Starting phenix.real_space_refine on Thu Dec 26 03:37:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xb5_38211/12_2024/8xb5_38211.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xb5_38211/12_2024/8xb5_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8xb5_38211/12_2024/8xb5_38211.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xb5_38211/12_2024/8xb5_38211.map" model { file = "/net/cci-nas-00/data/ceres_data/8xb5_38211/12_2024/8xb5_38211.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xb5_38211/12_2024/8xb5_38211.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.61s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: C, B, E, D, G, F, I, H, K, J, L Time building chain proxies: 11.78, per 1000 atoms: 0.27 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: 11.34 Conformation dependent library (CDL) restraints added in 5.2 seconds 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: 4.61 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: 19.26 Time building geometry restraints manager: 12.62 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: 0.00 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: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 1.500 Check model and map are aligned: 0.300 Set scattering table: 0.400 Process input model: 79.320 Find NCS groups from input model: 1.480 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.490 ------------------------------------------------------------------------------- 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= 0.174 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 : 9.93 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (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 TRP 0.013 0.001 TRP H 171 HIS 0.003 0.001 HIS K 299 PHE 0.010 0.001 PHE G 84 TYR 0.005 0.001 TYR E 62 ARG 0.005 0.000 ARG I 184 *********************** 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 : 5.016 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: 0.8096 (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: 0.6455 (mmp) 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: 0.5882 time to fit residues: 852.2496 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 : 5.239 ------------------------------------------------------------------------------- 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 455 optimal weight: 6.9990 chunk 409 optimal weight: 4.9990 chunk 227 optimal weight: 2.9990 chunk 139 optimal weight: 7.9990 chunk 276 optimal weight: 7.9990 chunk 218 optimal weight: 9.9990 chunk 423 optimal weight: 7.9990 chunk 163 optimal weight: 0.9990 chunk 257 optimal weight: 3.9990 chunk 315 optimal weight: 20.0000 chunk 490 optimal weight: 0.6980 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN A 299 HIS A 444 GLN B 195 GLN B 444 GLN C 195 GLN C 444 GLN D 195 GLN D 299 HIS D 444 GLN E 195 GLN E 444 GLN F 195 GLN F 444 GLN G 195 GLN G 299 HIS G 444 GLN H 6 ASN H 195 GLN H 444 GLN I 195 GLN I 444 GLN J 195 GLN J 299 HIS J 444 GLN K 195 GLN K 444 GLN L 195 GLN L 444 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 43908 Z= 0.270 Angle : 0.543 7.701 59388 Z= 0.288 Chirality : 0.041 0.167 6252 Planarity : 0.004 0.043 7860 Dihedral : 4.109 44.931 5918 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.13 % Allowed : 24.38 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.11), residues: 5352 helix: 1.98 (0.10), residues: 2424 sheet: -0.17 (0.19), residues: 720 loop : -0.47 (0.13), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 171 HIS 0.004 0.001 HIS J 299 PHE 0.014 0.002 PHE B 158 TYR 0.019 0.002 TYR B 62 ARG 0.005 0.000 ARG F 184 *********************** 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 1060 residues out of total 4524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 873 time to evaluate : 5.168 Fit side-chains REVERT: A 103 ASP cc_start: 0.7879 (p0) cc_final: 0.7592 (p0) REVERT: A 369 MET cc_start: 0.6210 (mmp) cc_final: 0.5973 (mmp) REVERT: A 415 ASP cc_start: 0.7335 (m-30) cc_final: 0.7052 (m-30) REVERT: B 103 ASP cc_start: 0.7654 (p0) cc_final: 0.7429 (p0) REVERT: B 158 PHE cc_start: 0.8608 (t80) cc_final: 0.8103 (t80) REVERT: B 165 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8862 (pp) REVERT: B 180 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8946 (tp) REVERT: B 184 ARG cc_start: 0.8735 (tmm-80) cc_final: 0.8357 (ttm-80) REVERT: B 225 TYR cc_start: 0.4764 (m-80) cc_final: 0.4510 (m-10) REVERT: B 329 GLN cc_start: 0.8934 (OUTLIER) cc_final: 0.8039 (pm20) REVERT: B 398 MET cc_start: 0.8483 (mtt) cc_final: 0.8004 (mtm) REVERT: B 455 ASP cc_start: 0.7180 (p0) cc_final: 0.6961 (m-30) REVERT: C 65 ARG cc_start: 0.8584 (mmm160) cc_final: 0.8230 (tpt170) REVERT: C 84 PHE cc_start: 0.9109 (m-80) cc_final: 0.8850 (m-80) REVERT: C 165 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8864 (pp) REVERT: C 199 GLU cc_start: 0.7966 (pp20) cc_final: 0.7745 (pp20) REVERT: C 369 MET cc_start: 0.6975 (mmp) cc_final: 0.6606 (mmp) REVERT: D 103 ASP cc_start: 0.7771 (p0) cc_final: 0.7472 (p0) REVERT: D 225 TYR cc_start: 0.5114 (m-10) cc_final: 0.4886 (m-10) REVERT: D 415 ASP cc_start: 0.7069 (m-30) cc_final: 0.6800 (m-30) REVERT: E 98 ASP cc_start: 0.8372 (t0) cc_final: 0.8080 (t0) REVERT: E 158 PHE cc_start: 0.8669 (t80) cc_final: 0.8158 (t80) REVERT: E 165 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8805 (pp) REVERT: E 184 ARG cc_start: 0.8679 (tmm-80) cc_final: 0.8314 (ttm-80) REVERT: E 225 TYR cc_start: 0.4778 (m-80) cc_final: 0.4412 (m-10) REVERT: E 322 ASN cc_start: 0.8526 (m-40) cc_final: 0.8315 (m-40) REVERT: E 329 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.7890 (pm20) REVERT: E 398 MET cc_start: 0.8445 (mtt) cc_final: 0.7984 (mtm) REVERT: E 455 ASP cc_start: 0.7246 (p0) cc_final: 0.6958 (m-30) REVERT: F 65 ARG cc_start: 0.8548 (mmm160) cc_final: 0.8190 (tpt170) REVERT: F 103 ASP cc_start: 0.7579 (p0) cc_final: 0.7294 (p0) REVERT: F 165 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8874 (pp) REVERT: F 176 LYS cc_start: 0.8157 (mmtt) cc_final: 0.7883 (mmtt) REVERT: F 199 GLU cc_start: 0.8121 (pp20) cc_final: 0.7863 (pp20) REVERT: F 217 TRP cc_start: 0.8660 (m100) cc_final: 0.8179 (m100) REVERT: F 302 LYS cc_start: 0.7823 (mppt) cc_final: 0.7480 (mppt) REVERT: F 369 MET cc_start: 0.6570 (mmp) cc_final: 0.6187 (mmp) REVERT: G 103 ASP cc_start: 0.7856 (p0) cc_final: 0.7617 (p0) REVERT: G 217 TRP cc_start: 0.8847 (m100) cc_final: 0.8570 (m100) REVERT: G 369 MET cc_start: 0.6290 (mmp) cc_final: 0.6061 (mmp) REVERT: G 415 ASP cc_start: 0.7243 (m-30) cc_final: 0.6966 (m-30) REVERT: H 103 ASP cc_start: 0.7805 (p0) cc_final: 0.7434 (p0) REVERT: H 158 PHE cc_start: 0.8613 (t80) cc_final: 0.8160 (t80) REVERT: H 184 ARG cc_start: 0.8772 (tmm-80) cc_final: 0.8530 (ttp80) REVERT: H 322 ASN cc_start: 0.8525 (m-40) cc_final: 0.8301 (m-40) REVERT: H 329 GLN cc_start: 0.8875 (OUTLIER) cc_final: 0.7852 (pm20) REVERT: H 398 MET cc_start: 0.8552 (mtt) cc_final: 0.8100 (mtm) REVERT: H 455 ASP cc_start: 0.7284 (p0) cc_final: 0.7015 (m-30) REVERT: I 65 ARG cc_start: 0.8561 (mmm160) cc_final: 0.8202 (tpt170) REVERT: I 103 ASP cc_start: 0.7451 (p0) cc_final: 0.7247 (p0) REVERT: I 165 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8843 (pp) REVERT: I 217 TRP cc_start: 0.8613 (m100) cc_final: 0.8242 (m100) REVERT: I 369 MET cc_start: 0.6747 (mmp) cc_final: 0.6457 (mmp) REVERT: I 383 LYS cc_start: 0.8267 (mmtp) cc_final: 0.8047 (mmtp) REVERT: J 103 ASP cc_start: 0.7861 (p0) cc_final: 0.7586 (p0) REVERT: J 217 TRP cc_start: 0.8852 (m100) cc_final: 0.8579 (m100) REVERT: K 103 ASP cc_start: 0.7820 (p0) cc_final: 0.7478 (p0) REVERT: K 165 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8756 (pp) REVERT: K 223 GLN cc_start: 0.2553 (OUTLIER) cc_final: 0.2234 (tp40) REVERT: K 329 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.7855 (pm20) REVERT: K 398 MET cc_start: 0.8526 (mtt) cc_final: 0.8063 (mtm) REVERT: L 98 ASP cc_start: 0.8050 (t0) cc_final: 0.7824 (t0) REVERT: L 165 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8850 (pp) REVERT: L 199 GLU cc_start: 0.8150 (pp20) cc_final: 0.7880 (pp20) REVERT: L 217 TRP cc_start: 0.8689 (m100) cc_final: 0.8274 (m100) REVERT: L 369 MET cc_start: 0.6273 (mmp) cc_final: 0.5883 (mmp) outliers start: 187 outliers final: 104 residues processed: 995 average time/residue: 0.5320 time to fit residues: 886.2460 Evaluate side-chains 953 residues out of total 4524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 836 time to evaluate : 4.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 321 VAL 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 B residue 165 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 216 THR 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 409 GLU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 165 LEU 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 317 VAL Chi-restraints excluded: chain C residue 321 VAL 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 125 LEU Chi-restraints excluded: chain D residue 258 ASP Chi-restraints excluded: chain D residue 299 HIS Chi-restraints excluded: chain D residue 317 VAL 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 E residue 165 LEU Chi-restraints excluded: chain E residue 216 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 409 GLU Chi-restraints excluded: chain E residue 416 ILE Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 165 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 317 VAL Chi-restraints excluded: chain F residue 321 VAL 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 246 VAL Chi-restraints excluded: chain G residue 258 ASP Chi-restraints excluded: chain G residue 299 HIS Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain G residue 321 VAL 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 H residue 6 ASN Chi-restraints excluded: chain H residue 216 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 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 125 LEU Chi-restraints excluded: chain I residue 165 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 317 VAL Chi-restraints excluded: chain I residue 321 VAL 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 246 VAL Chi-restraints excluded: chain J residue 258 ASP Chi-restraints excluded: chain J residue 317 VAL Chi-restraints excluded: chain J residue 321 VAL 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 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 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 357 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 125 LEU Chi-restraints excluded: chain L residue 165 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 317 VAL 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 436 ILE Chi-restraints excluded: chain L residue 457 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 272 optimal weight: 7.9990 chunk 152 optimal weight: 20.0000 chunk 408 optimal weight: 0.0060 chunk 333 optimal weight: 6.9990 chunk 135 optimal weight: 10.0000 chunk 491 optimal weight: 5.9990 chunk 530 optimal weight: 4.9990 chunk 437 optimal weight: 6.9990 chunk 487 optimal weight: 7.9990 chunk 167 optimal weight: 1.9990 chunk 394 optimal weight: 6.9990 overall best weight: 4.0004 ------------------------------------------------------------------------------- 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 303 ASN C 18 HIS C 303 ASN C 444 GLN D 18 HIS E 303 ASN F 18 HIS F 444 GLN G 18 HIS ** G 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 303 ASN I 18 HIS I 444 GLN J 18 HIS J 299 HIS J 444 GLN K 303 ASN L 18 HIS L 444 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 43908 Z= 0.365 Angle : 0.583 8.370 59388 Z= 0.307 Chirality : 0.042 0.158 6252 Planarity : 0.004 0.045 7860 Dihedral : 4.274 37.009 5884 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 6.45 % Allowed : 23.32 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.11), residues: 5352 helix: 1.83 (0.10), residues: 2412 sheet: -0.29 (0.19), residues: 720 loop : -0.68 (0.12), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP K 171 HIS 0.012 0.001 HIS D 299 PHE 0.016 0.002 PHE B 158 TYR 0.022 0.002 TYR A 62 ARG 0.005 0.001 ARG F 65 *********************** 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 1191 residues out of total 4524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 292 poor density : 899 time to evaluate : 5.063 Fit side-chains revert: symmetry clash REVERT: A 103 ASP cc_start: 0.7841 (p0) cc_final: 0.7612 (p0) REVERT: A 329 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8043 (pt0) REVERT: A 369 MET cc_start: 0.6252 (mmp) cc_final: 0.5886 (mmp) REVERT: A 415 ASP cc_start: 0.7291 (m-30) cc_final: 0.7047 (m-30) REVERT: B 103 ASP cc_start: 0.7759 (p0) cc_final: 0.7536 (p0) REVERT: B 157 LYS cc_start: 0.8430 (mmtp) cc_final: 0.8157 (mmtt) REVERT: B 165 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.8865 (pp) REVERT: B 184 ARG cc_start: 0.8749 (tmm-80) cc_final: 0.8266 (ttm-80) REVERT: B 329 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.7962 (pm20) REVERT: C 165 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.9005 (pp) REVERT: C 199 GLU cc_start: 0.7906 (pp20) cc_final: 0.7660 (pp20) REVERT: C 369 MET cc_start: 0.6458 (mmp) cc_final: 0.6005 (mmp) REVERT: D 103 ASP cc_start: 0.7782 (p0) cc_final: 0.7573 (p0) REVERT: D 133 ASP cc_start: 0.8475 (p0) cc_final: 0.8247 (p0) REVERT: D 217 TRP cc_start: 0.8766 (m100) cc_final: 0.8033 (m100) REVERT: D 415 ASP cc_start: 0.7157 (m-30) cc_final: 0.6909 (m-30) REVERT: D 418 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7782 (tttm) REVERT: E 157 LYS cc_start: 0.8444 (mmtp) cc_final: 0.8191 (mmtt) REVERT: E 165 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8745 (pp) REVERT: E 184 ARG cc_start: 0.8750 (tmm-80) cc_final: 0.8247 (ttm-80) REVERT: E 217 TRP cc_start: 0.8546 (m100) cc_final: 0.8345 (m-10) REVERT: E 322 ASN cc_start: 0.8677 (m-40) cc_final: 0.8411 (m-40) REVERT: E 329 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.7950 (pm20) REVERT: F 76 VAL cc_start: 0.9073 (OUTLIER) cc_final: 0.8865 (t) REVERT: F 165 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8935 (pp) REVERT: F 199 GLU cc_start: 0.7876 (pp20) cc_final: 0.7665 (pp20) REVERT: F 329 GLN cc_start: 0.8878 (OUTLIER) cc_final: 0.8207 (pm20) REVERT: F 369 MET cc_start: 0.6465 (mmp) cc_final: 0.6095 (mmp) REVERT: G 103 ASP cc_start: 0.7826 (p0) cc_final: 0.7595 (p0) REVERT: G 329 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8013 (pt0) REVERT: G 369 MET cc_start: 0.6248 (mmp) cc_final: 0.5889 (mmp) REVERT: H 103 ASP cc_start: 0.7833 (p0) cc_final: 0.7535 (p0) REVERT: H 165 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8764 (pp) REVERT: H 217 TRP cc_start: 0.8665 (m100) cc_final: 0.8436 (m-10) REVERT: H 322 ASN cc_start: 0.8678 (m-40) cc_final: 0.8412 (m-40) REVERT: H 329 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.7925 (pm20) REVERT: I 102 ASN cc_start: 0.7736 (m-40) cc_final: 0.7509 (m-40) REVERT: I 165 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8922 (pp) REVERT: I 176 LYS cc_start: 0.8638 (mmtp) cc_final: 0.8399 (mmtt) REVERT: I 199 GLU cc_start: 0.8001 (pp20) cc_final: 0.7759 (pp20) REVERT: I 217 TRP cc_start: 0.8707 (m100) cc_final: 0.8304 (m100) REVERT: I 302 LYS cc_start: 0.7937 (mppt) cc_final: 0.7550 (mppt) REVERT: I 329 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.8160 (pm20) REVERT: I 369 MET cc_start: 0.6989 (mmp) cc_final: 0.6542 (mmp) REVERT: J 103 ASP cc_start: 0.7843 (p0) cc_final: 0.7624 (p0) REVERT: J 329 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.8044 (pt0) REVERT: J 415 ASP cc_start: 0.7244 (m-30) cc_final: 0.6871 (m-30) REVERT: K 103 ASP cc_start: 0.7852 (p0) cc_final: 0.7567 (p0) REVERT: K 165 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8763 (pp) REVERT: K 217 TRP cc_start: 0.8654 (m100) cc_final: 0.8435 (m-10) REVERT: K 223 GLN cc_start: 0.2666 (OUTLIER) cc_final: 0.2046 (tp40) REVERT: K 329 GLN cc_start: 0.8916 (OUTLIER) cc_final: 0.7963 (pm20) REVERT: K 331 GLU cc_start: 0.8479 (pm20) cc_final: 0.8238 (pm20) REVERT: K 383 LYS cc_start: 0.8528 (mmtp) cc_final: 0.8073 (mmtt) REVERT: L 76 VAL cc_start: 0.9077 (OUTLIER) cc_final: 0.8867 (t) REVERT: L 165 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8902 (pp) REVERT: L 199 GLU cc_start: 0.7993 (pp20) cc_final: 0.7748 (pp20) REVERT: L 217 TRP cc_start: 0.8753 (m100) cc_final: 0.8389 (m100) REVERT: L 329 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8661 (pm20) REVERT: L 369 MET cc_start: 0.6485 (mmp) cc_final: 0.6019 (mmp) REVERT: L 383 LYS cc_start: 0.8599 (ttmt) cc_final: 0.8135 (mmtp) REVERT: L 418 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7763 (tttt) outliers start: 292 outliers final: 196 residues processed: 1107 average time/residue: 0.5752 time to fit residues: 1057.0582 Evaluate side-chains 1084 residues out of total 4524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 219 poor density : 865 time to evaluate : 4.887 ------------------------------------------------------------------------------- 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 125 LEU 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 258 ASP 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 321 VAL Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 379 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 125 LEU 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 321 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 19 LYS Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 165 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 299 HIS Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 317 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 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 258 ASP 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 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 418 LYS Chi-restraints excluded: chain D residue 419 MET Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 186 GLU Chi-restraints excluded: chain E residue 216 THR 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 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 379 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 76 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 165 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 310 VAL Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 321 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 457 ASP Chi-restraints excluded: chain G residue 18 HIS Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 216 THR Chi-restraints excluded: chain G residue 246 VAL Chi-restraints excluded: chain G residue 258 ASP Chi-restraints excluded: chain G residue 278 ASP Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain G residue 321 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 6 ASN 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 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 354 LEU Chi-restraints excluded: chain H residue 357 SER Chi-restraints excluded: chain H residue 376 SER Chi-restraints excluded: chain H residue 379 SER Chi-restraints excluded: chain H residue 409 GLU Chi-restraints excluded: chain H residue 410 LEU 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 164 ILE Chi-restraints excluded: chain I residue 165 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 310 VAL Chi-restraints excluded: chain I residue 317 VAL Chi-restraints excluded: chain I residue 321 VAL Chi-restraints excluded: chain I residue 329 GLN Chi-restraints excluded: chain I residue 357 SER Chi-restraints excluded: chain I residue 379 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 I residue 457 ASP Chi-restraints excluded: chain J residue 18 HIS Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 125 LEU 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 258 ASP 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 321 VAL Chi-restraints excluded: chain J residue 329 GLN Chi-restraints excluded: chain J residue 357 SER Chi-restraints excluded: chain J residue 379 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 216 THR 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 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 379 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 76 VAL Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 164 ILE Chi-restraints excluded: chain L residue 165 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 317 VAL Chi-restraints excluded: chain L residue 321 VAL Chi-restraints excluded: chain L residue 329 GLN 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 418 LYS Chi-restraints excluded: chain L residue 436 ILE Chi-restraints excluded: chain L residue 457 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 485 optimal weight: 9.9990 chunk 369 optimal weight: 4.9990 chunk 254 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 chunk 234 optimal weight: 5.9990 chunk 329 optimal weight: 7.9990 chunk 493 optimal weight: 7.9990 chunk 521 optimal weight: 4.9990 chunk 257 optimal weight: 0.9980 chunk 467 optimal weight: 8.9990 chunk 140 optimal weight: 1.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 ASN ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 HIS C 18 HIS C 444 GLN E 18 HIS F 18 HIS F 303 ASN F 444 GLN H 18 HIS I 18 HIS I 444 GLN J 6 ASN ** J 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 18 HIS L 303 ASN L 444 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 43908 Z= 0.344 Angle : 0.563 8.386 59388 Z= 0.298 Chirality : 0.042 0.172 6252 Planarity : 0.004 0.045 7860 Dihedral : 4.348 37.827 5884 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 6.37 % Allowed : 23.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.11), residues: 5352 helix: 1.78 (0.10), residues: 2412 sheet: -0.18 (0.18), residues: 816 loop : -0.67 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 171 HIS 0.019 0.001 HIS J 18 PHE 0.014 0.002 PHE B 158 TYR 0.021 0.002 TYR D 62 ARG 0.005 0.001 ARG L 184 *********************** 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 1176 residues out of total 4524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 288 poor density : 888 time to evaluate : 5.028 Fit side-chains revert: symmetry clash REVERT: A 103 ASP cc_start: 0.7773 (p0) cc_final: 0.7563 (p0) REVERT: A 223 GLN cc_start: 0.1839 (OUTLIER) cc_final: 0.1375 (pm20) REVERT: A 369 MET cc_start: 0.6293 (mmp) cc_final: 0.5922 (mmp) REVERT: A 415 ASP cc_start: 0.7311 (m-30) cc_final: 0.7035 (m-30) REVERT: B 103 ASP cc_start: 0.7732 (p0) cc_final: 0.7522 (p0) REVERT: B 165 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8814 (pp) REVERT: B 217 TRP cc_start: 0.8542 (m100) cc_final: 0.8309 (m-10) REVERT: B 240 PHE cc_start: 0.9019 (OUTLIER) cc_final: 0.7913 (m-80) REVERT: B 329 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8221 (pt0) REVERT: C 165 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8990 (pp) REVERT: C 176 LYS cc_start: 0.8589 (mmtp) cc_final: 0.8223 (tptt) REVERT: C 369 MET cc_start: 0.6472 (mmp) cc_final: 0.6103 (mmp) REVERT: C 454 GLU cc_start: 0.7886 (mp0) cc_final: 0.7272 (mp0) REVERT: D 217 TRP cc_start: 0.8782 (m100) cc_final: 0.8119 (m100) REVERT: D 326 GLU cc_start: 0.7850 (tt0) cc_final: 0.7623 (tt0) REVERT: D 418 LYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7664 (tttm) REVERT: E 165 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8748 (pp) REVERT: E 184 ARG cc_start: 0.8703 (tmm-80) cc_final: 0.8293 (ttm-80) REVERT: E 217 TRP cc_start: 0.8540 (m100) cc_final: 0.8331 (m-10) REVERT: E 240 PHE cc_start: 0.9032 (OUTLIER) cc_final: 0.8030 (m-80) REVERT: E 329 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8303 (pt0) REVERT: F 165 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8951 (pp) REVERT: F 329 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8175 (pm20) REVERT: F 369 MET cc_start: 0.6456 (mmp) cc_final: 0.5999 (mmp) REVERT: F 454 GLU cc_start: 0.7856 (mp0) cc_final: 0.7221 (mp0) REVERT: F 458 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.6670 (ttp) REVERT: G 103 ASP cc_start: 0.7732 (p0) cc_final: 0.7522 (p0) REVERT: G 369 MET cc_start: 0.6276 (mmp) cc_final: 0.5910 (mmp) REVERT: H 103 ASP cc_start: 0.7805 (p0) cc_final: 0.7550 (p0) REVERT: H 165 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8816 (pp) REVERT: H 240 PHE cc_start: 0.9011 (OUTLIER) cc_final: 0.8002 (m-80) REVERT: H 329 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.8308 (pt0) REVERT: I 99 MET cc_start: 0.7730 (OUTLIER) cc_final: 0.7481 (ptp) REVERT: I 329 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8207 (pm20) REVERT: I 369 MET cc_start: 0.7004 (mmp) cc_final: 0.6529 (mmp) REVERT: J 103 ASP cc_start: 0.7759 (p0) cc_final: 0.7547 (p0) REVERT: J 415 ASP cc_start: 0.7281 (m-30) cc_final: 0.6862 (m-30) REVERT: K 103 ASP cc_start: 0.7820 (p0) cc_final: 0.7564 (p0) REVERT: K 165 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8811 (pp) REVERT: K 223 GLN cc_start: 0.2672 (OUTLIER) cc_final: 0.2014 (tp40) REVERT: K 329 GLN cc_start: 0.8938 (OUTLIER) cc_final: 0.8314 (pt0) REVERT: K 331 GLU cc_start: 0.8488 (pm20) cc_final: 0.8078 (pm20) REVERT: K 383 LYS cc_start: 0.8480 (mmtp) cc_final: 0.8173 (mmtt) REVERT: L 165 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8933 (pp) REVERT: L 199 GLU cc_start: 0.7872 (pp20) cc_final: 0.7600 (pp20) REVERT: L 329 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.8049 (pm20) REVERT: L 369 MET cc_start: 0.6495 (mmp) cc_final: 0.5988 (mmp) REVERT: L 458 MET cc_start: 0.8019 (OUTLIER) cc_final: 0.6614 (ttp) outliers start: 288 outliers final: 217 residues processed: 1089 average time/residue: 0.5369 time to fit residues: 974.2852 Evaluate side-chains 1099 residues out of total 4524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 240 poor density : 859 time to evaluate : 5.197 ------------------------------------------------------------------------------- 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 125 LEU Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 223 GLN Chi-restraints excluded: chain A residue 225 TYR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 258 ASP 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 321 VAL Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 382 SER 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 457 ASP Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 125 LEU 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 321 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 379 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 13 ASP Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 165 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 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 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 C residue 457 ASP Chi-restraints excluded: chain D residue 13 ASP 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 164 ILE Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 258 ASP 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 379 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 418 LYS Chi-restraints excluded: chain D residue 419 MET Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 457 ASP 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 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 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 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 321 VAL Chi-restraints excluded: chain F residue 329 GLN Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 357 SER Chi-restraints excluded: chain F residue 379 SER Chi-restraints excluded: chain F residue 416 ILE Chi-restraints excluded: chain F residue 436 ILE Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain F residue 458 MET Chi-restraints excluded: chain G residue 13 ASP Chi-restraints excluded: chain G residue 19 LYS Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 164 ILE Chi-restraints excluded: chain G residue 216 THR Chi-restraints excluded: chain G residue 246 VAL Chi-restraints excluded: chain G residue 258 ASP 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 310 VAL Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain G residue 357 SER Chi-restraints excluded: chain G residue 379 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 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 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 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 379 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 99 MET 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 321 VAL Chi-restraints excluded: chain I residue 329 GLN Chi-restraints excluded: chain I residue 354 LEU Chi-restraints excluded: chain I residue 357 SER Chi-restraints excluded: chain I residue 379 SER Chi-restraints excluded: chain I residue 416 ILE Chi-restraints excluded: chain I residue 436 ILE Chi-restraints excluded: chain I residue 457 ASP Chi-restraints excluded: chain J residue 13 ASP Chi-restraints excluded: chain J residue 19 LYS Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 164 ILE 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 258 ASP 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 310 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 379 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 13 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 223 GLN 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 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 186 GLU 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 321 VAL Chi-restraints excluded: chain L residue 329 GLN Chi-restraints excluded: chain L residue 354 LEU Chi-restraints excluded: chain L residue 357 SER Chi-restraints excluded: chain L residue 416 ILE Chi-restraints excluded: chain L residue 436 ILE Chi-restraints excluded: chain L residue 457 ASP Chi-restraints excluded: chain L residue 458 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 434 optimal weight: 3.9990 chunk 296 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 chunk 388 optimal weight: 0.0040 chunk 215 optimal weight: 9.9990 chunk 445 optimal weight: 1.9990 chunk 360 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 266 optimal weight: 0.9980 chunk 468 optimal weight: 6.9990 chunk 131 optimal weight: 8.9990 overall best weight: 1.5396 ------------------------------------------------------------------------------- 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 342 GLN 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 J 6 ASN J 18 HIS ** J 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 18 HIS L 18 HIS L 444 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 43908 Z= 0.185 Angle : 0.481 7.153 59388 Z= 0.258 Chirality : 0.039 0.184 6252 Planarity : 0.004 0.044 7860 Dihedral : 4.057 34.520 5884 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 5.59 % Allowed : 23.89 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.11), residues: 5352 helix: 2.05 (0.10), residues: 2412 sheet: -0.15 (0.18), residues: 816 loop : -0.53 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 171 HIS 0.004 0.001 HIS C 18 PHE 0.011 0.001 PHE B 183 TYR 0.014 0.001 TYR A 62 ARG 0.005 0.000 ARG F 184 *********************** 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 1127 residues out of total 4524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 253 poor density : 874 time to evaluate : 4.876 Fit side-chains REVERT: A 103 ASP cc_start: 0.7698 (p0) cc_final: 0.7488 (p0) REVERT: A 217 TRP cc_start: 0.8752 (m100) cc_final: 0.8410 (m100) REVERT: A 240 PHE cc_start: 0.8947 (OUTLIER) cc_final: 0.7848 (m-80) REVERT: A 329 GLN cc_start: 0.8859 (OUTLIER) cc_final: 0.8040 (pt0) REVERT: A 369 MET cc_start: 0.6364 (mmp) cc_final: 0.5989 (mmp) REVERT: A 455 ASP cc_start: 0.8290 (m-30) cc_final: 0.6917 (t0) REVERT: B 19 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8586 (ttmm) REVERT: B 103 ASP cc_start: 0.7653 (p0) cc_final: 0.7420 (p0) REVERT: B 165 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8773 (pp) REVERT: B 180 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8968 (tp) REVERT: B 209 ASP cc_start: 0.8136 (p0) cc_final: 0.7924 (p0) REVERT: B 217 TRP cc_start: 0.8521 (m100) cc_final: 0.8287 (m-10) REVERT: B 240 PHE cc_start: 0.9020 (OUTLIER) cc_final: 0.7849 (m-80) REVERT: B 329 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.7921 (pm20) REVERT: B 447 LYS cc_start: 0.7902 (OUTLIER) cc_final: 0.7688 (tttp) REVERT: C 65 ARG cc_start: 0.8517 (mmm160) cc_final: 0.8161 (tpt170) REVERT: C 103 ASP cc_start: 0.7948 (p0) cc_final: 0.7616 (p0) REVERT: C 171 TRP cc_start: 0.7268 (m100) cc_final: 0.7003 (m100) REVERT: C 176 LYS cc_start: 0.8533 (mmtp) cc_final: 0.8174 (tptt) REVERT: C 369 MET cc_start: 0.6962 (mmp) cc_final: 0.6548 (mmp) REVERT: C 454 GLU cc_start: 0.8015 (mp0) cc_final: 0.7432 (mp0) REVERT: C 458 MET cc_start: 0.7829 (OUTLIER) cc_final: 0.6483 (ttp) REVERT: D 217 TRP cc_start: 0.8679 (m100) cc_final: 0.8294 (m100) REVERT: D 240 PHE cc_start: 0.8943 (OUTLIER) cc_final: 0.7705 (m-80) REVERT: D 326 GLU cc_start: 0.7945 (tt0) cc_final: 0.7661 (tt0) REVERT: D 329 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.8184 (pt0) REVERT: D 444 GLN cc_start: 0.8590 (mm110) cc_final: 0.8334 (mm-40) REVERT: D 455 ASP cc_start: 0.8310 (m-30) cc_final: 0.6961 (t0) REVERT: E 165 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8752 (pp) REVERT: E 180 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8997 (tp) REVERT: E 217 TRP cc_start: 0.8528 (m100) cc_final: 0.8085 (m100) REVERT: E 240 PHE cc_start: 0.9041 (OUTLIER) cc_final: 0.7972 (m-80) REVERT: E 329 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.7889 (pm20) REVERT: F 65 ARG cc_start: 0.8533 (mmm160) cc_final: 0.8103 (tpt170) REVERT: F 217 TRP cc_start: 0.8583 (m100) cc_final: 0.8133 (m100) REVERT: F 329 GLN cc_start: 0.8903 (OUTLIER) cc_final: 0.8223 (pm20) REVERT: F 369 MET cc_start: 0.7049 (mmp) cc_final: 0.6651 (mmp) REVERT: F 454 GLU cc_start: 0.7975 (mp0) cc_final: 0.7392 (mp0) REVERT: G 103 ASP cc_start: 0.7647 (p0) cc_final: 0.7447 (p0) REVERT: G 217 TRP cc_start: 0.8768 (m100) cc_final: 0.8388 (m100) REVERT: G 240 PHE cc_start: 0.8950 (OUTLIER) cc_final: 0.7821 (m-80) REVERT: G 369 MET cc_start: 0.6345 (mmp) cc_final: 0.5982 (mmp) REVERT: G 415 ASP cc_start: 0.7196 (m-30) cc_final: 0.6862 (m-30) REVERT: G 455 ASP cc_start: 0.8230 (m-30) cc_final: 0.7034 (t0) REVERT: G 458 MET cc_start: 0.8058 (OUTLIER) cc_final: 0.7068 (ttp) REVERT: H 103 ASP cc_start: 0.7677 (p0) cc_final: 0.7444 (p0) REVERT: H 165 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8724 (pp) REVERT: H 217 TRP cc_start: 0.8583 (m100) cc_final: 0.8002 (m100) REVERT: H 240 PHE cc_start: 0.9021 (OUTLIER) cc_final: 0.7944 (m-80) REVERT: H 329 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.8211 (pt0) REVERT: I 65 ARG cc_start: 0.8519 (mmm160) cc_final: 0.8136 (tpt170) REVERT: I 176 LYS cc_start: 0.8729 (mmtp) cc_final: 0.8200 (tptt) REVERT: I 217 TRP cc_start: 0.8677 (m100) cc_final: 0.8248 (m100) REVERT: I 329 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8205 (pm20) REVERT: I 369 MET cc_start: 0.7003 (mmp) cc_final: 0.6529 (mmp) REVERT: I 450 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.8264 (mmt180) REVERT: I 458 MET cc_start: 0.7891 (OUTLIER) cc_final: 0.6453 (ttp) REVERT: J 103 ASP cc_start: 0.7679 (p0) cc_final: 0.7473 (p0) REVERT: J 217 TRP cc_start: 0.8751 (m100) cc_final: 0.8415 (m100) REVERT: J 240 PHE cc_start: 0.8951 (OUTLIER) cc_final: 0.7843 (m-80) REVERT: J 329 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.8049 (pt0) REVERT: J 415 ASP cc_start: 0.7299 (m-30) cc_final: 0.6881 (m-30) REVERT: J 455 ASP cc_start: 0.8255 (m-30) cc_final: 0.7008 (t0) REVERT: K 19 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8670 (ttmm) REVERT: K 103 ASP cc_start: 0.7705 (p0) cc_final: 0.7478 (p0) REVERT: K 165 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8736 (pp) REVERT: K 217 TRP cc_start: 0.8573 (m100) cc_final: 0.8008 (m100) REVERT: K 223 GLN cc_start: 0.2452 (OUTLIER) cc_final: 0.2078 (tp40) REVERT: K 240 PHE cc_start: 0.9028 (OUTLIER) cc_final: 0.8002 (m-80) REVERT: K 329 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.7892 (pm20) REVERT: K 331 GLU cc_start: 0.8376 (pm20) cc_final: 0.8016 (pm20) REVERT: K 383 LYS cc_start: 0.8475 (mmtp) cc_final: 0.8189 (mmtt) REVERT: K 447 LYS cc_start: 0.7908 (OUTLIER) cc_final: 0.7696 (tttp) REVERT: L 65 ARG cc_start: 0.8521 (mmm160) cc_final: 0.8146 (tpt170) REVERT: L 76 VAL cc_start: 0.9048 (OUTLIER) cc_final: 0.8823 (t) REVERT: L 171 TRP cc_start: 0.7719 (m100) cc_final: 0.7415 (m100) REVERT: L 217 TRP cc_start: 0.8697 (m100) cc_final: 0.8250 (m100) REVERT: L 329 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8058 (pm20) REVERT: L 369 MET cc_start: 0.6472 (mmp) cc_final: 0.6105 (mmp) REVERT: L 447 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7944 (mmmt) REVERT: L 450 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.8346 (mmt180) outliers start: 253 outliers final: 170 residues processed: 1048 average time/residue: 0.5906 time to fit residues: 1035.0612 Evaluate side-chains 1060 residues out of total 4524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 854 time to evaluate : 5.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 125 LEU 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 278 ASP Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 354 LEU 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 B residue 19 LYS Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 180 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 296 LEU 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 125 LEU Chi-restraints excluded: chain C residue 186 GLU 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 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 C residue 457 ASP Chi-restraints excluded: chain C residue 458 MET 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 240 PHE Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 278 ASP Chi-restraints excluded: chain D residue 304 VAL 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 379 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 13 ASP Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 186 GLU Chi-restraints excluded: chain E residue 240 PHE Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 299 HIS 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 13 ASP Chi-restraints excluded: chain F residue 19 LYS 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 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 329 GLN 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 125 LEU 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 304 VAL Chi-restraints excluded: chain G residue 310 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 379 SER 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 13 ASP Chi-restraints excluded: chain H residue 165 LEU Chi-restraints excluded: chain H residue 186 GLU Chi-restraints excluded: chain H residue 240 PHE Chi-restraints excluded: chain H residue 290 THR Chi-restraints excluded: chain H residue 296 LEU 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 13 ASP 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 329 GLN 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 I residue 450 ARG Chi-restraints excluded: chain I residue 457 ASP Chi-restraints excluded: chain I residue 458 MET Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 216 THR 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 304 VAL Chi-restraints excluded: chain J residue 310 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 409 GLU Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 419 MET Chi-restraints excluded: chain K residue 19 LYS 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 240 PHE 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 329 GLN Chi-restraints excluded: chain K residue 338 GLU Chi-restraints excluded: chain K residue 354 LEU Chi-restraints excluded: chain K residue 376 SER Chi-restraints excluded: chain K residue 379 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 K residue 447 LYS Chi-restraints excluded: chain L residue 56 VAL Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 186 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 317 VAL Chi-restraints excluded: chain L residue 329 GLN Chi-restraints excluded: chain L residue 354 LEU 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 447 LYS Chi-restraints excluded: chain L residue 450 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 175 optimal weight: 8.9990 chunk 470 optimal weight: 20.0000 chunk 103 optimal weight: 6.9990 chunk 306 optimal weight: 1.9990 chunk 128 optimal weight: 7.9990 chunk 522 optimal weight: 0.9990 chunk 433 optimal weight: 2.9990 chunk 241 optimal weight: 9.9990 chunk 43 optimal weight: 7.9990 chunk 172 optimal weight: 0.9990 chunk 274 optimal weight: 8.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 303 ASN C 444 GLN D 18 HIS ** D 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 HIS F 18 HIS F 303 ASN F 444 GLN G 6 ASN G 18 HIS H 18 HIS I 18 HIS I 444 GLN J 18 HIS ** J 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 18 HIS L 303 ASN L 444 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 43908 Z= 0.271 Angle : 0.525 7.694 59388 Z= 0.278 Chirality : 0.040 0.195 6252 Planarity : 0.004 0.044 7860 Dihedral : 4.189 36.111 5884 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 6.52 % Allowed : 23.32 % Favored : 70.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.11), residues: 5352 helix: 1.99 (0.10), residues: 2412 sheet: -0.04 (0.18), residues: 804 loop : -0.62 (0.13), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 171 HIS 0.005 0.000 HIS I 18 PHE 0.013 0.002 PHE B 183 TYR 0.021 0.002 TYR H 62 ARG 0.006 0.000 ARG C 184 *********************** 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 1183 residues out of total 4524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 295 poor density : 888 time to evaluate : 5.236 Fit side-chains REVERT: A 240 PHE cc_start: 0.9000 (OUTLIER) cc_final: 0.7974 (m-80) REVERT: A 369 MET cc_start: 0.6367 (mmp) cc_final: 0.6022 (mmp) REVERT: A 455 ASP cc_start: 0.8268 (m-30) cc_final: 0.7018 (t0) REVERT: A 458 MET cc_start: 0.8146 (OUTLIER) cc_final: 0.6980 (ttp) REVERT: B 19 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8639 (ttmm) REVERT: B 103 ASP cc_start: 0.7665 (p0) cc_final: 0.7455 (p0) REVERT: B 157 LYS cc_start: 0.8253 (mmtp) cc_final: 0.8030 (mmtt) REVERT: B 165 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8795 (pp) REVERT: B 217 TRP cc_start: 0.8546 (m100) cc_final: 0.8301 (m-10) REVERT: B 240 PHE cc_start: 0.9057 (OUTLIER) cc_final: 0.7957 (m-80) REVERT: B 329 GLN cc_start: 0.8875 (OUTLIER) cc_final: 0.8270 (pt0) REVERT: B 447 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.7728 (tttp) REVERT: B 450 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.8493 (mmt180) REVERT: C 103 ASP cc_start: 0.7873 (p0) cc_final: 0.7463 (p0) REVERT: C 176 LYS cc_start: 0.8662 (mmtp) cc_final: 0.8125 (tptt) REVERT: C 240 PHE cc_start: 0.8976 (OUTLIER) cc_final: 0.8292 (m-80) REVERT: C 242 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7943 (pm20) REVERT: C 369 MET cc_start: 0.7106 (mmp) cc_final: 0.6661 (mmp) REVERT: C 454 GLU cc_start: 0.8101 (mp0) cc_final: 0.7538 (mp0) REVERT: C 458 MET cc_start: 0.7900 (OUTLIER) cc_final: 0.6587 (ttp) REVERT: D 103 ASP cc_start: 0.7638 (p0) cc_final: 0.7335 (p0) REVERT: D 240 PHE cc_start: 0.8993 (OUTLIER) cc_final: 0.7878 (m-80) REVERT: D 326 GLU cc_start: 0.8104 (tt0) cc_final: 0.7818 (tt0) REVERT: D 329 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8251 (pt0) REVERT: D 455 ASP cc_start: 0.8088 (m-30) cc_final: 0.6760 (t0) REVERT: E 103 ASP cc_start: 0.7810 (p0) cc_final: 0.7547 (p0) REVERT: E 165 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8754 (pp) REVERT: E 217 TRP cc_start: 0.8552 (m100) cc_final: 0.7954 (m100) REVERT: E 240 PHE cc_start: 0.9056 (OUTLIER) cc_final: 0.7925 (m-80) REVERT: E 329 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.8320 (pt0) REVERT: F 76 VAL cc_start: 0.9100 (OUTLIER) cc_final: 0.8864 (t) REVERT: F 240 PHE cc_start: 0.8975 (OUTLIER) cc_final: 0.8268 (m-80) REVERT: F 329 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8196 (pm20) REVERT: F 369 MET cc_start: 0.6987 (mmp) cc_final: 0.6504 (mmp) REVERT: F 450 ARG cc_start: 0.8802 (OUTLIER) cc_final: 0.8584 (mmt180) REVERT: F 454 GLU cc_start: 0.8067 (mp0) cc_final: 0.7513 (mp0) REVERT: F 458 MET cc_start: 0.7964 (OUTLIER) cc_final: 0.6561 (ttp) REVERT: G 103 ASP cc_start: 0.7676 (p0) cc_final: 0.7468 (p0) REVERT: G 217 TRP cc_start: 0.8771 (m100) cc_final: 0.8435 (m100) REVERT: G 240 PHE cc_start: 0.9003 (OUTLIER) cc_final: 0.7981 (m-80) REVERT: G 329 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.8168 (pt0) REVERT: G 369 MET cc_start: 0.6354 (mmp) cc_final: 0.6028 (mmp) REVERT: G 415 ASP cc_start: 0.7279 (m-30) cc_final: 0.6925 (m-30) REVERT: G 455 ASP cc_start: 0.8215 (m-30) cc_final: 0.6928 (t0) REVERT: G 458 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.7114 (ttp) REVERT: H 165 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8773 (pp) REVERT: H 217 TRP cc_start: 0.8607 (m100) cc_final: 0.8002 (m100) REVERT: H 240 PHE cc_start: 0.9053 (OUTLIER) cc_final: 0.8026 (m-80) REVERT: H 329 GLN cc_start: 0.8894 (OUTLIER) cc_final: 0.8329 (pt0) REVERT: H 422 GLU cc_start: 0.7700 (mp0) cc_final: 0.7482 (mp0) REVERT: H 450 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.8560 (mmt180) REVERT: I 99 MET cc_start: 0.7790 (OUTLIER) cc_final: 0.7518 (ptp) REVERT: I 176 LYS cc_start: 0.8705 (mmtp) cc_final: 0.8306 (tptt) REVERT: I 217 TRP cc_start: 0.8711 (m100) cc_final: 0.8310 (m100) REVERT: I 240 PHE cc_start: 0.8962 (OUTLIER) cc_final: 0.8382 (m-80) REVERT: I 329 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.8226 (pm20) REVERT: I 369 MET cc_start: 0.6950 (mmp) cc_final: 0.6581 (mmp) REVERT: I 447 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.8007 (mmmt) REVERT: I 450 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.8388 (mmt180) REVERT: I 458 MET cc_start: 0.7939 (OUTLIER) cc_final: 0.6638 (ttp) REVERT: J 103 ASP cc_start: 0.7692 (p0) cc_final: 0.7480 (p0) REVERT: J 240 PHE cc_start: 0.9008 (OUTLIER) cc_final: 0.7973 (m-80) REVERT: J 329 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.8110 (pt0) REVERT: J 455 ASP cc_start: 0.8106 (m-30) cc_final: 0.6803 (t0) REVERT: J 458 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.7015 (ttp) REVERT: K 19 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8707 (ttmm) REVERT: K 103 ASP cc_start: 0.7704 (p0) cc_final: 0.7496 (p0) REVERT: K 165 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8772 (pp) REVERT: K 217 TRP cc_start: 0.8599 (m100) cc_final: 0.8001 (m100) REVERT: K 223 GLN cc_start: 0.2613 (OUTLIER) cc_final: 0.2058 (tp40) REVERT: K 240 PHE cc_start: 0.9058 (OUTLIER) cc_final: 0.7996 (m-80) REVERT: K 329 GLN cc_start: 0.8881 (OUTLIER) cc_final: 0.8289 (pt0) REVERT: K 331 GLU cc_start: 0.8519 (pm20) cc_final: 0.8119 (pm20) REVERT: K 383 LYS cc_start: 0.8504 (mmtp) cc_final: 0.8231 (mmtt) REVERT: K 447 LYS cc_start: 0.7862 (OUTLIER) cc_final: 0.7661 (tttp) REVERT: L 76 VAL cc_start: 0.9096 (OUTLIER) cc_final: 0.8861 (t) REVERT: L 217 TRP cc_start: 0.8714 (m100) cc_final: 0.8305 (m100) REVERT: L 240 PHE cc_start: 0.8945 (OUTLIER) cc_final: 0.8354 (m-80) REVERT: L 329 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.7996 (pm20) REVERT: L 369 MET cc_start: 0.6998 (mmp) cc_final: 0.6562 (mmp) REVERT: L 447 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7999 (mmmt) REVERT: L 450 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.8440 (mmt180) REVERT: L 458 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.6569 (ttp) outliers start: 295 outliers final: 221 residues processed: 1085 average time/residue: 0.5472 time to fit residues: 986.4488 Evaluate side-chains 1131 residues out of total 4524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 270 poor density : 861 time to evaluate : 4.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASP Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 125 LEU 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 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 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 457 ASP Chi-restraints excluded: chain A residue 458 MET Chi-restraints excluded: chain B residue 19 LYS 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 296 LEU 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 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 379 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 B residue 450 ARG Chi-restraints excluded: chain C residue 19 LYS Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 258 ASP 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 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 C residue 457 ASP Chi-restraints excluded: chain C residue 458 MET 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 125 LEU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 240 PHE 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 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 379 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 D residue 457 ASP Chi-restraints excluded: chain E residue 13 ASP 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 216 THR Chi-restraints excluded: chain E residue 240 PHE Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 296 LEU 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 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 379 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 13 ASP Chi-restraints excluded: chain F residue 19 LYS Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 76 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 240 PHE 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 329 GLN 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 F residue 450 ARG Chi-restraints excluded: chain F residue 458 MET Chi-restraints excluded: chain G residue 13 ASP Chi-restraints excluded: chain G residue 18 HIS Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 216 THR Chi-restraints excluded: chain G residue 240 PHE 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 310 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 379 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 13 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 240 PHE Chi-restraints excluded: chain H residue 290 THR Chi-restraints excluded: chain H residue 296 LEU 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 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 H residue 450 ARG Chi-restraints excluded: chain I residue 13 ASP Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 99 MET 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 240 PHE 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 321 VAL Chi-restraints excluded: chain I residue 329 GLN 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 I residue 447 LYS Chi-restraints excluded: chain I residue 450 ARG Chi-restraints excluded: chain I residue 457 ASP Chi-restraints excluded: chain I residue 458 MET Chi-restraints excluded: chain J residue 13 ASP Chi-restraints excluded: chain J residue 18 HIS Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 125 LEU 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 278 ASP Chi-restraints excluded: chain J residue 290 THR Chi-restraints excluded: chain J residue 299 HIS Chi-restraints excluded: chain J residue 310 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 379 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 13 ASP Chi-restraints excluded: chain K residue 19 LYS 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 223 GLN Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain K residue 290 THR Chi-restraints excluded: chain K residue 296 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 321 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 379 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 K residue 447 LYS Chi-restraints excluded: chain L residue 13 ASP Chi-restraints excluded: chain L residue 56 VAL Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 186 GLU Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain L residue 216 THR Chi-restraints excluded: chain L residue 240 PHE 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 317 VAL Chi-restraints excluded: chain L residue 321 VAL Chi-restraints excluded: chain L residue 329 GLN Chi-restraints excluded: chain L residue 354 LEU 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 447 LYS Chi-restraints excluded: chain L residue 450 ARG Chi-restraints excluded: chain L residue 457 ASP Chi-restraints excluded: chain L residue 458 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 503 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 297 optimal weight: 5.9990 chunk 381 optimal weight: 3.9990 chunk 295 optimal weight: 0.9980 chunk 439 optimal weight: 0.3980 chunk 291 optimal weight: 6.9990 chunk 520 optimal weight: 4.9990 chunk 325 optimal weight: 7.9990 chunk 317 optimal weight: 2.9990 chunk 240 optimal weight: 8.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- 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 444 GLN C 444 GLN D 18 HIS ** D 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 HIS F 444 GLN G 6 ASN G 18 HIS H 18 HIS I 444 GLN J 18 HIS ** J 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 444 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 43908 Z= 0.260 Angle : 0.517 7.770 59388 Z= 0.274 Chirality : 0.040 0.197 6252 Planarity : 0.004 0.044 7860 Dihedral : 4.191 37.439 5884 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 7.12 % Allowed : 22.99 % Favored : 69.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.11), residues: 5352 helix: 1.99 (0.10), residues: 2412 sheet: -0.01 (0.19), residues: 804 loop : -0.59 (0.13), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 171 HIS 0.015 0.001 HIS J 18 PHE 0.013 0.001 PHE B 183 TYR 0.019 0.002 TYR A 62 ARG 0.007 0.000 ARG F 184 *********************** 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 1212 residues out of total 4524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 322 poor density : 890 time to evaluate : 4.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 PHE cc_start: 0.9023 (OUTLIER) cc_final: 0.8017 (m-80) REVERT: A 329 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.8151 (pt0) REVERT: A 369 MET cc_start: 0.6358 (mmp) cc_final: 0.6023 (mmp) REVERT: A 447 LYS cc_start: 0.7930 (OUTLIER) cc_final: 0.7728 (mmmt) REVERT: A 455 ASP cc_start: 0.8212 (m-30) cc_final: 0.6947 (t0) REVERT: A 458 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.6947 (ttp) REVERT: B 19 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8658 (ttmm) REVERT: B 103 ASP cc_start: 0.7680 (p0) cc_final: 0.7429 (p0) REVERT: B 165 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8802 (pp) REVERT: B 217 TRP cc_start: 0.8614 (m100) cc_final: 0.8372 (m-10) REVERT: B 240 PHE cc_start: 0.9101 (OUTLIER) cc_final: 0.7860 (m-80) REVERT: B 329 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.8291 (pt0) REVERT: B 447 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7705 (tttp) REVERT: C 103 ASP cc_start: 0.7865 (p0) cc_final: 0.7448 (p0) REVERT: C 176 LYS cc_start: 0.8666 (mmtp) cc_final: 0.8444 (tptt) REVERT: C 240 PHE cc_start: 0.8983 (OUTLIER) cc_final: 0.8307 (m-80) REVERT: C 242 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7888 (pm20) REVERT: C 458 MET cc_start: 0.7927 (OUTLIER) cc_final: 0.6623 (ttp) REVERT: D 103 ASP cc_start: 0.7516 (p0) cc_final: 0.7236 (p0) REVERT: D 217 TRP cc_start: 0.8431 (m100) cc_final: 0.8218 (m100) REVERT: D 240 PHE cc_start: 0.9000 (OUTLIER) cc_final: 0.7923 (m-80) REVERT: D 326 GLU cc_start: 0.8006 (tt0) cc_final: 0.7732 (tt0) REVERT: D 329 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.8255 (pt0) REVERT: D 450 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.8239 (mmt180) REVERT: D 455 ASP cc_start: 0.8105 (m-30) cc_final: 0.6767 (t0) REVERT: E 19 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8650 (ttmm) REVERT: E 103 ASP cc_start: 0.7806 (p0) cc_final: 0.7549 (p0) REVERT: E 165 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8760 (pp) REVERT: E 217 TRP cc_start: 0.8580 (m100) cc_final: 0.8002 (m100) REVERT: E 240 PHE cc_start: 0.9118 (OUTLIER) cc_final: 0.7878 (m-80) REVERT: E 329 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.8297 (pt0) REVERT: F 11 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.7717 (ttt180) REVERT: F 76 VAL cc_start: 0.9089 (OUTLIER) cc_final: 0.8850 (t) REVERT: F 240 PHE cc_start: 0.8941 (OUTLIER) cc_final: 0.8234 (m-80) REVERT: F 329 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.8239 (pm20) REVERT: F 369 MET cc_start: 0.7129 (mmp) cc_final: 0.6652 (mmp) REVERT: F 450 ARG cc_start: 0.8806 (OUTLIER) cc_final: 0.8599 (mmt180) REVERT: F 458 MET cc_start: 0.7935 (OUTLIER) cc_final: 0.6538 (ttp) REVERT: G 240 PHE cc_start: 0.9025 (OUTLIER) cc_final: 0.7927 (m-80) REVERT: G 329 GLN cc_start: 0.8859 (OUTLIER) cc_final: 0.8173 (pt0) REVERT: G 369 MET cc_start: 0.6359 (mmp) cc_final: 0.6031 (mmp) REVERT: G 415 ASP cc_start: 0.7288 (m-30) cc_final: 0.6926 (m-30) REVERT: G 455 ASP cc_start: 0.8232 (m-30) cc_final: 0.6930 (t0) REVERT: G 458 MET cc_start: 0.8116 (OUTLIER) cc_final: 0.7038 (ttp) REVERT: H 165 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8764 (pp) REVERT: H 217 TRP cc_start: 0.8643 (m100) cc_final: 0.8104 (m100) REVERT: H 240 PHE cc_start: 0.9059 (OUTLIER) cc_final: 0.7965 (m-80) REVERT: H 329 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.8304 (pt0) REVERT: H 422 GLU cc_start: 0.7707 (mp0) cc_final: 0.7478 (mp0) REVERT: H 450 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8497 (mmt180) REVERT: I 217 TRP cc_start: 0.8702 (m100) cc_final: 0.8305 (m100) REVERT: I 240 PHE cc_start: 0.8905 (OUTLIER) cc_final: 0.8179 (m-80) REVERT: I 329 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.8227 (pm20) REVERT: I 369 MET cc_start: 0.7119 (mmp) cc_final: 0.6694 (mmp) REVERT: I 447 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7992 (mmmt) REVERT: I 450 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.8373 (mmt180) REVERT: I 458 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.6553 (ttp) REVERT: J 240 PHE cc_start: 0.9018 (OUTLIER) cc_final: 0.8016 (m-80) REVERT: J 329 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.8159 (pt0) REVERT: J 415 ASP cc_start: 0.7261 (m-30) cc_final: 0.6956 (m-30) REVERT: J 455 ASP cc_start: 0.8127 (m-30) cc_final: 0.6809 (t0) REVERT: J 458 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.6862 (ttp) REVERT: K 19 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8696 (ttmm) REVERT: K 165 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8771 (pp) REVERT: K 217 TRP cc_start: 0.8640 (m100) cc_final: 0.8062 (m100) REVERT: K 223 GLN cc_start: 0.2570 (OUTLIER) cc_final: 0.2054 (tp40) REVERT: K 240 PHE cc_start: 0.9053 (OUTLIER) cc_final: 0.7895 (m-80) REVERT: K 329 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.8301 (pt0) REVERT: K 331 GLU cc_start: 0.8521 (pm20) cc_final: 0.8124 (pm20) REVERT: K 383 LYS cc_start: 0.8501 (mmtp) cc_final: 0.8108 (mmtt) REVERT: K 447 LYS cc_start: 0.7902 (OUTLIER) cc_final: 0.7693 (tttp) REVERT: L 76 VAL cc_start: 0.9087 (OUTLIER) cc_final: 0.8851 (t) REVERT: L 98 ASP cc_start: 0.7981 (t0) cc_final: 0.7447 (m-30) REVERT: L 170 ARG cc_start: 0.7426 (tpp80) cc_final: 0.7107 (tpt90) REVERT: L 217 TRP cc_start: 0.8719 (m100) cc_final: 0.8302 (m100) REVERT: L 240 PHE cc_start: 0.8914 (OUTLIER) cc_final: 0.8200 (m-80) REVERT: L 329 GLN cc_start: 0.8917 (OUTLIER) cc_final: 0.8027 (pm20) REVERT: L 369 MET cc_start: 0.6979 (mmp) cc_final: 0.6670 (mmp) REVERT: L 447 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7984 (mmmt) REVERT: L 450 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.8599 (mmt180) REVERT: L 458 MET cc_start: 0.7990 (OUTLIER) cc_final: 0.6497 (ttp) outliers start: 322 outliers final: 228 residues processed: 1114 average time/residue: 0.5677 time to fit residues: 1045.8889 Evaluate side-chains 1151 residues out of total 4524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 280 poor density : 871 time to evaluate : 5.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASP Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 125 LEU 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 246 VAL Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 278 ASP 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 379 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 447 LYS Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 458 MET Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 19 LYS 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 296 LEU 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 379 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 13 ASP Chi-restraints excluded: chain C residue 19 LYS Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 242 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 C residue 457 ASP Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain D residue 13 ASP 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 240 PHE Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 278 ASP 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 379 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 D residue 450 ARG Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 13 ASP 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 186 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 296 LEU 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 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 416 ILE Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain F residue 11 ARG Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 19 LYS Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 164 ILE 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 240 PHE Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 278 ASP 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 321 VAL Chi-restraints excluded: chain F residue 329 GLN 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 F residue 450 ARG Chi-restraints excluded: chain F residue 458 MET Chi-restraints excluded: chain G residue 13 ASP Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 125 LEU 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 246 VAL Chi-restraints excluded: chain G residue 258 ASP Chi-restraints excluded: chain G residue 278 ASP Chi-restraints excluded: chain G residue 299 HIS Chi-restraints excluded: chain G residue 310 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 379 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 13 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 240 PHE Chi-restraints excluded: chain H residue 290 THR Chi-restraints excluded: chain H residue 296 LEU 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 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 H residue 450 ARG Chi-restraints excluded: chain I residue 13 ASP Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 164 ILE 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 240 PHE 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 329 GLN 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 379 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 I residue 447 LYS Chi-restraints excluded: chain I residue 450 ARG Chi-restraints excluded: chain I residue 457 ASP Chi-restraints excluded: chain I residue 458 MET Chi-restraints excluded: chain J residue 13 ASP Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 185 GLU 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 258 ASP 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 310 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 379 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 19 LYS 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 223 GLN Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain K residue 290 THR Chi-restraints excluded: chain K residue 296 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 379 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 K residue 447 LYS Chi-restraints excluded: chain L residue 13 ASP Chi-restraints excluded: chain L residue 56 VAL Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 164 ILE Chi-restraints excluded: chain L residue 186 GLU Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain L residue 216 THR Chi-restraints excluded: chain L residue 240 PHE Chi-restraints excluded: chain L residue 246 VAL Chi-restraints excluded: chain L residue 278 ASP 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 329 GLN Chi-restraints excluded: chain L residue 338 GLU Chi-restraints excluded: chain L residue 354 LEU 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 447 LYS Chi-restraints excluded: chain L residue 450 ARG Chi-restraints excluded: chain L residue 457 ASP Chi-restraints excluded: chain L residue 458 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 321 optimal weight: 1.9990 chunk 207 optimal weight: 8.9990 chunk 310 optimal weight: 0.6980 chunk 156 optimal weight: 8.9990 chunk 102 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 chunk 330 optimal weight: 8.9990 chunk 354 optimal weight: 0.1980 chunk 257 optimal weight: 0.0670 chunk 48 optimal weight: 2.9990 chunk 409 optimal weight: 0.0040 overall best weight: 0.5932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS A 444 GLN B 18 HIS C 18 HIS C 303 ASN C 444 GLN D 6 ASN D 18 HIS D 444 GLN E 18 HIS F 18 HIS F 444 GLN G 18 HIS H 18 HIS I 18 HIS I 444 GLN J 6 ASN J 18 HIS L 18 HIS L 303 ASN L 444 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 43908 Z= 0.137 Angle : 0.455 6.381 59388 Z= 0.247 Chirality : 0.038 0.187 6252 Planarity : 0.004 0.044 7860 Dihedral : 3.857 30.951 5884 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 4.93 % Allowed : 25.44 % Favored : 69.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.12), residues: 5352 helix: 2.23 (0.10), residues: 2424 sheet: 0.14 (0.20), residues: 732 loop : -0.37 (0.13), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 300 HIS 0.004 0.000 HIS L 18 PHE 0.013 0.001 PHE B 183 TYR 0.015 0.001 TYR B 225 ARG 0.006 0.000 ARG F 184 *********************** 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 1141 residues out of total 4524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 223 poor density : 918 time to evaluate : 4.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 PHE cc_start: 0.8985 (OUTLIER) cc_final: 0.7958 (m-80) REVERT: A 369 MET cc_start: 0.6295 (mmp) cc_final: 0.5946 (mmp) REVERT: A 455 ASP cc_start: 0.8224 (m-30) cc_final: 0.6970 (t0) REVERT: A 459 ARG cc_start: 0.7362 (OUTLIER) cc_final: 0.7064 (mtp180) REVERT: B 103 ASP cc_start: 0.7633 (p0) cc_final: 0.7347 (p0) REVERT: B 165 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8620 (pp) REVERT: B 240 PHE cc_start: 0.9009 (OUTLIER) cc_final: 0.7912 (m-80) REVERT: B 447 LYS cc_start: 0.7833 (OUTLIER) cc_final: 0.7587 (tttp) REVERT: C 65 ARG cc_start: 0.8428 (mmm160) cc_final: 0.8098 (tpt170) REVERT: C 176 LYS cc_start: 0.8598 (mmtp) cc_final: 0.8344 (tptt) REVERT: C 194 TYR cc_start: 0.7369 (m-80) cc_final: 0.7026 (m-10) REVERT: C 209 ASP cc_start: 0.8240 (p0) cc_final: 0.8039 (p0) REVERT: C 217 TRP cc_start: 0.8539 (m100) cc_final: 0.8057 (m100) REVERT: C 240 PHE cc_start: 0.8981 (OUTLIER) cc_final: 0.8318 (m-80) REVERT: C 242 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7737 (pm20) REVERT: C 338 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8359 (pt0) REVERT: D 103 ASP cc_start: 0.7584 (p0) cc_final: 0.7296 (p0) REVERT: D 217 TRP cc_start: 0.8418 (m100) cc_final: 0.8178 (m100) REVERT: D 240 PHE cc_start: 0.8976 (OUTLIER) cc_final: 0.7849 (m-80) REVERT: D 326 GLU cc_start: 0.7910 (tt0) cc_final: 0.7604 (tt0) REVERT: D 329 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.8256 (pt0) REVERT: D 450 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.8105 (mmt180) REVERT: D 455 ASP cc_start: 0.8204 (m-30) cc_final: 0.6940 (t0) REVERT: E 165 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8645 (pp) REVERT: E 204 GLU cc_start: 0.8421 (tt0) cc_final: 0.8062 (tt0) REVERT: E 217 TRP cc_start: 0.8562 (m100) cc_final: 0.8216 (m100) REVERT: E 240 PHE cc_start: 0.9040 (OUTLIER) cc_final: 0.7933 (m-80) REVERT: F 65 ARG cc_start: 0.8443 (mmm160) cc_final: 0.8122 (tpt170) REVERT: F 76 VAL cc_start: 0.9010 (OUTLIER) cc_final: 0.8790 (t) REVERT: F 84 PHE cc_start: 0.9118 (m-80) cc_final: 0.8900 (m-80) REVERT: F 209 ASP cc_start: 0.8226 (p0) cc_final: 0.7954 (p0) REVERT: F 217 TRP cc_start: 0.8519 (m100) cc_final: 0.8052 (m100) REVERT: F 240 PHE cc_start: 0.8977 (OUTLIER) cc_final: 0.8319 (m-80) REVERT: F 329 GLN cc_start: 0.8979 (OUTLIER) cc_final: 0.8236 (pm20) REVERT: F 369 MET cc_start: 0.7073 (mmp) cc_final: 0.6772 (mmp) REVERT: G 217 TRP cc_start: 0.8435 (m100) cc_final: 0.8164 (m100) REVERT: G 240 PHE cc_start: 0.8989 (OUTLIER) cc_final: 0.7967 (m-80) REVERT: G 369 MET cc_start: 0.6304 (mmp) cc_final: 0.6028 (mmp) REVERT: G 450 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.8056 (mmt180) REVERT: G 455 ASP cc_start: 0.8273 (m-30) cc_final: 0.7042 (t0) REVERT: H 165 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8722 (pp) REVERT: H 217 TRP cc_start: 0.8610 (m100) cc_final: 0.8290 (m100) REVERT: H 240 PHE cc_start: 0.9030 (OUTLIER) cc_final: 0.7911 (m-80) REVERT: I 65 ARG cc_start: 0.8433 (mmm160) cc_final: 0.8081 (tpt170) REVERT: I 217 TRP cc_start: 0.8676 (m100) cc_final: 0.8103 (m100) REVERT: I 240 PHE cc_start: 0.8991 (OUTLIER) cc_final: 0.8325 (m-80) REVERT: I 329 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8211 (pm20) REVERT: I 447 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7900 (mmmt) REVERT: I 458 MET cc_start: 0.7770 (OUTLIER) cc_final: 0.6302 (ttp) REVERT: J 240 PHE cc_start: 0.8981 (OUTLIER) cc_final: 0.7960 (m-80) REVERT: J 329 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8111 (pt0) REVERT: J 455 ASP cc_start: 0.8218 (m-30) cc_final: 0.6967 (t0) REVERT: K 165 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8697 (pp) REVERT: K 217 TRP cc_start: 0.8608 (m100) cc_final: 0.8288 (m100) REVERT: K 223 GLN cc_start: 0.2461 (OUTLIER) cc_final: 0.2235 (tp40) REVERT: K 240 PHE cc_start: 0.9009 (OUTLIER) cc_final: 0.7961 (m-80) REVERT: K 383 LYS cc_start: 0.8425 (mmtp) cc_final: 0.8180 (mmtt) REVERT: K 422 GLU cc_start: 0.7749 (mp0) cc_final: 0.7530 (mp0) REVERT: K 447 LYS cc_start: 0.7776 (OUTLIER) cc_final: 0.7504 (tttp) REVERT: L 65 ARG cc_start: 0.8437 (mmm160) cc_final: 0.8082 (tpt170) REVERT: L 76 VAL cc_start: 0.9011 (OUTLIER) cc_final: 0.8793 (t) REVERT: L 84 PHE cc_start: 0.9118 (m-80) cc_final: 0.8878 (m-80) REVERT: L 217 TRP cc_start: 0.8669 (m100) cc_final: 0.8121 (m100) REVERT: L 240 PHE cc_start: 0.8977 (OUTLIER) cc_final: 0.8315 (m-80) REVERT: L 329 GLN cc_start: 0.8982 (OUTLIER) cc_final: 0.8244 (pm20) REVERT: L 338 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8132 (tt0) outliers start: 223 outliers final: 147 residues processed: 1065 average time/residue: 0.5752 time to fit residues: 1011.9671 Evaluate side-chains 1052 residues out of total 4524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 871 time to evaluate : 5.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 278 ASP 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 379 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 A residue 459 ARG 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 310 VAL Chi-restraints excluded: chain B residue 317 VAL 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 186 GLU Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 242 GLU 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 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 240 PHE Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 278 ASP 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 379 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 D residue 450 ARG 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 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 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 76 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 240 PHE Chi-restraints excluded: chain F residue 278 ASP 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 329 GLN Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 409 GLU Chi-restraints excluded: chain F residue 416 ILE Chi-restraints excluded: chain G residue 185 GLU Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 278 ASP Chi-restraints excluded: chain G residue 310 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 379 SER Chi-restraints excluded: chain G residue 409 GLU Chi-restraints excluded: chain G residue 416 ILE Chi-restraints excluded: chain G residue 450 ARG 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 299 HIS Chi-restraints excluded: chain H residue 310 VAL 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 125 LEU Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 186 GLU Chi-restraints excluded: chain I residue 199 GLU Chi-restraints excluded: chain I residue 240 PHE Chi-restraints excluded: chain I residue 278 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 329 GLN Chi-restraints excluded: chain I residue 354 LEU Chi-restraints excluded: chain I residue 409 GLU Chi-restraints excluded: chain I residue 416 ILE Chi-restraints excluded: chain I residue 447 LYS Chi-restraints excluded: chain I residue 457 ASP Chi-restraints excluded: chain I residue 458 MET Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 185 GLU 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 310 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 409 GLU Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 436 ILE Chi-restraints excluded: chain K residue 18 HIS Chi-restraints excluded: chain K residue 165 LEU Chi-restraints excluded: chain K residue 186 GLU Chi-restraints excluded: chain K residue 223 GLN Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain K residue 290 THR Chi-restraints excluded: chain K residue 296 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 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 K residue 447 LYS Chi-restraints excluded: chain L residue 13 ASP Chi-restraints excluded: chain L residue 56 VAL Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 186 GLU Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain L residue 240 PHE Chi-restraints excluded: chain L residue 278 ASP 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 329 GLN Chi-restraints excluded: chain L residue 338 GLU Chi-restraints excluded: chain L residue 354 LEU 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 457 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 473 optimal weight: 8.9990 chunk 498 optimal weight: 5.9990 chunk 454 optimal weight: 0.0020 chunk 485 optimal weight: 7.9990 chunk 291 optimal weight: 10.0000 chunk 211 optimal weight: 6.9990 chunk 380 optimal weight: 9.9990 chunk 148 optimal weight: 2.9990 chunk 438 optimal weight: 6.9990 chunk 458 optimal weight: 1.9990 chunk 483 optimal weight: 1.9990 overall best weight: 2.5996 ------------------------------------------------------------------------------- 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 44 HIS C 303 ASN C 444 GLN D 18 HIS D 44 HIS E 18 HIS F 44 HIS F 444 GLN G 18 HIS G 44 HIS H 18 HIS I 44 HIS J 18 HIS J 44 HIS ** J 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 44 HIS L 303 ASN L 444 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 43908 Z= 0.259 Angle : 0.519 12.772 59388 Z= 0.275 Chirality : 0.041 0.219 6252 Planarity : 0.004 0.044 7860 Dihedral : 4.035 35.400 5878 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 5.44 % Allowed : 24.78 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.12), residues: 5352 helix: 2.14 (0.10), residues: 2424 sheet: 0.14 (0.19), residues: 804 loop : -0.50 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 171 HIS 0.008 0.001 HIS F 44 PHE 0.013 0.001 PHE B 183 TYR 0.020 0.002 TYR A 62 ARG 0.007 0.000 ARG L 170 *********************** 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 1127 residues out of total 4524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 246 poor density : 881 time to evaluate : 5.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 240 PHE cc_start: 0.9028 (OUTLIER) cc_final: 0.8050 (m-80) REVERT: A 241 ASP cc_start: 0.8020 (p0) cc_final: 0.7808 (p0) REVERT: A 329 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.8092 (pt0) REVERT: A 369 MET cc_start: 0.6262 (mmp) cc_final: 0.5967 (mmp) REVERT: A 455 ASP cc_start: 0.8134 (m-30) cc_final: 0.6774 (t0) REVERT: A 459 ARG cc_start: 0.7376 (OUTLIER) cc_final: 0.7081 (mtp180) REVERT: B 19 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8632 (ttmm) REVERT: B 103 ASP cc_start: 0.7681 (p0) cc_final: 0.7441 (p0) REVERT: B 165 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8824 (pp) REVERT: B 217 TRP cc_start: 0.8292 (m-10) cc_final: 0.8060 (m100) REVERT: B 240 PHE cc_start: 0.9063 (OUTLIER) cc_final: 0.7964 (m-80) REVERT: B 447 LYS cc_start: 0.7911 (OUTLIER) cc_final: 0.7658 (tttp) REVERT: C 11 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.7767 (ttt180) REVERT: C 176 LYS cc_start: 0.8666 (mmtp) cc_final: 0.8361 (tptt) REVERT: C 240 PHE cc_start: 0.8956 (OUTLIER) cc_final: 0.8275 (m-80) REVERT: C 242 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7847 (pm20) REVERT: C 338 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8280 (tt0) REVERT: C 458 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.6606 (ttp) REVERT: D 103 ASP cc_start: 0.7628 (p0) cc_final: 0.7362 (p0) REVERT: D 217 TRP cc_start: 0.8474 (m100) cc_final: 0.8203 (m100) REVERT: D 240 PHE cc_start: 0.8997 (OUTLIER) cc_final: 0.7929 (m-80) REVERT: D 326 GLU cc_start: 0.8017 (tt0) cc_final: 0.7729 (tt0) REVERT: D 329 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8247 (pt0) REVERT: D 450 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.8109 (mmt90) REVERT: E 165 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8798 (pp) REVERT: E 217 TRP cc_start: 0.8614 (m100) cc_final: 0.8236 (m100) REVERT: E 240 PHE cc_start: 0.9078 (OUTLIER) cc_final: 0.7974 (m-80) REVERT: F 194 TYR cc_start: 0.7571 (m-10) cc_final: 0.7367 (m-10) REVERT: F 240 PHE cc_start: 0.8959 (OUTLIER) cc_final: 0.8274 (m-80) REVERT: F 329 GLN cc_start: 0.8889 (OUTLIER) cc_final: 0.8206 (pm20) REVERT: F 383 LYS cc_start: 0.8288 (mmtp) cc_final: 0.8076 (mmtp) REVERT: G 240 PHE cc_start: 0.9020 (OUTLIER) cc_final: 0.7947 (m-80) REVERT: G 241 ASP cc_start: 0.8034 (p0) cc_final: 0.7824 (p0) REVERT: G 369 MET cc_start: 0.6324 (mmp) cc_final: 0.6053 (mmp) REVERT: G 450 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.8093 (mmt90) REVERT: G 455 ASP cc_start: 0.8143 (m-30) cc_final: 0.6866 (t0) REVERT: G 458 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.6965 (ttp) REVERT: H 103 ASP cc_start: 0.7878 (p0) cc_final: 0.7669 (p0) REVERT: H 165 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8833 (pp) REVERT: H 171 TRP cc_start: 0.7421 (m100) cc_final: 0.6630 (m100) REVERT: H 217 TRP cc_start: 0.8613 (m100) cc_final: 0.8298 (m100) REVERT: H 240 PHE cc_start: 0.9060 (OUTLIER) cc_final: 0.8003 (m-80) REVERT: H 450 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.8443 (mmt180) REVERT: I 176 LYS cc_start: 0.8736 (mmtp) cc_final: 0.8258 (tptt) REVERT: I 209 ASP cc_start: 0.8290 (p0) cc_final: 0.8049 (p0) REVERT: I 217 TRP cc_start: 0.8678 (m100) cc_final: 0.8172 (m100) REVERT: I 240 PHE cc_start: 0.8946 (OUTLIER) cc_final: 0.8259 (m-80) REVERT: I 242 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7870 (pm20) REVERT: I 329 GLN cc_start: 0.8885 (OUTLIER) cc_final: 0.8197 (pm20) REVERT: I 447 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7980 (mmmt) REVERT: I 458 MET cc_start: 0.7955 (OUTLIER) cc_final: 0.6498 (ttp) REVERT: J 240 PHE cc_start: 0.9028 (OUTLIER) cc_final: 0.8076 (m-80) REVERT: J 329 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.8155 (pt0) REVERT: J 450 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.8108 (mmt180) REVERT: K 19 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8633 (ttmm) REVERT: K 165 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8741 (pp) REVERT: K 217 TRP cc_start: 0.8644 (m100) cc_final: 0.8061 (m100) REVERT: K 223 GLN cc_start: 0.2470 (OUTLIER) cc_final: 0.2029 (tp40) REVERT: K 240 PHE cc_start: 0.9027 (OUTLIER) cc_final: 0.8023 (m-80) REVERT: K 331 GLU cc_start: 0.8340 (pm20) cc_final: 0.7989 (pm20) REVERT: K 422 GLU cc_start: 0.7732 (mp0) cc_final: 0.7491 (mp0) REVERT: K 447 LYS cc_start: 0.7895 (OUTLIER) cc_final: 0.7639 (tttp) REVERT: L 76 VAL cc_start: 0.9038 (OUTLIER) cc_final: 0.8828 (t) REVERT: L 217 TRP cc_start: 0.8668 (m100) cc_final: 0.8181 (m100) REVERT: L 240 PHE cc_start: 0.8947 (OUTLIER) cc_final: 0.8278 (m-80) REVERT: L 329 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8020 (pm20) REVERT: L 450 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.8611 (mmt180) outliers start: 246 outliers final: 186 residues processed: 1047 average time/residue: 0.5770 time to fit residues: 999.8766 Evaluate side-chains 1102 residues out of total 4524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 228 poor density : 874 time to evaluate : 4.869 ------------------------------------------------------------------------------- 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 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 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 379 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 459 ARG Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 19 LYS 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 299 HIS Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 317 VAL 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 11 ARG Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 242 GLU 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 409 GLU Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 458 MET 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 246 VAL 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 379 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 D residue 450 ARG Chi-restraints excluded: chain E residue 13 ASP 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 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 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 13 ASP 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 240 PHE Chi-restraints excluded: chain F residue 278 ASP 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 329 GLN Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain F residue 354 LEU 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 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 310 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 379 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 450 ARG Chi-restraints excluded: chain G residue 457 ASP Chi-restraints excluded: chain G residue 458 MET Chi-restraints excluded: chain H residue 13 ASP Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 76 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 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 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 H residue 450 ARG 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 240 PHE Chi-restraints excluded: chain I residue 242 GLU Chi-restraints excluded: chain I residue 278 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 329 GLN 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 447 LYS Chi-restraints excluded: chain I residue 458 MET Chi-restraints excluded: chain J residue 13 ASP Chi-restraints excluded: chain J residue 18 HIS Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 185 GLU Chi-restraints excluded: chain J residue 216 THR 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 310 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 379 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 450 ARG Chi-restraints excluded: chain K residue 13 ASP Chi-restraints excluded: chain K residue 19 LYS Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain K residue 76 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 240 PHE Chi-restraints excluded: chain K residue 290 THR Chi-restraints excluded: chain K residue 296 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 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 K residue 447 LYS Chi-restraints excluded: chain L residue 13 ASP Chi-restraints excluded: chain L residue 56 VAL Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 186 GLU Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain L residue 240 PHE Chi-restraints excluded: chain L residue 278 ASP 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 329 GLN Chi-restraints excluded: chain L residue 338 GLU Chi-restraints excluded: chain L residue 354 LEU 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 450 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 318 optimal weight: 3.9990 chunk 512 optimal weight: 3.9990 chunk 313 optimal weight: 7.9990 chunk 243 optimal weight: 4.9990 chunk 356 optimal weight: 0.9990 chunk 537 optimal weight: 3.9990 chunk 495 optimal weight: 0.0040 chunk 428 optimal weight: 8.9990 chunk 44 optimal weight: 5.9990 chunk 330 optimal weight: 0.9980 chunk 262 optimal weight: 3.9990 overall best weight: 1.9998 ------------------------------------------------------------------------------- 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 18 HIS E 18 HIS F 444 GLN G 18 HIS H 18 HIS J 18 HIS ** J 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 444 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 43908 Z= 0.215 Angle : 0.504 11.815 59388 Z= 0.269 Chirality : 0.040 0.208 6252 Planarity : 0.004 0.044 7860 Dihedral : 4.032 34.848 5878 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 5.22 % Allowed : 24.80 % Favored : 69.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.12), residues: 5352 helix: 2.12 (0.10), residues: 2424 sheet: 0.15 (0.19), residues: 804 loop : -0.47 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP H 171 HIS 0.006 0.001 HIS F 44 PHE 0.013 0.001 PHE B 183 TYR 0.017 0.001 TYR A 62 ARG 0.007 0.000 ARG A 170 ********************** 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 1108 residues out of total 4524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 236 poor density : 872 time to evaluate : 5.177 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 240 PHE cc_start: 0.8992 (OUTLIER) cc_final: 0.8024 (m-80) REVERT: A 329 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8182 (pt0) REVERT: A 369 MET cc_start: 0.6263 (mmp) cc_final: 0.5971 (mmp) REVERT: A 455 ASP cc_start: 0.8095 (m-30) cc_final: 0.6754 (t0) REVERT: A 459 ARG cc_start: 0.7383 (OUTLIER) cc_final: 0.7092 (mtp180) REVERT: B 19 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8660 (ttmm) REVERT: B 103 ASP cc_start: 0.7644 (p0) cc_final: 0.7392 (p0) REVERT: B 165 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8755 (pp) REVERT: B 217 TRP cc_start: 0.8285 (m-10) cc_final: 0.8084 (m100) REVERT: B 240 PHE cc_start: 0.9067 (OUTLIER) cc_final: 0.7857 (m-80) REVERT: B 447 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7654 (tttp) REVERT: C 11 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.7711 (ttt180) REVERT: C 176 LYS cc_start: 0.8717 (mmtp) cc_final: 0.8302 (tptt) REVERT: C 240 PHE cc_start: 0.8958 (OUTLIER) cc_final: 0.8282 (m-80) REVERT: C 242 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7868 (pm20) REVERT: C 458 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.6498 (ttp) REVERT: D 103 ASP cc_start: 0.7623 (p0) cc_final: 0.7348 (p0) REVERT: D 217 TRP cc_start: 0.8473 (m100) cc_final: 0.8195 (m100) REVERT: D 240 PHE cc_start: 0.8997 (OUTLIER) cc_final: 0.7933 (m-80) REVERT: D 326 GLU cc_start: 0.8013 (tt0) cc_final: 0.7723 (tt0) REVERT: D 329 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.8244 (pt0) REVERT: D 450 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.8098 (mmt90) REVERT: E 165 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8783 (pp) REVERT: E 217 TRP cc_start: 0.8594 (m100) cc_final: 0.8043 (m100) REVERT: E 240 PHE cc_start: 0.9079 (OUTLIER) cc_final: 0.7866 (m-80) REVERT: F 65 ARG cc_start: 0.8539 (mmm160) cc_final: 0.8111 (tpt170) REVERT: F 240 PHE cc_start: 0.8964 (OUTLIER) cc_final: 0.8282 (m-80) REVERT: F 329 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.8230 (pm20) REVERT: G 240 PHE cc_start: 0.8986 (OUTLIER) cc_final: 0.8019 (m-80) REVERT: G 369 MET cc_start: 0.6327 (mmp) cc_final: 0.5993 (mmp) REVERT: G 415 ASP cc_start: 0.7285 (m-30) cc_final: 0.7013 (m-30) REVERT: G 450 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.8038 (mmt90) REVERT: G 455 ASP cc_start: 0.8258 (m-30) cc_final: 0.7049 (t0) REVERT: G 458 MET cc_start: 0.8056 (OUTLIER) cc_final: 0.6874 (ttp) REVERT: H 103 ASP cc_start: 0.7855 (p0) cc_final: 0.7633 (p0) REVERT: H 165 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8775 (pp) REVERT: H 217 TRP cc_start: 0.8625 (m100) cc_final: 0.8301 (m100) REVERT: H 240 PHE cc_start: 0.9082 (OUTLIER) cc_final: 0.8008 (m-80) REVERT: H 450 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.8411 (mmt180) REVERT: I 65 ARG cc_start: 0.8549 (mmm160) cc_final: 0.8130 (tpt170) REVERT: I 176 LYS cc_start: 0.8775 (mmtp) cc_final: 0.8332 (tptt) REVERT: I 209 ASP cc_start: 0.8305 (p0) cc_final: 0.8076 (p0) REVERT: I 217 TRP cc_start: 0.8671 (m100) cc_final: 0.8165 (m100) REVERT: I 240 PHE cc_start: 0.8952 (OUTLIER) cc_final: 0.8256 (m-80) REVERT: I 242 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7869 (pm20) REVERT: I 329 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.8181 (pm20) REVERT: I 447 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7963 (mmmt) REVERT: I 458 MET cc_start: 0.7924 (OUTLIER) cc_final: 0.6466 (ttp) REVERT: J 11 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.7984 (ttt180) REVERT: J 240 PHE cc_start: 0.9025 (OUTLIER) cc_final: 0.8080 (m-80) REVERT: J 329 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.8164 (pt0) REVERT: J 450 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.8099 (mmt180) REVERT: J 455 ASP cc_start: 0.8031 (m-30) cc_final: 0.6824 (t0) REVERT: K 19 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8652 (ttmm) REVERT: K 165 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8762 (pp) REVERT: K 217 TRP cc_start: 0.8619 (m100) cc_final: 0.8074 (m100) REVERT: K 223 GLN cc_start: 0.2407 (OUTLIER) cc_final: 0.2024 (tp40) REVERT: K 240 PHE cc_start: 0.9031 (OUTLIER) cc_final: 0.8051 (m-80) REVERT: K 331 GLU cc_start: 0.8334 (pm20) cc_final: 0.7991 (pm20) REVERT: K 383 LYS cc_start: 0.8484 (mmtp) cc_final: 0.8210 (mmtt) REVERT: K 422 GLU cc_start: 0.7730 (mp0) cc_final: 0.7495 (mp0) REVERT: K 447 LYS cc_start: 0.7928 (OUTLIER) cc_final: 0.7694 (tttp) REVERT: L 76 VAL cc_start: 0.9005 (OUTLIER) cc_final: 0.8803 (t) REVERT: L 170 ARG cc_start: 0.7515 (tpp80) cc_final: 0.7154 (tpt90) REVERT: L 217 TRP cc_start: 0.8660 (m100) cc_final: 0.8175 (m100) REVERT: L 240 PHE cc_start: 0.8964 (OUTLIER) cc_final: 0.8285 (m-80) REVERT: L 329 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8062 (pm20) REVERT: L 450 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.8444 (mmt180) outliers start: 236 outliers final: 181 residues processed: 1026 average time/residue: 0.5566 time to fit residues: 945.3763 Evaluate side-chains 1076 residues out of total 4524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 223 poor density : 853 time to evaluate : 5.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 379 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 459 ARG Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 19 LYS 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 299 HIS Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 317 VAL 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 11 ARG Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 185 GLU Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 242 GLU 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 409 GLU Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain D residue 13 ASP 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 246 VAL 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 379 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 D residue 450 ARG Chi-restraints excluded: chain E residue 13 ASP 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 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 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 199 GLU Chi-restraints excluded: chain F residue 240 PHE Chi-restraints excluded: chain F residue 278 ASP 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 329 GLN Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain F residue 354 LEU 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 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 310 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 379 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 450 ARG Chi-restraints excluded: chain G residue 457 ASP Chi-restraints excluded: chain G residue 458 MET Chi-restraints excluded: chain H residue 13 ASP Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 76 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 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 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 H residue 450 ARG Chi-restraints excluded: chain I residue 13 ASP 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 240 PHE Chi-restraints excluded: chain I residue 242 GLU Chi-restraints excluded: chain I residue 278 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 329 GLN 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 447 LYS Chi-restraints excluded: chain I residue 458 MET Chi-restraints excluded: chain J residue 11 ARG Chi-restraints excluded: chain J residue 13 ASP Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 185 GLU 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 310 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 379 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 450 ARG Chi-restraints excluded: chain K residue 13 ASP Chi-restraints excluded: chain K residue 19 LYS Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain K residue 76 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 240 PHE Chi-restraints excluded: chain K residue 290 THR Chi-restraints excluded: chain K residue 296 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 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 K residue 447 LYS Chi-restraints excluded: chain L residue 13 ASP Chi-restraints excluded: chain L residue 56 VAL Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 186 GLU Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain L residue 240 PHE Chi-restraints excluded: chain L residue 278 ASP 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 329 GLN Chi-restraints excluded: chain L residue 354 LEU 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 450 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 340 optimal weight: 0.7980 chunk 456 optimal weight: 5.9990 chunk 131 optimal weight: 9.9990 chunk 395 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 119 optimal weight: 0.0170 chunk 429 optimal weight: 0.6980 chunk 179 optimal weight: 6.9990 chunk 440 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 overall best weight: 2.1022 ------------------------------------------------------------------------------- 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 444 GLN D 18 HIS E 18 HIS F 444 GLN G 18 HIS H 18 HIS J 18 HIS ** J 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 444 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.138851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.114027 restraints weight = 59014.108| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.24 r_work: 0.3039 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 43908 Z= 0.223 Angle : 0.507 11.591 59388 Z= 0.270 Chirality : 0.040 0.205 6252 Planarity : 0.004 0.043 7860 Dihedral : 4.054 34.718 5878 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 5.77 % Allowed : 24.29 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.12), residues: 5352 helix: 2.15 (0.10), residues: 2412 sheet: 0.15 (0.19), residues: 804 loop : -0.48 (0.13), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP J 171 HIS 0.005 0.001 HIS F 44 PHE 0.014 0.001 PHE B 183 TYR 0.017 0.001 TYR E 62 ARG 0.007 0.000 ARG A 170 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14042.12 seconds wall clock time: 253 minutes 27.96 seconds (15207.96 seconds total)