144| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.26 r_work: 0.3067 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 43908 Z= 0.222 Angle : 0.588 11.393 59388 Z= 0.308 Chirality : 0.042 0.165 6252 Planarity : 0.004 0.044 7860 Dihedral : 4.068 36.078 5870 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 5.90 % Allowed : 23.47 % Favored : 70.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.11), residues: 5352 helix: 1.96 (0.10), residues: 2412 sheet: -0.13 (0.19), residues: 720 loop : -0.68 (0.12), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 184 TYR 0.023 0.002 TYR B 62 PHE 0.015 0.002 PHE E 158 TRP 0.027 0.002 TRP F 171 HIS 0.005 0.001 HIS L 299 Details of bonding type rmsd covalent geometry : bond 0.00523 (43908) covalent geometry : angle 0.58830 (59388) hydrogen bonds : bond 0.04761 ( 2124) hydrogen bonds : angle 4.49826 ( 6156) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10704 Ramachandran restraints generated. 5352 Oldfield, 0 Emsley, 5352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10704 Ramachandran restraints generated. 5352 Oldfield, 0 Emsley, 5352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1174 residues out of total 4524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 267 poor density : 907 time to evaluate : 1.586 Fit side-chains REVERT: A 103 ASP cc_start: 0.7996 (p0) cc_final: 0.7729 (p0) REVERT: A 217 TRP cc_start: 0.8914 (m100) cc_final: 0.8460 (m100) REVERT: A 329 GLN cc_start: 0.8968 (OUTLIER) cc_final: 0.8102 (pt0) REVERT: A 369 MET cc_start: 0.6292 (mmp) cc_final: 0.5762 (mmp) REVERT: A 415 ASP cc_start: 0.7573 (m-30) cc_final: 0.7280 (m-30) REVERT: A 418 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7907 (tttp) REVERT: B 103 ASP cc_start: 0.7846 (p0) cc_final: 0.7588 (p0) REVERT: B 165 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8802 (pp) REVERT: B 217 TRP cc_start: 0.8616 (m100) cc_final: 0.8399 (m-10) REVERT: B 322 ASN cc_start: 0.8711 (m-40) cc_final: 0.8486 (m-40) REVERT: B 329 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.8094 (pm20) REVERT: B 398 MET cc_start: 0.8474 (mtt) cc_final: 0.7928 (mtm) REVERT: C 103 ASP cc_start: 0.7903 (p0) cc_final: 0.7404 (p0) REVERT: C 176 LYS cc_start: 0.8510 (mmtp) cc_final: 0.8209 (mmtt) REVERT: C 217 TRP cc_start: 0.8691 (m100) cc_final: 0.8000 (m100) REVERT: C 369 MET cc_start: 0.6845 (mmp) cc_final: 0.6380 (mmp) REVERT: D 35 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8702 (mttm) REVERT: D 103 ASP cc_start: 0.7901 (p0) cc_final: 0.7649 (p0) REVERT: D 217 TRP cc_start: 0.8860 (m100) cc_final: 0.8334 (m100) REVERT: D 415 ASP cc_start: 0.7358 (m-30) cc_final: 0.7074 (m-30) REVERT: E 165 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8747 (pp) REVERT: E 200 GLU cc_start: 0.8270 (mt-10) cc_final: 0.8068 (mt-10) REVERT: E 329 GLN cc_start: 0.9004 (OUTLIER) cc_final: 0.8092 (pm20) REVERT: E 383 LYS cc_start: 0.8570 (mmtp) cc_final: 0.8057 (mmtt) REVERT: E 398 MET cc_start: 0.8488 (mtt) cc_final: 0.7956 (mtm) REVERT: E 455 ASP cc_start: 0.7275 (p0) cc_final: 0.7040 (m-30) REVERT: F 165 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8866 (pp) REVERT: F 369 MET cc_start: 0.6879 (mmp) cc_final: 0.6376 (mmp) REVERT: F 405 LYS cc_start: 0.8613 (mmtp) cc_final: 0.8235 (pttm) REVERT: G 103 ASP cc_start: 0.7978 (p0) cc_final: 0.7672 (p0) REVERT: G 217 TRP cc_start: 0.8991 (m100) cc_final: 0.8494 (m100) REVERT: G 225 TYR cc_start: 0.5749 (m-10) cc_final: 0.5480 (m-10) REVERT: G 329 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8122 (pt0) REVERT: G 369 MET cc_start: 0.6459 (mmp) cc_final: 0.5971 (mmp) REVERT: G 415 ASP cc_start: 0.7482 (m-30) cc_final: 0.7179 (m-30) REVERT: H 103 ASP cc_start: 0.7961 (p0) cc_final: 0.7647 (p0) REVERT: H 165 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8800 (pp) REVERT: H 186 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8288 (tp30) REVERT: H 217 TRP cc_start: 0.8542 (m-10) cc_final: 0.8135 (m100) REVERT: H 223 GLN cc_start: 0.2440 (OUTLIER) cc_final: 0.2022 (tp40) REVERT: H 329 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.8008 (pm20) REVERT: H 398 MET cc_start: 0.8540 (mtt) cc_final: 0.8026 (mtm) REVERT: I 165 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8951 (pp) REVERT: I 176 LYS cc_start: 0.8285 (mmtt) cc_final: 0.8022 (mmtt) REVERT: I 217 TRP cc_start: 0.8673 (m100) cc_final: 0.8204 (m100) REVERT: J 103 ASP cc_start: 0.7991 (p0) cc_final: 0.7699 (p0) REVERT: J 217 TRP cc_start: 0.8988 (m100) cc_final: 0.8526 (m100) REVERT: J 329 GLN cc_start: 0.8964 (OUTLIER) cc_final: 0.8113 (pt0) REVERT: J 369 MET cc_start: 0.6358 (mmp) cc_final: 0.5867 (mmp) REVERT: K 165 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8825 (pp) REVERT: K 184 ARG cc_start: 0.9025 (tmm-80) cc_final: 0.8761 (ttm-80) REVERT: K 217 TRP cc_start: 0.8791 (m100) cc_final: 0.8257 (m100) REVERT: K 223 GLN cc_start: 0.2461 (OUTLIER) cc_final: 0.2032 (tp40) REVERT: K 329 GLN cc_start: 0.9013 (OUTLIER) cc_final: 0.8082 (pm20) REVERT: K 383 LYS cc_start: 0.8573 (mmtp) cc_final: 0.8058 (mmtt) REVERT: L 165 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8906 (pp) REVERT: L 217 TRP cc_start: 0.8796 (m100) cc_final: 0.8316 (m100) REVERT: L 369 MET cc_start: 0.6372 (mmp) cc_final: 0.5868 (mmp) REVERT: L 383 LYS cc_start: 0.8624 (ttmt) cc_final: 0.7941 (mmtp) outliers start: 267 outliers final: 171 residues processed: 1097 average time/residue: 0.2259 time to fit residues: 410.8404 Evaluate side-chains 1055 residues out of total 4524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 865 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 225 TYR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 418 LYS Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 329 GLN Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 409 GLU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain C residue 19 LYS Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain C residue 409 GLU Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain D residue 35 LYS Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 357 SER Chi-restraints excluded: chain D residue 409 GLU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 419 MET Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 329 GLN Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 357 SER Chi-restraints excluded: chain E residue 376 SER Chi-restraints excluded: chain E residue 409 GLU Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 416 ILE Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain F residue 19 LYS Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 186 GLU Chi-restraints excluded: chain F residue 196 ILE Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 321 VAL Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 357 SER Chi-restraints excluded: chain F residue 409 GLU Chi-restraints excluded: chain F residue 416 ILE Chi-restraints excluded: chain F residue 436 ILE Chi-restraints excluded: chain G residue 18 HIS Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 211 THR Chi-restraints excluded: chain G residue 216 THR Chi-restraints excluded: chain G residue 246 VAL Chi-restraints excluded: chain G residue 278 ASP Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain G residue 329 GLN Chi-restraints excluded: chain G residue 354 LEU Chi-restraints excluded: chain G residue 357 SER Chi-restraints excluded: chain G residue 409 GLU Chi-restraints excluded: chain G residue 416 ILE Chi-restraints excluded: chain G residue 419 MET Chi-restraints excluded: chain G residue 436 ILE Chi-restraints excluded: chain G residue 457 ASP Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 165 LEU Chi-restraints excluded: chain H residue 186 GLU Chi-restraints excluded: chain H residue 216 THR Chi-restraints excluded: chain H residue 223 GLN Chi-restraints excluded: chain H residue 290 THR Chi-restraints excluded: chain H residue 310 VAL Chi-restraints excluded: chain H residue 317 VAL Chi-restraints excluded: chain H residue 321 VAL Chi-restraints excluded: chain H residue 329 GLN Chi-restraints excluded: chain H residue 354 LEU Chi-restraints excluded: chain H residue 357 SER Chi-restraints excluded: chain H residue 376 SER Chi-restraints excluded: chain H residue 409 GLU Chi-restraints excluded: chain H residue 416 ILE Chi-restraints excluded: chain H residue 436 ILE Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 186 GLU Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 246 VAL Chi-restraints excluded: chain I residue 310 VAL Chi-restraints excluded: chain I residue 321 VAL Chi-restraints excluded: chain I residue 354 LEU Chi-restraints excluded: chain I residue 357 SER Chi-restraints excluded: chain I residue 409 GLU Chi-restraints excluded: chain I residue 416 ILE Chi-restraints excluded: chain I residue 436 ILE Chi-restraints excluded: chain J residue 18 HIS Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 211 THR Chi-restraints excluded: chain J residue 216 THR Chi-restraints excluded: chain J residue 225 TYR Chi-restraints excluded: chain J residue 246 VAL Chi-restraints excluded: chain J residue 278 ASP Chi-restraints excluded: chain J residue 290 THR Chi-restraints excluded: chain J residue 317 VAL Chi-restraints excluded: chain J residue 329 GLN Chi-restraints excluded: chain J residue 354 LEU Chi-restraints excluded: chain J residue 357 SER Chi-restraints excluded: chain J residue 409 GLU Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 419 MET Chi-restraints excluded: chain J residue 436 ILE Chi-restraints excluded: chain J residue 457 ASP Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain K residue 165 LEU Chi-restraints excluded: chain K residue 216 THR Chi-restraints excluded: chain K residue 223 GLN Chi-restraints excluded: chain K residue 299 HIS Chi-restraints excluded: chain K residue 310 VAL Chi-restraints excluded: chain K residue 317 VAL Chi-restraints excluded: chain K residue 321 VAL Chi-restraints excluded: chain K residue 329 GLN Chi-restraints excluded: chain K residue 354 LEU Chi-restraints excluded: chain K residue 357 SER Chi-restraints excluded: chain K residue 376 SER Chi-restraints excluded: chain K residue 409 GLU Chi-restraints excluded: chain K residue 410 LEU Chi-restraints excluded: chain K residue 416 ILE Chi-restraints excluded: chain K residue 436 ILE Chi-restraints excluded: chain L residue 19 LYS Chi-restraints excluded: chain L residue 56 VAL Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 165 LEU Chi-restraints excluded: chain L residue 180 LEU Chi-restraints excluded: chain L residue 186 GLU Chi-restraints excluded: chain L residue 196 ILE Chi-restraints excluded: chain L residue 216 THR Chi-restraints excluded: chain L residue 246 VAL Chi-restraints excluded: chain L residue 299 HIS Chi-restraints excluded: chain L residue 321 VAL Chi-restraints excluded: chain L residue 357 SER Chi-restraints excluded: chain L residue 409 GLU Chi-restraints excluded: chain L residue 416 ILE Chi-restraints excluded: chain L residue 436 ILE Chi-restraints excluded: chain L residue 457 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 383 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 chunk 348 optimal weight: 7.9990 chunk 146 optimal weight: 0.9990 chunk 433 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS B 18 HIS C 18 HIS C 444 GLN D 18 HIS E 18 HIS F 18 HIS F 444 GLN G 18 HIS H 18 HIS I 18 HIS I 444 GLN ** K 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 18 HIS L 444 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.146027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.121652 restraints weight = 58179.919| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.17 r_work: 0.3116 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 43908 Z= 0.118 Angle : 0.478 9.152 59388 Z= 0.255 Chirality : 0.039 0.158 6252 Planarity : 0.004 0.042 7860 Dihedral : 3.795 30.715 5870 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 5.11 % Allowed : 23.96 % Favored : 70.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.11), residues: 5352 helix: 2.14 (0.10), residues: 2412 sheet: 0.05 (0.18), residues: 816 loop : -0.53 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 184 TYR 0.015 0.001 TYR H 389 PHE 0.012 0.001 PHE B 183 TRP 0.020 0.001 TRP I 171 HIS 0.018 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00266 (43908) covalent geometry : angle 0.47760 (59388) hydrogen bonds : bond 0.03764 ( 2124) hydrogen bonds : angle 4.28549 ( 6156) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10704 Ramachandran restraints generated. 5352 Oldfield, 0 Emsley, 5352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10704 Ramachandran restraints generated. 5352 Oldfield, 0 Emsley, 5352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1116 residues out of total 4524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 231 poor density : 885 time to evaluate : 1.374 Fit side-chains REVERT: A 103 ASP cc_start: 0.7848 (p0) cc_final: 0.7537 (p0) REVERT: A 217 TRP cc_start: 0.8964 (m100) cc_final: 0.8551 (m100) REVERT: A 329 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8078 (pt0) REVERT: A 415 ASP cc_start: 0.7564 (m-30) cc_final: 0.7254 (m-30) REVERT: A 444 GLN cc_start: 0.8677 (mm-40) cc_final: 0.8470 (mm110) REVERT: B 103 ASP cc_start: 0.7727 (p0) cc_final: 0.7459 (p0) REVERT: B 165 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8709 (pp) REVERT: B 217 TRP cc_start: 0.8543 (m100) cc_final: 0.8329 (m-10) REVERT: B 322 ASN cc_start: 0.8684 (m-40) cc_final: 0.8472 (m-40) REVERT: B 329 GLN cc_start: 0.8983 (OUTLIER) cc_final: 0.8082 (pm20) REVERT: B 398 MET cc_start: 0.8479 (mtt) cc_final: 0.7951 (mtm) REVERT: B 447 LYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7716 (tttp) REVERT: C 7 ILE cc_start: 0.9079 (tp) cc_final: 0.8741 (tt) REVERT: C 84 PHE cc_start: 0.9025 (m-80) cc_final: 0.8754 (m-80) REVERT: C 103 ASP cc_start: 0.7991 (p0) cc_final: 0.7502 (p0) REVERT: C 217 TRP cc_start: 0.8686 (m100) cc_final: 0.8011 (m100) REVERT: C 369 MET cc_start: 0.6826 (mmp) cc_final: 0.6342 (mmp) REVERT: C 409 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7509 (tm-30) REVERT: D 103 ASP cc_start: 0.7765 (p0) cc_final: 0.7496 (p0) REVERT: D 185 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8070 (tt0) REVERT: D 217 TRP cc_start: 0.8880 (m100) cc_final: 0.8371 (m100) REVERT: D 415 ASP cc_start: 0.7411 (m-30) cc_final: 0.7082 (m-30) REVERT: D 444 GLN cc_start: 0.8683 (mm-40) cc_final: 0.8454 (mm-40) REVERT: E 19 LYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8606 (ttmm) REVERT: E 103 ASP cc_start: 0.7844 (p0) cc_final: 0.7579 (p0) REVERT: E 165 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8680 (pp) REVERT: E 217 TRP cc_start: 0.8461 (m-10) cc_final: 0.8022 (m100) REVERT: E 329 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.8050 (pm20) REVERT: E 383 LYS cc_start: 0.8423 (mmtp) cc_final: 0.8178 (mmtt) REVERT: E 398 MET cc_start: 0.8488 (mtt) cc_final: 0.7963 (mtm) REVERT: E 455 ASP cc_start: 0.7253 (p0) cc_final: 0.7034 (m-30) REVERT: F 7 ILE cc_start: 0.9039 (tp) cc_final: 0.8694 (tt) REVERT: F 84 PHE cc_start: 0.9013 (m-80) cc_final: 0.8759 (m-80) REVERT: F 103 ASP cc_start: 0.7902 (p0) cc_final: 0.7594 (p0) REVERT: F 217 TRP cc_start: 0.8624 (m100) cc_final: 0.8110 (m100) REVERT: F 369 MET cc_start: 0.6923 (mmp) cc_final: 0.6439 (mmp) REVERT: G 103 ASP cc_start: 0.7900 (p0) cc_final: 0.7589 (p0) REVERT: G 217 TRP cc_start: 0.8986 (m100) cc_final: 0.8534 (m100) REVERT: G 329 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.8090 (pt0) REVERT: G 369 MET cc_start: 0.6338 (mmp) cc_final: 0.5980 (mmp) REVERT: G 415 ASP cc_start: 0.7449 (m-30) cc_final: 0.7129 (m-30) REVERT: H 103 ASP cc_start: 0.7858 (p0) cc_final: 0.7520 (p0) REVERT: H 165 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8755 (pp) REVERT: H 217 TRP cc_start: 0.8446 (m-10) cc_final: 0.8087 (m100) REVERT: H 223 GLN cc_start: 0.2447 (OUTLIER) cc_final: 0.2134 (tp40) REVERT: H 329 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.7997 (pm20) REVERT: H 398 MET cc_start: 0.8493 (mtt) cc_final: 0.7999 (mtm) REVERT: I 176 LYS cc_start: 0.8383 (mmtt) cc_final: 0.8130 (mmtt) REVERT: I 217 TRP cc_start: 0.8690 (m100) cc_final: 0.8280 (m100) REVERT: J 103 ASP cc_start: 0.7906 (p0) cc_final: 0.7583 (p0) REVERT: J 217 TRP cc_start: 0.8954 (m100) cc_final: 0.8547 (m100) REVERT: J 329 GLN cc_start: 0.8935 (OUTLIER) cc_final: 0.8068 (pt0) REVERT: J 369 MET cc_start: 0.6381 (mmp) cc_final: 0.5985 (mmp) REVERT: K 165 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8747 (pp) REVERT: K 217 TRP cc_start: 0.8760 (m100) cc_final: 0.8331 (m100) REVERT: K 223 GLN cc_start: 0.2396 (OUTLIER) cc_final: 0.2122 (tp40) REVERT: K 329 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.7958 (pm20) REVERT: K 383 LYS cc_start: 0.8396 (mmtp) cc_final: 0.8150 (mmtt) REVERT: L 98 ASP cc_start: 0.8010 (t0) cc_final: 0.7410 (m-30) REVERT: L 217 TRP cc_start: 0.8748 (m100) cc_final: 0.8309 (m100) REVERT: L 369 MET cc_start: 0.6894 (mmp) cc_final: 0.6392 (mmp) REVERT: L 383 LYS cc_start: 0.8575 (ttmt) cc_final: 0.8268 (mmtp) outliers start: 231 outliers final: 163 residues processed: 1042 average time/residue: 0.2235 time to fit residues: 388.9785 Evaluate side-chains 1028 residues out of total 4524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 849 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 225 TYR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 299 HIS Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 329 GLN Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 409 GLU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 447 LYS Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 299 HIS Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain C residue 409 GLU Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 278 ASP Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 299 HIS Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 357 SER Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 409 GLU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 419 MET Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 299 HIS Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 329 GLN Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 376 SER Chi-restraints excluded: chain E residue 409 GLU Chi-restraints excluded: chain E residue 416 ILE Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain F residue 19 LYS Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 186 GLU Chi-restraints excluded: chain F residue 199 GLU Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 299 HIS Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 357 SER Chi-restraints excluded: chain F residue 409 GLU Chi-restraints excluded: chain F residue 416 ILE Chi-restraints excluded: chain F residue 436 ILE Chi-restraints excluded: chain G residue 19 LYS Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 216 THR Chi-restraints excluded: chain G residue 246 VAL Chi-restraints excluded: chain G residue 278 ASP Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 299 HIS Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain G residue 329 GLN Chi-restraints excluded: chain G residue 354 LEU Chi-restraints excluded: chain G residue 357 SER Chi-restraints excluded: chain G residue 382 SER Chi-restraints excluded: chain G residue 409 GLU Chi-restraints excluded: chain G residue 416 ILE Chi-restraints excluded: chain G residue 419 MET Chi-restraints excluded: chain G residue 436 ILE Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 165 LEU Chi-restraints excluded: chain H residue 223 GLN Chi-restraints excluded: chain H residue 290 THR Chi-restraints excluded: chain H residue 299 HIS Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 310 VAL Chi-restraints excluded: chain H residue 317 VAL Chi-restraints excluded: chain H residue 329 GLN Chi-restraints excluded: chain H residue 354 LEU Chi-restraints excluded: chain H residue 357 SER Chi-restraints excluded: chain H residue 376 SER Chi-restraints excluded: chain H residue 409 GLU Chi-restraints excluded: chain H residue 416 ILE Chi-restraints excluded: chain H residue 436 ILE Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 186 GLU Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 246 VAL Chi-restraints excluded: chain I residue 299 HIS Chi-restraints excluded: chain I residue 304 VAL Chi-restraints excluded: chain I residue 310 VAL Chi-restraints excluded: chain I residue 317 VAL Chi-restraints excluded: chain I residue 354 LEU Chi-restraints excluded: chain I residue 357 SER Chi-restraints excluded: chain I residue 409 GLU Chi-restraints excluded: chain I residue 416 ILE Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 216 THR Chi-restraints excluded: chain J residue 225 TYR Chi-restraints excluded: chain J residue 246 VAL Chi-restraints excluded: chain J residue 278 ASP Chi-restraints excluded: chain J residue 290 THR Chi-restraints excluded: chain J residue 299 HIS Chi-restraints excluded: chain J residue 317 VAL Chi-restraints excluded: chain J residue 329 GLN Chi-restraints excluded: chain J residue 354 LEU Chi-restraints excluded: chain J residue 357 SER Chi-restraints excluded: chain J residue 382 SER Chi-restraints excluded: chain J residue 409 GLU Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 419 MET Chi-restraints excluded: chain J residue 436 ILE Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain K residue 165 LEU Chi-restraints excluded: chain K residue 223 GLN Chi-restraints excluded: chain K residue 304 VAL Chi-restraints excluded: chain K residue 310 VAL Chi-restraints excluded: chain K residue 317 VAL Chi-restraints excluded: chain K residue 329 GLN Chi-restraints excluded: chain K residue 338 GLU Chi-restraints excluded: chain K residue 354 LEU Chi-restraints excluded: chain K residue 357 SER Chi-restraints excluded: chain K residue 376 SER Chi-restraints excluded: chain K residue 409 GLU Chi-restraints excluded: chain K residue 416 ILE Chi-restraints excluded: chain K residue 436 ILE Chi-restraints excluded: chain L residue 19 LYS Chi-restraints excluded: chain L residue 56 VAL Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 186 GLU Chi-restraints excluded: chain L residue 216 THR Chi-restraints excluded: chain L residue 246 VAL Chi-restraints excluded: chain L residue 304 VAL Chi-restraints excluded: chain L residue 317 VAL Chi-restraints excluded: chain L residue 357 SER Chi-restraints excluded: chain L residue 409 GLU Chi-restraints excluded: chain L residue 416 ILE Chi-restraints excluded: chain L residue 436 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 87 optimal weight: 2.9990 chunk 153 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 chunk 418 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 167 optimal weight: 0.7980 chunk 125 optimal weight: 10.0000 chunk 509 optimal weight: 0.3980 chunk 510 optimal weight: 7.9990 chunk 244 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 ASN A 18 HIS B 18 HIS C 18 HIS C 444 GLN D 18 HIS E 18 HIS F 18 HIS G 6 ASN G 18 HIS H 18 HIS I 18 HIS I 444 GLN J 18 HIS K 18 HIS ** K 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 18 HIS L 444 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.148480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.123812 restraints weight = 58252.238| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.20 r_work: 0.3141 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 43908 Z= 0.105 Angle : 0.460 8.152 59388 Z= 0.245 Chirality : 0.038 0.172 6252 Planarity : 0.003 0.042 7860 Dihedral : 3.653 29.791 5870 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 4.89 % Allowed : 24.58 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.12), residues: 5352 helix: 2.27 (0.10), residues: 2424 sheet: 0.15 (0.20), residues: 744 loop : -0.37 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 184 TYR 0.013 0.001 TYR B 389 PHE 0.013 0.001 PHE B 183 TRP 0.017 0.001 TRP L 171 HIS 0.011 0.001 HIS D 18 Details of bonding type rmsd covalent geometry : bond 0.00233 (43908) covalent geometry : angle 0.45961 (59388) hydrogen bonds : bond 0.03514 ( 2124) hydrogen bonds : angle 4.14831 ( 6156) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10704 Ramachandran restraints generated. 5352 Oldfield, 0 Emsley, 5352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10704 Ramachandran restraints generated. 5352 Oldfield, 0 Emsley, 5352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1095 residues out of total 4524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 221 poor density : 874 time to evaluate : 1.432 Fit side-chains revert: symmetry clash REVERT: A 103 ASP cc_start: 0.7842 (p0) cc_final: 0.7497 (p0) REVERT: A 217 TRP cc_start: 0.8951 (m100) cc_final: 0.8552 (m100) REVERT: A 329 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8078 (pt0) REVERT: A 415 ASP cc_start: 0.7462 (m-30) cc_final: 0.7152 (m-30) REVERT: B 103 ASP cc_start: 0.7710 (p0) cc_final: 0.7438 (p0) REVERT: B 165 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8701 (pp) REVERT: B 329 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.8008 (pm20) REVERT: B 398 MET cc_start: 0.8454 (mtt) cc_final: 0.7928 (mtm) REVERT: B 447 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7682 (tttp) REVERT: C 7 ILE cc_start: 0.9031 (tp) cc_final: 0.8673 (tt) REVERT: C 84 PHE cc_start: 0.9015 (m-80) cc_final: 0.8743 (m-80) REVERT: C 103 ASP cc_start: 0.7968 (p0) cc_final: 0.7494 (p0) REVERT: C 217 TRP cc_start: 0.8689 (m100) cc_final: 0.8020 (m100) REVERT: C 369 MET cc_start: 0.6843 (mmp) cc_final: 0.6386 (mmp) REVERT: C 409 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7464 (tm-30) REVERT: D 103 ASP cc_start: 0.7736 (p0) cc_final: 0.7459 (p0) REVERT: D 185 GLU cc_start: 0.8410 (tm-30) cc_final: 0.8019 (tt0) REVERT: D 217 TRP cc_start: 0.8896 (m100) cc_final: 0.8438 (m100) REVERT: D 241 ASP cc_start: 0.8213 (p0) cc_final: 0.7810 (p0) REVERT: D 242 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.7895 (pm20) REVERT: D 415 ASP cc_start: 0.7587 (m-30) cc_final: 0.7301 (m-30) REVERT: D 455 ASP cc_start: 0.8299 (m-30) cc_final: 0.6980 (t0) REVERT: E 103 ASP cc_start: 0.7797 (p0) cc_final: 0.7552 (p0) REVERT: E 165 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8695 (pp) REVERT: E 217 TRP cc_start: 0.8506 (m-10) cc_final: 0.8084 (m100) REVERT: E 329 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.7989 (pm20) REVERT: E 398 MET cc_start: 0.8474 (mtt) cc_final: 0.7958 (mtm) REVERT: E 455 ASP cc_start: 0.7256 (p0) cc_final: 0.7054 (m-30) REVERT: F 7 ILE cc_start: 0.9033 (tp) cc_final: 0.8685 (tt) REVERT: F 84 PHE cc_start: 0.9006 (m-80) cc_final: 0.8741 (m-80) REVERT: F 103 ASP cc_start: 0.7898 (p0) cc_final: 0.7633 (p0) REVERT: F 217 TRP cc_start: 0.8630 (m100) cc_final: 0.8134 (m100) REVERT: F 369 MET cc_start: 0.7001 (mmp) cc_final: 0.6534 (mmp) REVERT: G 103 ASP cc_start: 0.7861 (p0) cc_final: 0.7544 (p0) REVERT: G 217 TRP cc_start: 0.8953 (m100) cc_final: 0.8510 (m100) REVERT: G 329 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.8051 (pt0) REVERT: G 369 MET cc_start: 0.6329 (mmp) cc_final: 0.5987 (mmp) REVERT: G 415 ASP cc_start: 0.7418 (m-30) cc_final: 0.7110 (m-30) REVERT: G 455 ASP cc_start: 0.8338 (m-30) cc_final: 0.6964 (t0) REVERT: H 103 ASP cc_start: 0.7829 (p0) cc_final: 0.7496 (p0) REVERT: H 165 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8665 (pp) REVERT: H 186 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.8132 (tp30) REVERT: H 217 TRP cc_start: 0.8483 (m-10) cc_final: 0.8125 (m100) REVERT: H 223 GLN cc_start: 0.2379 (OUTLIER) cc_final: 0.2123 (tp40) REVERT: H 329 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.7961 (pm20) REVERT: I 84 PHE cc_start: 0.9021 (m-80) cc_final: 0.8756 (m-80) REVERT: I 98 ASP cc_start: 0.8004 (t0) cc_final: 0.7574 (m-30) REVERT: I 217 TRP cc_start: 0.8678 (m100) cc_final: 0.8248 (m100) REVERT: J 103 ASP cc_start: 0.7893 (p0) cc_final: 0.7556 (p0) REVERT: J 217 TRP cc_start: 0.8973 (m100) cc_final: 0.8574 (m100) REVERT: J 329 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8034 (pt0) REVERT: J 369 MET cc_start: 0.6339 (mmp) cc_final: 0.6016 (mmp) REVERT: J 455 ASP cc_start: 0.8269 (m-30) cc_final: 0.6940 (t0) REVERT: K 165 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8700 (pp) REVERT: K 184 ARG cc_start: 0.8904 (tmm-80) cc_final: 0.8661 (ttm-80) REVERT: K 199 GLU cc_start: 0.7740 (pp20) cc_final: 0.7516 (pp20) REVERT: K 217 TRP cc_start: 0.8738 (m100) cc_final: 0.8344 (m100) REVERT: K 329 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.7919 (pm20) REVERT: K 398 MET cc_start: 0.8475 (mtt) cc_final: 0.7915 (mtm) REVERT: L 84 PHE cc_start: 0.8986 (m-80) cc_final: 0.8728 (m-80) REVERT: L 217 TRP cc_start: 0.8665 (m100) cc_final: 0.8259 (m100) REVERT: L 369 MET cc_start: 0.6968 (mmp) cc_final: 0.6501 (mmp) REVERT: L 383 LYS cc_start: 0.8601 (ttmt) cc_final: 0.8289 (mmtp) outliers start: 221 outliers final: 172 residues processed: 1015 average time/residue: 0.2164 time to fit residues: 367.7624 Evaluate side-chains 1034 residues out of total 4524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 846 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 225 TYR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 299 HIS Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 329 GLN Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 409 GLU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 447 LYS Chi-restraints excluded: chain C residue 19 LYS Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 299 HIS Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain C residue 409 GLU Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain D residue 19 LYS Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 278 ASP Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 299 HIS Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 357 SER Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 409 GLU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 419 MET Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 299 HIS Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 329 GLN Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 357 SER Chi-restraints excluded: chain E residue 376 SER Chi-restraints excluded: chain E residue 409 GLU Chi-restraints excluded: chain E residue 416 ILE Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain F residue 19 LYS Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 199 GLU Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 283 CYS Chi-restraints excluded: chain F residue 299 HIS Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 357 SER Chi-restraints excluded: chain F residue 409 GLU Chi-restraints excluded: chain F residue 416 ILE Chi-restraints excluded: chain F residue 436 ILE Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 216 THR Chi-restraints excluded: chain G residue 246 VAL Chi-restraints excluded: chain G residue 278 ASP Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 299 HIS Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain G residue 329 GLN Chi-restraints excluded: chain G residue 354 LEU Chi-restraints excluded: chain G residue 357 SER Chi-restraints excluded: chain G residue 409 GLU Chi-restraints excluded: chain G residue 416 ILE Chi-restraints excluded: chain G residue 419 MET Chi-restraints excluded: chain G residue 436 ILE Chi-restraints excluded: chain H residue 165 LEU Chi-restraints excluded: chain H residue 186 GLU Chi-restraints excluded: chain H residue 223 GLN Chi-restraints excluded: chain H residue 290 THR Chi-restraints excluded: chain H residue 299 HIS Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 310 VAL Chi-restraints excluded: chain H residue 317 VAL Chi-restraints excluded: chain H residue 329 GLN Chi-restraints excluded: chain H residue 338 GLU Chi-restraints excluded: chain H residue 354 LEU Chi-restraints excluded: chain H residue 357 SER Chi-restraints excluded: chain H residue 376 SER Chi-restraints excluded: chain H residue 409 GLU Chi-restraints excluded: chain H residue 416 ILE Chi-restraints excluded: chain H residue 436 ILE Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 186 GLU Chi-restraints excluded: chain I residue 199 GLU Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 246 VAL Chi-restraints excluded: chain I residue 258 ASP Chi-restraints excluded: chain I residue 299 HIS Chi-restraints excluded: chain I residue 304 VAL Chi-restraints excluded: chain I residue 310 VAL Chi-restraints excluded: chain I residue 317 VAL Chi-restraints excluded: chain I residue 354 LEU Chi-restraints excluded: chain I residue 357 SER Chi-restraints excluded: chain I residue 409 GLU Chi-restraints excluded: chain I residue 416 ILE Chi-restraints excluded: chain I residue 436 ILE Chi-restraints excluded: chain J residue 18 HIS Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 216 THR Chi-restraints excluded: chain J residue 278 ASP Chi-restraints excluded: chain J residue 290 THR Chi-restraints excluded: chain J residue 299 HIS Chi-restraints excluded: chain J residue 317 VAL Chi-restraints excluded: chain J residue 329 GLN Chi-restraints excluded: chain J residue 354 LEU Chi-restraints excluded: chain J residue 357 SER Chi-restraints excluded: chain J residue 409 GLU Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 419 MET Chi-restraints excluded: chain J residue 436 ILE Chi-restraints excluded: chain J residue 457 ASP Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain K residue 165 LEU Chi-restraints excluded: chain K residue 299 HIS Chi-restraints excluded: chain K residue 304 VAL Chi-restraints excluded: chain K residue 310 VAL Chi-restraints excluded: chain K residue 317 VAL Chi-restraints excluded: chain K residue 329 GLN Chi-restraints excluded: chain K residue 354 LEU Chi-restraints excluded: chain K residue 357 SER Chi-restraints excluded: chain K residue 376 SER Chi-restraints excluded: chain K residue 409 GLU Chi-restraints excluded: chain K residue 416 ILE Chi-restraints excluded: chain K residue 436 ILE Chi-restraints excluded: chain L residue 19 LYS Chi-restraints excluded: chain L residue 56 VAL Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 186 GLU Chi-restraints excluded: chain L residue 216 THR Chi-restraints excluded: chain L residue 246 VAL Chi-restraints excluded: chain L residue 278 ASP Chi-restraints excluded: chain L residue 283 CYS Chi-restraints excluded: chain L residue 299 HIS Chi-restraints excluded: chain L residue 317 VAL Chi-restraints excluded: chain L residue 357 SER Chi-restraints excluded: chain L residue 409 GLU Chi-restraints excluded: chain L residue 416 ILE Chi-restraints excluded: chain L residue 436 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 121 optimal weight: 0.0980 chunk 253 optimal weight: 0.0970 chunk 200 optimal weight: 20.0000 chunk 272 optimal weight: 0.7980 chunk 406 optimal weight: 5.9990 chunk 167 optimal weight: 0.8980 chunk 285 optimal weight: 0.7980 chunk 263 optimal weight: 6.9990 chunk 29 optimal weight: 0.2980 chunk 51 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS B 18 HIS C 444 GLN ** D 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 HIS G 18 HIS H 18 HIS I 444 GLN J 18 HIS K 18 HIS L 444 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.147385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.122701 restraints weight = 58404.191| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.21 r_work: 0.3158 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 43908 Z= 0.089 Angle : 0.441 7.310 59388 Z= 0.235 Chirality : 0.038 0.161 6252 Planarity : 0.003 0.042 7860 Dihedral : 3.481 27.322 5870 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 4.69 % Allowed : 24.38 % Favored : 70.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (0.12), residues: 5352 helix: 2.43 (0.10), residues: 2424 sheet: 0.42 (0.20), residues: 720 loop : -0.34 (0.13), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 184 TYR 0.015 0.001 TYR E 225 PHE 0.013 0.001 PHE B 183 TRP 0.012 0.001 TRP F 171 HIS 0.019 0.001 HIS J 18 Details of bonding type rmsd covalent geometry : bond 0.00193 (43908) covalent geometry : angle 0.44140 (59388) hydrogen bonds : bond 0.03174 ( 2124) hydrogen bonds : angle 4.01123 ( 6156) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10704 Ramachandran restraints generated. 5352 Oldfield, 0 Emsley, 5352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10704 Ramachandran restraints generated. 5352 Oldfield, 0 Emsley, 5352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1107 residues out of total 4524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 212 poor density : 895 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 ASP cc_start: 0.7803 (p0) cc_final: 0.7464 (p0) REVERT: A 158 PHE cc_start: 0.8508 (t80) cc_final: 0.8281 (t80) REVERT: A 217 TRP cc_start: 0.8933 (m100) cc_final: 0.8518 (m100) REVERT: A 369 MET cc_start: 0.6434 (mmp) cc_final: 0.6177 (mmp) REVERT: A 415 ASP cc_start: 0.7576 (m-30) cc_final: 0.7302 (m-30) REVERT: B 62 TYR cc_start: 0.8769 (t80) cc_final: 0.8297 (t80) REVERT: B 103 ASP cc_start: 0.7667 (p0) cc_final: 0.7327 (p0) REVERT: B 165 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8468 (pp) REVERT: B 204 GLU cc_start: 0.8485 (tt0) cc_final: 0.8229 (tt0) REVERT: B 217 TRP cc_start: 0.8439 (m-10) cc_final: 0.7918 (m100) REVERT: B 240 PHE cc_start: 0.8855 (OUTLIER) cc_final: 0.7750 (m-80) REVERT: B 329 GLN cc_start: 0.8928 (OUTLIER) cc_final: 0.7948 (pm20) REVERT: B 398 MET cc_start: 0.8475 (mtt) cc_final: 0.7937 (mtm) REVERT: B 447 LYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7570 (tttp) REVERT: C 7 ILE cc_start: 0.9022 (tp) cc_final: 0.8744 (tt) REVERT: C 84 PHE cc_start: 0.8930 (m-80) cc_final: 0.8635 (m-80) REVERT: C 103 ASP cc_start: 0.7977 (p0) cc_final: 0.7511 (p0) REVERT: C 217 TRP cc_start: 0.8685 (m100) cc_final: 0.8029 (m100) REVERT: C 409 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7407 (tm-30) REVERT: D 103 ASP cc_start: 0.7697 (p0) cc_final: 0.7394 (p0) REVERT: D 185 GLU cc_start: 0.8353 (tm-30) cc_final: 0.7980 (tt0) REVERT: D 217 TRP cc_start: 0.8878 (m100) cc_final: 0.8405 (m100) REVERT: D 241 ASP cc_start: 0.8201 (p0) cc_final: 0.7867 (p0) REVERT: D 242 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.7908 (pm20) REVERT: D 310 VAL cc_start: 0.8399 (OUTLIER) cc_final: 0.8146 (m) REVERT: D 329 GLN cc_start: 0.8952 (OUTLIER) cc_final: 0.8304 (pt0) REVERT: D 415 ASP cc_start: 0.7576 (m-30) cc_final: 0.7306 (m-30) REVERT: D 455 ASP cc_start: 0.8197 (m-30) cc_final: 0.6833 (t0) REVERT: E 62 TYR cc_start: 0.8836 (t80) cc_final: 0.8295 (t80) REVERT: E 103 ASP cc_start: 0.7842 (p0) cc_final: 0.7560 (p0) REVERT: E 165 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8571 (pp) REVERT: E 217 TRP cc_start: 0.8495 (m-10) cc_final: 0.7990 (m100) REVERT: E 240 PHE cc_start: 0.8817 (OUTLIER) cc_final: 0.7863 (m-80) REVERT: E 322 ASN cc_start: 0.8318 (m-40) cc_final: 0.8108 (m-40) REVERT: E 329 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.7910 (pm20) REVERT: E 398 MET cc_start: 0.8473 (mtt) cc_final: 0.7958 (mtm) REVERT: F 7 ILE cc_start: 0.9009 (tp) cc_final: 0.8663 (tt) REVERT: F 84 PHE cc_start: 0.8919 (m-80) cc_final: 0.8634 (m-80) REVERT: F 103 ASP cc_start: 0.7961 (p0) cc_final: 0.7712 (p0) REVERT: F 194 TYR cc_start: 0.7458 (m-80) cc_final: 0.7237 (m-10) REVERT: F 217 TRP cc_start: 0.8669 (m100) cc_final: 0.8136 (m100) REVERT: G 103 ASP cc_start: 0.7842 (p0) cc_final: 0.7500 (p0) REVERT: G 217 TRP cc_start: 0.8942 (m100) cc_final: 0.8487 (m100) REVERT: G 329 GLN cc_start: 0.8927 (OUTLIER) cc_final: 0.8026 (pt0) REVERT: G 369 MET cc_start: 0.6386 (mmp) cc_final: 0.6119 (mmp) REVERT: G 415 ASP cc_start: 0.7471 (m-30) cc_final: 0.7175 (m-30) REVERT: G 455 ASP cc_start: 0.8299 (m-30) cc_final: 0.6934 (t0) REVERT: H 103 ASP cc_start: 0.7828 (p0) cc_final: 0.7501 (p0) REVERT: H 165 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8521 (pp) REVERT: H 204 GLU cc_start: 0.8671 (tt0) cc_final: 0.8458 (tt0) REVERT: H 217 TRP cc_start: 0.8460 (m-10) cc_final: 0.8093 (m100) REVERT: H 329 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.7912 (pm20) REVERT: H 398 MET cc_start: 0.8465 (mtt) cc_final: 0.7946 (mtm) REVERT: I 84 PHE cc_start: 0.8931 (m-80) cc_final: 0.8640 (m-80) REVERT: I 194 TYR cc_start: 0.7522 (m-80) cc_final: 0.7212 (m-10) REVERT: I 217 TRP cc_start: 0.8662 (m100) cc_final: 0.8098 (m100) REVERT: I 452 TYR cc_start: 0.8887 (p90) cc_final: 0.8567 (p90) REVERT: J 103 ASP cc_start: 0.7871 (p0) cc_final: 0.7510 (p0) REVERT: J 158 PHE cc_start: 0.8511 (t80) cc_final: 0.8305 (t80) REVERT: J 217 TRP cc_start: 0.8920 (m100) cc_final: 0.8515 (m100) REVERT: J 329 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.8017 (pt0) REVERT: J 369 MET cc_start: 0.6259 (mmp) cc_final: 0.5976 (mmp) REVERT: J 455 ASP cc_start: 0.8200 (m-30) cc_final: 0.6933 (t0) REVERT: K 62 TYR cc_start: 0.8838 (t80) cc_final: 0.8314 (t80) REVERT: K 165 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8605 (pp) REVERT: K 199 GLU cc_start: 0.7638 (pp20) cc_final: 0.7373 (pp20) REVERT: K 217 TRP cc_start: 0.8689 (m100) cc_final: 0.8292 (m100) REVERT: K 329 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.7843 (pm20) REVERT: K 398 MET cc_start: 0.8458 (mtt) cc_final: 0.7926 (mtm) REVERT: L 64 GLU cc_start: 0.8361 (mm-30) cc_final: 0.8154 (mm-30) REVERT: L 84 PHE cc_start: 0.8899 (m-80) cc_final: 0.8617 (m-80) REVERT: L 217 TRP cc_start: 0.8636 (m100) cc_final: 0.8051 (m100) REVERT: L 283 CYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8538 (t) REVERT: L 383 LYS cc_start: 0.8529 (ttmt) cc_final: 0.8293 (mmtp) outliers start: 212 outliers final: 158 residues processed: 1029 average time/residue: 0.2197 time to fit residues: 378.6526 Evaluate side-chains 1034 residues out of total 4524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 858 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 299 HIS Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 329 GLN Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 409 GLU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 447 LYS Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 299 HIS Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain C residue 409 GLU Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 278 ASP Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 329 GLN Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 357 SER Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 409 GLU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 419 MET Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 186 GLU Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain E residue 240 PHE Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 299 HIS Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 329 GLN Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 357 SER Chi-restraints excluded: chain E residue 376 SER Chi-restraints excluded: chain E residue 409 GLU Chi-restraints excluded: chain E residue 416 ILE Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 199 GLU Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 357 SER Chi-restraints excluded: chain F residue 409 GLU Chi-restraints excluded: chain F residue 416 ILE Chi-restraints excluded: chain F residue 436 ILE Chi-restraints excluded: chain G residue 18 HIS Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 216 THR Chi-restraints excluded: chain G residue 278 ASP Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain G residue 329 GLN Chi-restraints excluded: chain G residue 354 LEU Chi-restraints excluded: chain G residue 357 SER Chi-restraints excluded: chain G residue 409 GLU Chi-restraints excluded: chain G residue 416 ILE Chi-restraints excluded: chain G residue 436 ILE Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 165 LEU Chi-restraints excluded: chain H residue 290 THR Chi-restraints excluded: chain H residue 299 HIS Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 310 VAL Chi-restraints excluded: chain H residue 329 GLN Chi-restraints excluded: chain H residue 338 GLU Chi-restraints excluded: chain H residue 354 LEU Chi-restraints excluded: chain H residue 357 SER Chi-restraints excluded: chain H residue 376 SER Chi-restraints excluded: chain H residue 409 GLU Chi-restraints excluded: chain H residue 416 ILE Chi-restraints excluded: chain H residue 436 ILE Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 186 GLU Chi-restraints excluded: chain I residue 199 GLU Chi-restraints excluded: chain I residue 246 VAL Chi-restraints excluded: chain I residue 278 ASP Chi-restraints excluded: chain I residue 304 VAL Chi-restraints excluded: chain I residue 310 VAL Chi-restraints excluded: chain I residue 317 VAL Chi-restraints excluded: chain I residue 354 LEU Chi-restraints excluded: chain I residue 357 SER Chi-restraints excluded: chain I residue 409 GLU Chi-restraints excluded: chain I residue 416 ILE Chi-restraints excluded: chain I residue 436 ILE Chi-restraints excluded: chain J residue 19 LYS Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 216 THR Chi-restraints excluded: chain J residue 225 TYR Chi-restraints excluded: chain J residue 278 ASP Chi-restraints excluded: chain J residue 290 THR Chi-restraints excluded: chain J residue 317 VAL Chi-restraints excluded: chain J residue 329 GLN Chi-restraints excluded: chain J residue 354 LEU Chi-restraints excluded: chain J residue 357 SER Chi-restraints excluded: chain J residue 382 SER Chi-restraints excluded: chain J residue 409 GLU Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 419 MET Chi-restraints excluded: chain J residue 436 ILE Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain K residue 165 LEU Chi-restraints excluded: chain K residue 186 GLU Chi-restraints excluded: chain K residue 299 HIS Chi-restraints excluded: chain K residue 304 VAL Chi-restraints excluded: chain K residue 310 VAL Chi-restraints excluded: chain K residue 317 VAL Chi-restraints excluded: chain K residue 329 GLN Chi-restraints excluded: chain K residue 354 LEU Chi-restraints excluded: chain K residue 357 SER Chi-restraints excluded: chain K residue 376 SER Chi-restraints excluded: chain K residue 409 GLU Chi-restraints excluded: chain K residue 416 ILE Chi-restraints excluded: chain K residue 436 ILE Chi-restraints excluded: chain L residue 56 VAL Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain L residue 246 VAL Chi-restraints excluded: chain L residue 278 ASP Chi-restraints excluded: chain L residue 283 CYS Chi-restraints excluded: chain L residue 299 HIS Chi-restraints excluded: chain L residue 304 VAL Chi-restraints excluded: chain L residue 310 VAL Chi-restraints excluded: chain L residue 317 VAL Chi-restraints excluded: chain L residue 357 SER Chi-restraints excluded: chain L residue 409 GLU Chi-restraints excluded: chain L residue 416 ILE Chi-restraints excluded: chain L residue 436 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 39 optimal weight: 3.9990 chunk 326 optimal weight: 10.0000 chunk 113 optimal weight: 7.9990 chunk 171 optimal weight: 4.9990 chunk 293 optimal weight: 4.9990 chunk 494 optimal weight: 6.9990 chunk 249 optimal weight: 3.9990 chunk 262 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 184 optimal weight: 9.9990 chunk 470 optimal weight: 10.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS A 299 HIS B 18 HIS B 303 ASN C 18 HIS C 303 ASN C 444 GLN D 18 HIS D 299 HIS ** D 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 HIS E 299 HIS F 18 HIS F 303 ASN F 444 GLN G 18 HIS G 299 HIS G 444 GLN H 18 HIS H 299 HIS I 18 HIS I 303 ASN I 444 GLN J 18 HIS J 299 HIS K 18 HIS L 18 HIS L 299 HIS L 444 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.140443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.115079 restraints weight = 58679.441| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.24 r_work: 0.3101 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 43908 Z= 0.218 Angle : 0.573 9.064 59388 Z= 0.298 Chirality : 0.042 0.189 6252 Planarity : 0.004 0.043 7860 Dihedral : 3.994 37.048 5870 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 5.31 % Allowed : 23.98 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.11), residues: 5352 helix: 2.14 (0.10), residues: 2412 sheet: 0.11 (0.19), residues: 816 loop : -0.59 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 274 TYR 0.024 0.002 TYR B 62 PHE 0.016 0.002 PHE C 158 TRP 0.034 0.002 TRP F 171 HIS 0.006 0.001 HIS I 18 Details of bonding type rmsd covalent geometry : bond 0.00518 (43908) covalent geometry : angle 0.57259 (59388) hydrogen bonds : bond 0.04494 ( 2124) hydrogen bonds : angle 4.30251 ( 6156) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10704 Ramachandran restraints generated. 5352 Oldfield, 0 Emsley, 5352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10704 Ramachandran restraints generated. 5352 Oldfield, 0 Emsley, 5352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1103 residues out of total 4524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 240 poor density : 863 time to evaluate : 1.279 Fit side-chains revert: symmetry clash REVERT: A 103 ASP cc_start: 0.7876 (p0) cc_final: 0.7550 (p0) REVERT: A 240 PHE cc_start: 0.8939 (OUTLIER) cc_final: 0.7797 (m-80) REVERT: A 369 MET cc_start: 0.6391 (mmp) cc_final: 0.6172 (mmp) REVERT: A 458 MET cc_start: 0.8184 (OUTLIER) cc_final: 0.6786 (ttp) REVERT: B 103 ASP cc_start: 0.7782 (p0) cc_final: 0.7559 (p0) REVERT: B 165 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8706 (pp) REVERT: B 217 TRP cc_start: 0.8426 (m-10) cc_final: 0.7779 (m100) REVERT: B 240 PHE cc_start: 0.8908 (OUTLIER) cc_final: 0.7820 (m-80) REVERT: B 322 ASN cc_start: 0.8726 (m-40) cc_final: 0.8499 (m-40) REVERT: B 329 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.8427 (pt0) REVERT: B 398 MET cc_start: 0.8442 (mtt) cc_final: 0.7913 (mtm) REVERT: C 11 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7716 (ttt180) REVERT: C 103 ASP cc_start: 0.8049 (p0) cc_final: 0.7667 (p0) REVERT: C 217 TRP cc_start: 0.8730 (m100) cc_final: 0.8083 (m100) REVERT: C 409 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7572 (tm-30) REVERT: C 454 GLU cc_start: 0.8401 (mp0) cc_final: 0.7880 (mp0) REVERT: D 103 ASP cc_start: 0.7876 (p0) cc_final: 0.7625 (p0) REVERT: D 185 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8222 (tt0) REVERT: D 217 TRP cc_start: 0.8856 (m100) cc_final: 0.8419 (m100) REVERT: D 241 ASP cc_start: 0.8217 (p0) cc_final: 0.7754 (p0) REVERT: D 242 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.7902 (pm20) REVERT: D 329 GLN cc_start: 0.8909 (OUTLIER) cc_final: 0.8270 (pt0) REVERT: E 103 ASP cc_start: 0.7864 (p0) cc_final: 0.7425 (p0) REVERT: E 165 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8751 (pp) REVERT: E 217 TRP cc_start: 0.8471 (m-10) cc_final: 0.8028 (m100) REVERT: E 240 PHE cc_start: 0.8937 (OUTLIER) cc_final: 0.7798 (m-80) REVERT: E 329 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.8438 (pt0) REVERT: E 398 MET cc_start: 0.8573 (mtt) cc_final: 0.8091 (mtm) REVERT: F 7 ILE cc_start: 0.9034 (tp) cc_final: 0.8721 (tt) REVERT: F 103 ASP cc_start: 0.7978 (p0) cc_final: 0.7768 (p0) REVERT: F 454 GLU cc_start: 0.8309 (mp0) cc_final: 0.7787 (mp0) REVERT: G 103 ASP cc_start: 0.7946 (p0) cc_final: 0.7660 (p0) REVERT: G 217 TRP cc_start: 0.8947 (m100) cc_final: 0.8553 (m100) REVERT: G 329 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8161 (pt0) REVERT: G 369 MET cc_start: 0.6369 (mmp) cc_final: 0.5973 (mmm) REVERT: G 458 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.6902 (ttp) REVERT: H 103 ASP cc_start: 0.7867 (p0) cc_final: 0.7626 (p0) REVERT: H 165 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8813 (pp) REVERT: H 217 TRP cc_start: 0.8540 (m-10) cc_final: 0.8116 (m100) REVERT: H 240 PHE cc_start: 0.9001 (OUTLIER) cc_final: 0.7995 (m-80) REVERT: H 329 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.8409 (pt0) REVERT: I 217 TRP cc_start: 0.8778 (m100) cc_final: 0.8216 (m100) REVERT: J 103 ASP cc_start: 0.7946 (p0) cc_final: 0.7627 (p0) REVERT: J 217 TRP cc_start: 0.8957 (m100) cc_final: 0.8565 (m100) REVERT: J 240 PHE cc_start: 0.8941 (OUTLIER) cc_final: 0.7819 (m-80) REVERT: J 329 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8121 (pt0) REVERT: J 369 MET cc_start: 0.6354 (mmp) cc_final: 0.5966 (mmm) REVERT: J 458 MET cc_start: 0.8269 (OUTLIER) cc_final: 0.6965 (ttp) REVERT: K 165 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8817 (pp) REVERT: K 217 TRP cc_start: 0.8808 (m100) cc_final: 0.8445 (m100) REVERT: K 240 PHE cc_start: 0.8999 (OUTLIER) cc_final: 0.8017 (m-80) REVERT: K 329 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.8402 (pt0) REVERT: L 98 ASP cc_start: 0.7876 (t0) cc_final: 0.7427 (m-30) REVERT: L 217 TRP cc_start: 0.8772 (m100) cc_final: 0.8359 (m100) REVERT: L 310 VAL cc_start: 0.9025 (OUTLIER) cc_final: 0.8747 (m) REVERT: L 383 LYS cc_start: 0.8561 (ttmt) cc_final: 0.8052 (mmtp) outliers start: 240 outliers final: 169 residues processed: 1022 average time/residue: 0.2228 time to fit residues: 380.6985 Evaluate side-chains 1033 residues out of total 4524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 840 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASP Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 225 TYR Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 458 MET Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 329 GLN Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 409 GLU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain C residue 11 ARG Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 299 HIS Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain C residue 409 GLU Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 329 GLN Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 357 SER Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 409 GLU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 419 MET Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 186 GLU Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 240 PHE Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 329 GLN Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 357 SER Chi-restraints excluded: chain E residue 376 SER Chi-restraints excluded: chain E residue 409 GLU Chi-restraints excluded: chain E residue 416 ILE Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 186 GLU Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 299 HIS Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 357 SER Chi-restraints excluded: chain F residue 409 GLU Chi-restraints excluded: chain F residue 416 ILE Chi-restraints excluded: chain F residue 436 ILE Chi-restraints excluded: chain G residue 13 ASP Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 185 GLU Chi-restraints excluded: chain G residue 216 THR Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 304 VAL Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain G residue 329 GLN Chi-restraints excluded: chain G residue 354 LEU Chi-restraints excluded: chain G residue 357 SER Chi-restraints excluded: chain G residue 382 SER Chi-restraints excluded: chain G residue 409 GLU Chi-restraints excluded: chain G residue 416 ILE Chi-restraints excluded: chain G residue 419 MET Chi-restraints excluded: chain G residue 436 ILE Chi-restraints excluded: chain G residue 457 ASP Chi-restraints excluded: chain G residue 458 MET Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 165 LEU Chi-restraints excluded: chain H residue 216 THR Chi-restraints excluded: chain H residue 240 PHE Chi-restraints excluded: chain H residue 290 THR Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 310 VAL Chi-restraints excluded: chain H residue 317 VAL Chi-restraints excluded: chain H residue 321 VAL Chi-restraints excluded: chain H residue 329 GLN Chi-restraints excluded: chain H residue 338 GLU Chi-restraints excluded: chain H residue 354 LEU Chi-restraints excluded: chain H residue 357 SER Chi-restraints excluded: chain H residue 376 SER Chi-restraints excluded: chain H residue 409 GLU Chi-restraints excluded: chain H residue 416 ILE Chi-restraints excluded: chain H residue 436 ILE Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 186 GLU Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 246 VAL Chi-restraints excluded: chain I residue 299 HIS Chi-restraints excluded: chain I residue 304 VAL Chi-restraints excluded: chain I residue 310 VAL Chi-restraints excluded: chain I residue 354 LEU Chi-restraints excluded: chain I residue 357 SER Chi-restraints excluded: chain I residue 409 GLU Chi-restraints excluded: chain I residue 416 ILE Chi-restraints excluded: chain I residue 436 ILE Chi-restraints excluded: chain J residue 13 ASP Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 99 MET Chi-restraints excluded: chain J residue 216 THR Chi-restraints excluded: chain J residue 225 TYR Chi-restraints excluded: chain J residue 240 PHE Chi-restraints excluded: chain J residue 246 VAL Chi-restraints excluded: chain J residue 290 THR Chi-restraints excluded: chain J residue 304 VAL Chi-restraints excluded: chain J residue 317 VAL Chi-restraints excluded: chain J residue 329 GLN Chi-restraints excluded: chain J residue 354 LEU Chi-restraints excluded: chain J residue 357 SER Chi-restraints excluded: chain J residue 382 SER Chi-restraints excluded: chain J residue 409 GLU Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 419 MET Chi-restraints excluded: chain J residue 436 ILE Chi-restraints excluded: chain J residue 457 ASP Chi-restraints excluded: chain J residue 458 MET Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain K residue 165 LEU Chi-restraints excluded: chain K residue 186 GLU Chi-restraints excluded: chain K residue 216 THR Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain K residue 299 HIS Chi-restraints excluded: chain K residue 304 VAL Chi-restraints excluded: chain K residue 310 VAL Chi-restraints excluded: chain K residue 317 VAL Chi-restraints excluded: chain K residue 329 GLN Chi-restraints excluded: chain K residue 338 GLU Chi-restraints excluded: chain K residue 354 LEU Chi-restraints excluded: chain K residue 357 SER Chi-restraints excluded: chain K residue 376 SER Chi-restraints excluded: chain K residue 409 GLU Chi-restraints excluded: chain K residue 416 ILE Chi-restraints excluded: chain K residue 436 ILE Chi-restraints excluded: chain L residue 56 VAL Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 216 THR Chi-restraints excluded: chain L residue 246 VAL Chi-restraints excluded: chain L residue 304 VAL Chi-restraints excluded: chain L residue 310 VAL Chi-restraints excluded: chain L residue 357 SER Chi-restraints excluded: chain L residue 409 GLU Chi-restraints excluded: chain L residue 416 ILE Chi-restraints excluded: chain L residue 436 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 81 optimal weight: 3.9990 chunk 523 optimal weight: 10.0000 chunk 490 optimal weight: 1.9990 chunk 508 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 285 optimal weight: 0.5980 chunk 468 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 chunk 121 optimal weight: 0.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS B 18 HIS B 299 HIS B 303 ASN C 444 GLN ** D 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 HIS F 444 GLN G 18 HIS H 18 HIS I 444 GLN J 18 HIS K 18 HIS L 444 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.142858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.117624 restraints weight = 58768.434| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.26 r_work: 0.3152 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 43908 Z= 0.108 Angle : 0.471 7.617 59388 Z= 0.250 Chirality : 0.039 0.171 6252 Planarity : 0.003 0.042 7860 Dihedral : 3.726 31.194 5870 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 4.49 % Allowed : 24.87 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.12), residues: 5352 helix: 2.31 (0.10), residues: 2412 sheet: 0.15 (0.19), residues: 816 loop : -0.47 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 184 TYR 0.014 0.001 TYR E 225 PHE 0.013 0.001 PHE B 183 TRP 0.023 0.001 TRP F 171 HIS 0.003 0.000 HIS J 18 Details of bonding type rmsd covalent geometry : bond 0.00244 (43908) covalent geometry : angle 0.47074 (59388) hydrogen bonds : bond 0.03524 ( 2124) hydrogen bonds : angle 4.09608 ( 6156) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10704 Ramachandran restraints generated. 5352 Oldfield, 0 Emsley, 5352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10704 Ramachandran restraints generated. 5352 Oldfield, 0 Emsley, 5352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1069 residues out of total 4524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 203 poor density : 866 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 ASP cc_start: 0.7774 (p0) cc_final: 0.7470 (p0) REVERT: A 217 TRP cc_start: 0.8871 (m100) cc_final: 0.8492 (m100) REVERT: A 240 PHE cc_start: 0.8893 (OUTLIER) cc_final: 0.7751 (m-80) REVERT: A 329 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.8122 (pt0) REVERT: A 369 MET cc_start: 0.6413 (mmp) cc_final: 0.6132 (mmp) REVERT: B 103 ASP cc_start: 0.7645 (p0) cc_final: 0.7391 (p0) REVERT: B 165 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8663 (pp) REVERT: B 217 TRP cc_start: 0.8366 (m-10) cc_final: 0.7847 (m100) REVERT: B 240 PHE cc_start: 0.8941 (OUTLIER) cc_final: 0.7907 (m-80) REVERT: B 329 GLN cc_start: 0.8915 (OUTLIER) cc_final: 0.7990 (pm20) REVERT: B 398 MET cc_start: 0.8381 (mtt) cc_final: 0.7872 (mtm) REVERT: C 84 PHE cc_start: 0.9006 (m-80) cc_final: 0.8743 (m-80) REVERT: C 103 ASP cc_start: 0.8008 (p0) cc_final: 0.7595 (p0) REVERT: C 217 TRP cc_start: 0.8695 (m100) cc_final: 0.8090 (m100) REVERT: C 409 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7480 (tm-30) REVERT: C 454 GLU cc_start: 0.8336 (mp0) cc_final: 0.7832 (mp0) REVERT: D 103 ASP cc_start: 0.7770 (p0) cc_final: 0.7408 (p0) REVERT: D 185 GLU cc_start: 0.8394 (tm-30) cc_final: 0.8068 (tt0) REVERT: D 217 TRP cc_start: 0.8904 (m100) cc_final: 0.8472 (m100) REVERT: D 329 GLN cc_start: 0.8973 (OUTLIER) cc_final: 0.8306 (pt0) REVERT: D 455 ASP cc_start: 0.8014 (m-30) cc_final: 0.6642 (t0) REVERT: E 103 ASP cc_start: 0.7761 (p0) cc_final: 0.7348 (p0) REVERT: E 165 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8692 (pp) REVERT: E 217 TRP cc_start: 0.8483 (m-10) cc_final: 0.8092 (m100) REVERT: E 240 PHE cc_start: 0.8933 (OUTLIER) cc_final: 0.7870 (m-80) REVERT: E 329 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.7990 (pm20) REVERT: E 398 MET cc_start: 0.8531 (mtt) cc_final: 0.8059 (mtm) REVERT: F 7 ILE cc_start: 0.9050 (tp) cc_final: 0.8709 (tt) REVERT: F 84 PHE cc_start: 0.8984 (m-80) cc_final: 0.8735 (m-80) REVERT: F 103 ASP cc_start: 0.8005 (p0) cc_final: 0.7801 (p0) REVERT: F 176 LYS cc_start: 0.8376 (mmtt) cc_final: 0.8113 (mmtt) REVERT: F 217 TRP cc_start: 0.8653 (m100) cc_final: 0.8186 (m100) REVERT: F 454 GLU cc_start: 0.8248 (mp0) cc_final: 0.7736 (mp0) REVERT: G 103 ASP cc_start: 0.7824 (p0) cc_final: 0.7553 (p0) REVERT: G 217 TRP cc_start: 0.8947 (m100) cc_final: 0.8533 (m100) REVERT: G 369 MET cc_start: 0.6319 (mmp) cc_final: 0.5929 (mmm) REVERT: G 455 ASP cc_start: 0.8309 (m-30) cc_final: 0.6944 (t0) REVERT: G 458 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.6564 (ttp) REVERT: H 103 ASP cc_start: 0.7769 (p0) cc_final: 0.7525 (p0) REVERT: H 165 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8687 (pp) REVERT: H 217 TRP cc_start: 0.8522 (m-10) cc_final: 0.8179 (m100) REVERT: H 240 PHE cc_start: 0.8976 (OUTLIER) cc_final: 0.7868 (m-80) REVERT: H 329 GLN cc_start: 0.8885 (OUTLIER) cc_final: 0.7943 (pm20) REVERT: H 398 MET cc_start: 0.8673 (mtt) cc_final: 0.8136 (mtm) REVERT: I 84 PHE cc_start: 0.9013 (m-80) cc_final: 0.8754 (m-80) REVERT: I 194 TYR cc_start: 0.7580 (m-80) cc_final: 0.7349 (m-10) REVERT: I 217 TRP cc_start: 0.8770 (m100) cc_final: 0.8134 (m100) REVERT: J 103 ASP cc_start: 0.7827 (p0) cc_final: 0.7502 (p0) REVERT: J 217 TRP cc_start: 0.8927 (m100) cc_final: 0.8542 (m100) REVERT: J 369 MET cc_start: 0.6311 (mmp) cc_final: 0.6046 (mmp) REVERT: J 455 ASP cc_start: 0.8037 (m-30) cc_final: 0.6794 (t0) REVERT: K 165 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8698 (pp) REVERT: K 217 TRP cc_start: 0.8752 (m100) cc_final: 0.8413 (m100) REVERT: K 240 PHE cc_start: 0.8969 (OUTLIER) cc_final: 0.7896 (m-80) REVERT: K 329 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.7876 (pm20) REVERT: K 398 MET cc_start: 0.8482 (mtt) cc_final: 0.7944 (mtm) REVERT: L 84 PHE cc_start: 0.8982 (m-80) cc_final: 0.8732 (m-80) REVERT: L 217 TRP cc_start: 0.8747 (m100) cc_final: 0.8248 (m100) REVERT: L 383 LYS cc_start: 0.8594 (ttmt) cc_final: 0.8288 (mmtp) outliers start: 203 outliers final: 159 residues processed: 995 average time/residue: 0.2257 time to fit residues: 376.1806 Evaluate side-chains 1021 residues out of total 4524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 845 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASP Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 329 GLN Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 409 GLU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 299 HIS Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain C residue 409 GLU Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 278 ASP Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 329 GLN Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 357 SER Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 409 GLU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 419 MET Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 186 GLU Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain E residue 240 PHE Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 329 GLN Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 357 SER Chi-restraints excluded: chain E residue 376 SER Chi-restraints excluded: chain E residue 409 GLU Chi-restraints excluded: chain E residue 416 ILE Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 199 GLU Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 299 HIS Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 357 SER Chi-restraints excluded: chain F residue 409 GLU Chi-restraints excluded: chain F residue 416 ILE Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 185 GLU Chi-restraints excluded: chain G residue 216 THR Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 304 VAL Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain G residue 354 LEU Chi-restraints excluded: chain G residue 357 SER Chi-restraints excluded: chain G residue 382 SER Chi-restraints excluded: chain G residue 409 GLU Chi-restraints excluded: chain G residue 416 ILE Chi-restraints excluded: chain G residue 419 MET Chi-restraints excluded: chain G residue 436 ILE Chi-restraints excluded: chain G residue 458 MET Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 165 LEU Chi-restraints excluded: chain H residue 240 PHE Chi-restraints excluded: chain H residue 290 THR Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 310 VAL Chi-restraints excluded: chain H residue 317 VAL Chi-restraints excluded: chain H residue 329 GLN Chi-restraints excluded: chain H residue 338 GLU Chi-restraints excluded: chain H residue 354 LEU Chi-restraints excluded: chain H residue 357 SER Chi-restraints excluded: chain H residue 376 SER Chi-restraints excluded: chain H residue 409 GLU Chi-restraints excluded: chain H residue 416 ILE Chi-restraints excluded: chain H residue 436 ILE Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 186 GLU Chi-restraints excluded: chain I residue 199 GLU Chi-restraints excluded: chain I residue 246 VAL Chi-restraints excluded: chain I residue 299 HIS Chi-restraints excluded: chain I residue 304 VAL Chi-restraints excluded: chain I residue 310 VAL Chi-restraints excluded: chain I residue 317 VAL Chi-restraints excluded: chain I residue 338 GLU Chi-restraints excluded: chain I residue 354 LEU Chi-restraints excluded: chain I residue 357 SER Chi-restraints excluded: chain I residue 409 GLU Chi-restraints excluded: chain I residue 416 ILE Chi-restraints excluded: chain I residue 436 ILE Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 216 THR Chi-restraints excluded: chain J residue 225 TYR Chi-restraints excluded: chain J residue 278 ASP Chi-restraints excluded: chain J residue 290 THR Chi-restraints excluded: chain J residue 304 VAL Chi-restraints excluded: chain J residue 317 VAL Chi-restraints excluded: chain J residue 354 LEU Chi-restraints excluded: chain J residue 357 SER Chi-restraints excluded: chain J residue 382 SER Chi-restraints excluded: chain J residue 409 GLU Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 419 MET Chi-restraints excluded: chain J residue 436 ILE Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain K residue 165 LEU Chi-restraints excluded: chain K residue 186 GLU Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain K residue 299 HIS Chi-restraints excluded: chain K residue 304 VAL Chi-restraints excluded: chain K residue 310 VAL Chi-restraints excluded: chain K residue 317 VAL Chi-restraints excluded: chain K residue 329 GLN Chi-restraints excluded: chain K residue 338 GLU Chi-restraints excluded: chain K residue 354 LEU Chi-restraints excluded: chain K residue 357 SER Chi-restraints excluded: chain K residue 376 SER Chi-restraints excluded: chain K residue 409 GLU Chi-restraints excluded: chain K residue 416 ILE Chi-restraints excluded: chain K residue 436 ILE Chi-restraints excluded: chain L residue 56 VAL Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain L residue 246 VAL Chi-restraints excluded: chain L residue 299 HIS Chi-restraints excluded: chain L residue 304 VAL Chi-restraints excluded: chain L residue 310 VAL Chi-restraints excluded: chain L residue 317 VAL Chi-restraints excluded: chain L residue 357 SER Chi-restraints excluded: chain L residue 409 GLU Chi-restraints excluded: chain L residue 416 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 488 optimal weight: 8.9990 chunk 393 optimal weight: 5.9990 chunk 353 optimal weight: 4.9990 chunk 189 optimal weight: 5.9990 chunk 154 optimal weight: 5.9990 chunk 360 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 335 optimal weight: 8.9990 chunk 504 optimal weight: 2.9990 chunk 183 optimal weight: 0.6980 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 HIS B 299 HIS C 303 ASN C 444 GLN D 6 ASN ** D 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 HIS F 303 ASN F 444 GLN H 18 HIS I 303 ASN I 444 GLN K 18 HIS L 444 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.138172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.113437 restraints weight = 59325.973| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.22 r_work: 0.3029 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 43908 Z= 0.242 Angle : 0.584 9.044 59388 Z= 0.304 Chirality : 0.043 0.210 6252 Planarity : 0.004 0.043 7860 Dihedral : 4.146 37.916 5870 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 4.80 % Allowed : 24.85 % Favored : 70.36 % 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: 0.99 (0.11), residues: 5352 helix: 1.97 (0.10), residues: 2412 sheet: 0.15 (0.19), residues: 804 loop : -0.65 (0.13), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG J 170 TYR 0.026 0.002 TYR B 62 PHE 0.015 0.002 PHE L 273 TRP 0.036 0.002 TRP I 171 HIS 0.004 0.001 HIS I 18 Details of bonding type rmsd covalent geometry : bond 0.00575 (43908) covalent geometry : angle 0.58388 (59388) hydrogen bonds : bond 0.04505 ( 2124) hydrogen bonds : angle 4.33754 ( 6156) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10704 Ramachandran restraints generated. 5352 Oldfield, 0 Emsley, 5352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10704 Ramachandran restraints generated. 5352 Oldfield, 0 Emsley, 5352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1077 residues out of total 4524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 217 poor density : 860 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 ASP cc_start: 0.7808 (p0) cc_final: 0.7505 (p0) REVERT: A 217 TRP cc_start: 0.8925 (m100) cc_final: 0.8537 (m100) REVERT: A 240 PHE cc_start: 0.8973 (OUTLIER) cc_final: 0.7864 (m-80) REVERT: A 369 MET cc_start: 0.6453 (mmp) cc_final: 0.6194 (mmp) REVERT: B 103 ASP cc_start: 0.7697 (p0) cc_final: 0.7469 (p0) REVERT: B 165 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8612 (pp) REVERT: B 240 PHE cc_start: 0.9033 (OUTLIER) cc_final: 0.7805 (m-80) REVERT: B 329 GLN cc_start: 0.9021 (OUTLIER) cc_final: 0.8498 (pt0) REVERT: B 447 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7732 (tttp) REVERT: C 103 ASP cc_start: 0.7999 (p0) cc_final: 0.7618 (p0) REVERT: C 409 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7608 (tm-30) REVERT: C 454 GLU cc_start: 0.8498 (mp0) cc_final: 0.7983 (mp0) REVERT: D 103 ASP cc_start: 0.7853 (p0) cc_final: 0.7459 (p0) REVERT: D 185 GLU cc_start: 0.8412 (tm-30) cc_final: 0.8109 (tt0) REVERT: D 240 PHE cc_start: 0.8960 (OUTLIER) cc_final: 0.7843 (m-80) REVERT: D 329 GLN cc_start: 0.8942 (OUTLIER) cc_final: 0.8300 (pt0) REVERT: E 56 VAL cc_start: 0.8590 (OUTLIER) cc_final: 0.8371 (t) REVERT: E 103 ASP cc_start: 0.7739 (p0) cc_final: 0.7321 (p0) REVERT: E 165 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8699 (pp) REVERT: E 217 TRP cc_start: 0.8521 (m-10) cc_final: 0.7976 (m100) REVERT: E 240 PHE cc_start: 0.8950 (OUTLIER) cc_final: 0.7852 (m-80) REVERT: E 329 GLN cc_start: 0.9037 (OUTLIER) cc_final: 0.8531 (pt0) REVERT: F 7 ILE cc_start: 0.9053 (tp) cc_final: 0.8745 (tt) REVERT: F 11 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7572 (ttt180) REVERT: F 103 ASP cc_start: 0.7915 (p0) cc_final: 0.7698 (p0) REVERT: F 338 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8390 (tt0) REVERT: F 454 GLU cc_start: 0.8411 (mp0) cc_final: 0.7889 (mp0) REVERT: G 103 ASP cc_start: 0.7844 (p0) cc_final: 0.7622 (p0) REVERT: G 217 TRP cc_start: 0.8939 (m100) cc_final: 0.8532 (m100) REVERT: G 240 PHE cc_start: 0.8964 (OUTLIER) cc_final: 0.7804 (m-80) REVERT: G 369 MET cc_start: 0.6368 (mmp) cc_final: 0.5972 (mmm) REVERT: G 458 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.6780 (ttp) REVERT: H 56 VAL cc_start: 0.8576 (OUTLIER) cc_final: 0.8352 (t) REVERT: H 103 ASP cc_start: 0.7776 (p0) cc_final: 0.7554 (p0) REVERT: H 165 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8754 (pp) REVERT: H 217 TRP cc_start: 0.8548 (m-10) cc_final: 0.7980 (m100) REVERT: H 240 PHE cc_start: 0.9022 (OUTLIER) cc_final: 0.7939 (m-80) REVERT: H 329 GLN cc_start: 0.9020 (OUTLIER) cc_final: 0.8501 (pt0) REVERT: I 98 ASP cc_start: 0.8001 (t0) cc_final: 0.7666 (m-30) REVERT: I 170 ARG cc_start: 0.7676 (tpp80) cc_final: 0.7201 (tpt90) REVERT: I 217 TRP cc_start: 0.8766 (m100) cc_final: 0.8383 (m100) REVERT: I 454 GLU cc_start: 0.8397 (mp0) cc_final: 0.7855 (mp0) REVERT: J 103 ASP cc_start: 0.7861 (p0) cc_final: 0.7561 (p0) REVERT: J 217 TRP cc_start: 0.8898 (m100) cc_final: 0.8511 (m100) REVERT: J 240 PHE cc_start: 0.8976 (OUTLIER) cc_final: 0.7914 (m-80) REVERT: J 369 MET cc_start: 0.6380 (mmp) cc_final: 0.5997 (mmm) REVERT: K 56 VAL cc_start: 0.8602 (OUTLIER) cc_final: 0.8380 (t) REVERT: K 165 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8781 (pp) REVERT: K 217 TRP cc_start: 0.8802 (m100) cc_final: 0.7793 (m100) REVERT: K 240 PHE cc_start: 0.8999 (OUTLIER) cc_final: 0.7951 (m-80) REVERT: K 329 GLN cc_start: 0.9006 (OUTLIER) cc_final: 0.8472 (pt0) REVERT: L 98 ASP cc_start: 0.7980 (t0) cc_final: 0.7371 (m-30) REVERT: L 310 VAL cc_start: 0.9093 (OUTLIER) cc_final: 0.8867 (m) REVERT: L 383 LYS cc_start: 0.8566 (ttmt) cc_final: 0.8269 (mmtp) REVERT: L 454 GLU cc_start: 0.8342 (mp0) cc_final: 0.7825 (mp0) REVERT: L 458 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.6314 (ttp) outliers start: 217 outliers final: 172 residues processed: 1010 average time/residue: 0.2215 time to fit residues: 372.5734 Evaluate side-chains 1037 residues out of total 4524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 838 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASP Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 329 GLN Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 409 GLU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 447 LYS Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 299 HIS Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain C residue 409 GLU Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 240 PHE Chi-restraints excluded: chain D residue 278 ASP Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 299 HIS Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 329 GLN Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 357 SER Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 409 GLU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 419 MET Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 186 GLU Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 240 PHE Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 299 HIS Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 329 GLN Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 357 SER Chi-restraints excluded: chain E residue 376 SER Chi-restraints excluded: chain E residue 409 GLU Chi-restraints excluded: chain E residue 416 ILE Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain F residue 11 ARG Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 299 HIS Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 357 SER Chi-restraints excluded: chain F residue 409 GLU Chi-restraints excluded: chain F residue 416 ILE Chi-restraints excluded: chain F residue 436 ILE Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 99 MET Chi-restraints excluded: chain G residue 185 GLU Chi-restraints excluded: chain G residue 216 THR Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 278 ASP Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 299 HIS Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain G residue 354 LEU Chi-restraints excluded: chain G residue 357 SER Chi-restraints excluded: chain G residue 382 SER Chi-restraints excluded: chain G residue 409 GLU Chi-restraints excluded: chain G residue 416 ILE Chi-restraints excluded: chain G residue 419 MET Chi-restraints excluded: chain G residue 436 ILE Chi-restraints excluded: chain G residue 458 MET Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 165 LEU Chi-restraints excluded: chain H residue 216 THR Chi-restraints excluded: chain H residue 240 PHE Chi-restraints excluded: chain H residue 290 THR Chi-restraints excluded: chain H residue 299 HIS Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 310 VAL Chi-restraints excluded: chain H residue 317 VAL Chi-restraints excluded: chain H residue 329 GLN Chi-restraints excluded: chain H residue 338 GLU Chi-restraints excluded: chain H residue 354 LEU Chi-restraints excluded: chain H residue 357 SER Chi-restraints excluded: chain H residue 376 SER Chi-restraints excluded: chain H residue 409 GLU Chi-restraints excluded: chain H residue 416 ILE Chi-restraints excluded: chain H residue 436 ILE Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 186 GLU Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 246 VAL Chi-restraints excluded: chain I residue 299 HIS Chi-restraints excluded: chain I residue 304 VAL Chi-restraints excluded: chain I residue 310 VAL Chi-restraints excluded: chain I residue 317 VAL Chi-restraints excluded: chain I residue 338 GLU Chi-restraints excluded: chain I residue 354 LEU Chi-restraints excluded: chain I residue 357 SER Chi-restraints excluded: chain I residue 409 GLU Chi-restraints excluded: chain I residue 416 ILE Chi-restraints excluded: chain I residue 436 ILE Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 98 ASP Chi-restraints excluded: chain J residue 99 MET Chi-restraints excluded: chain J residue 216 THR Chi-restraints excluded: chain J residue 225 TYR Chi-restraints excluded: chain J residue 240 PHE Chi-restraints excluded: chain J residue 278 ASP Chi-restraints excluded: chain J residue 290 THR Chi-restraints excluded: chain J residue 299 HIS Chi-restraints excluded: chain J residue 317 VAL Chi-restraints excluded: chain J residue 354 LEU Chi-restraints excluded: chain J residue 357 SER Chi-restraints excluded: chain J residue 382 SER Chi-restraints excluded: chain J residue 409 GLU Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 419 MET Chi-restraints excluded: chain J residue 436 ILE Chi-restraints excluded: chain J residue 457 ASP Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain K residue 165 LEU Chi-restraints excluded: chain K residue 186 GLU Chi-restraints excluded: chain K residue 216 THR Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain K residue 299 HIS Chi-restraints excluded: chain K residue 304 VAL Chi-restraints excluded: chain K residue 310 VAL Chi-restraints excluded: chain K residue 317 VAL Chi-restraints excluded: chain K residue 329 GLN Chi-restraints excluded: chain K residue 338 GLU Chi-restraints excluded: chain K residue 354 LEU Chi-restraints excluded: chain K residue 357 SER Chi-restraints excluded: chain K residue 376 SER Chi-restraints excluded: chain K residue 409 GLU Chi-restraints excluded: chain K residue 416 ILE Chi-restraints excluded: chain K residue 436 ILE Chi-restraints excluded: chain L residue 56 VAL Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 216 THR Chi-restraints excluded: chain L residue 246 VAL Chi-restraints excluded: chain L residue 299 HIS Chi-restraints excluded: chain L residue 304 VAL Chi-restraints excluded: chain L residue 310 VAL Chi-restraints excluded: chain L residue 338 GLU Chi-restraints excluded: chain L residue 357 SER Chi-restraints excluded: chain L residue 409 GLU Chi-restraints excluded: chain L residue 416 ILE Chi-restraints excluded: chain L residue 458 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 307 optimal weight: 0.9980 chunk 201 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 197 optimal weight: 20.0000 chunk 262 optimal weight: 0.8980 chunk 254 optimal weight: 10.0000 chunk 269 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 301 optimal weight: 7.9990 chunk 436 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 HIS B 299 HIS C 444 GLN ** D 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 HIS F 444 GLN H 18 HIS I 444 GLN K 18 HIS L 444 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.141818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.116960 restraints weight = 59148.970| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.24 r_work: 0.3156 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 43908 Z= 0.119 Angle : 0.489 7.722 59388 Z= 0.260 Chirality : 0.039 0.171 6252 Planarity : 0.004 0.042 7860 Dihedral : 3.865 33.024 5870 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.33 % Allowed : 25.55 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.12), residues: 5352 helix: 2.20 (0.10), residues: 2412 sheet: 0.19 (0.19), residues: 804 loop : -0.51 (0.13), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 184 TYR 0.015 0.001 TYR K 225 PHE 0.014 0.001 PHE B 183 TRP 0.024 0.001 TRP L 171 HIS 0.002 0.000 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00271 (43908) covalent geometry : angle 0.48877 (59388) hydrogen bonds : bond 0.03638 ( 2124) hydrogen bonds : angle 4.14404 ( 6156) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11160.14 seconds wall clock time: 191 minutes 5.40 seconds (11465.40 seconds total)