Starting phenix.real_space_refine on Fri Sep 27 04:05:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kfk_9974/09_2024/6kfk_9974.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kfk_9974/09_2024/6kfk_9974.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kfk_9974/09_2024/6kfk_9974.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kfk_9974/09_2024/6kfk_9974.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kfk_9974/09_2024/6kfk_9974.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kfk_9974/09_2024/6kfk_9974.cif" } resolution = 4.1 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 ------------------------------------------------------------------------------- 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= 0.009 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 176 5.16 5 C 40040 2.51 5 N 11242 2.21 5 O 13618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 286 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 65076 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 2958 Classifications: {'peptide': 402} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 387} Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, S, R, U, T, V Time building chain proxies: 11.15, per 1000 atoms: 0.17 Number of scatterers: 65076 At special positions: 0 Unit cell: (186.14, 187.78, 218.94, 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 176 16.00 O 13618 8.00 N 11242 7.00 C 40040 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: 13.39 Conformation dependent library (CDL) restraints added in 7.0 seconds 17600 Ramachandran restraints generated. 8800 Oldfield, 0 Emsley, 8800 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15972 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 198 sheets defined 17.2% alpha, 32.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.97 Creating SS restraints... Processing helix chain 'A' and resid 2 through 25 removed outlier: 4.895A pdb=" N GLY A 8 " --> pdb=" O GLN A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 28 No H-bonds generated for 'chain 'A' and resid 26 through 28' Processing helix chain 'A' and resid 173 through 177 Processing helix chain 'A' and resid 366 through 402 removed outlier: 4.530A pdb=" N VAL A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 25 removed outlier: 4.894A pdb=" N GLY B 8 " --> pdb=" O GLN B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 28 No H-bonds generated for 'chain 'B' and resid 26 through 28' Processing helix chain 'B' and resid 173 through 177 Processing helix chain 'B' and resid 366 through 402 removed outlier: 4.530A pdb=" N VAL B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 25 removed outlier: 4.894A pdb=" N GLY C 8 " --> pdb=" O GLN C 4 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 28 No H-bonds generated for 'chain 'C' and resid 26 through 28' Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 366 through 402 removed outlier: 4.530A pdb=" N VAL C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 25 removed outlier: 4.894A pdb=" N GLY D 8 " --> pdb=" O GLN D 4 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 28 No H-bonds generated for 'chain 'D' and resid 26 through 28' Processing helix chain 'D' and resid 173 through 177 Processing helix chain 'D' and resid 366 through 402 removed outlier: 4.530A pdb=" N VAL D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 25 removed outlier: 4.894A pdb=" N GLY E 8 " --> pdb=" O GLN E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 28 No H-bonds generated for 'chain 'E' and resid 26 through 28' Processing helix chain 'E' and resid 173 through 177 Processing helix chain 'E' and resid 366 through 402 removed outlier: 4.530A pdb=" N VAL E 372 " --> pdb=" O SER E 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 25 removed outlier: 4.895A pdb=" N GLY F 8 " --> pdb=" O GLN F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 28 No H-bonds generated for 'chain 'F' and resid 26 through 28' Processing helix chain 'F' and resid 173 through 177 Processing helix chain 'F' and resid 366 through 402 removed outlier: 4.530A pdb=" N VAL F 372 " --> pdb=" O SER F 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 25 removed outlier: 4.895A pdb=" N GLY G 8 " --> pdb=" O GLN G 4 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 28 No H-bonds generated for 'chain 'G' and resid 26 through 28' Processing helix chain 'G' and resid 173 through 177 Processing helix chain 'G' and resid 366 through 402 removed outlier: 4.530A pdb=" N VAL G 372 " --> pdb=" O SER G 368 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 25 removed outlier: 4.895A pdb=" N GLY H 8 " --> pdb=" O GLN H 4 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 28 No H-bonds generated for 'chain 'H' and resid 26 through 28' Processing helix chain 'H' and resid 173 through 177 Processing helix chain 'H' and resid 366 through 402 removed outlier: 4.530A pdb=" N VAL H 372 " --> pdb=" O SER H 368 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 25 removed outlier: 4.894A pdb=" N GLY I 8 " --> pdb=" O GLN I 4 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 28 No H-bonds generated for 'chain 'I' and resid 26 through 28' Processing helix chain 'I' and resid 173 through 177 Processing helix chain 'I' and resid 366 through 402 removed outlier: 4.530A pdb=" N VAL I 372 " --> pdb=" O SER I 368 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 25 removed outlier: 4.895A pdb=" N GLY J 8 " --> pdb=" O GLN J 4 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 28 No H-bonds generated for 'chain 'J' and resid 26 through 28' Processing helix chain 'J' and resid 173 through 177 Processing helix chain 'J' and resid 366 through 402 removed outlier: 4.530A pdb=" N VAL J 372 " --> pdb=" O SER J 368 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 25 removed outlier: 4.894A pdb=" N GLY K 8 " --> pdb=" O GLN K 4 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 28 No H-bonds generated for 'chain 'K' and resid 26 through 28' Processing helix chain 'K' and resid 173 through 177 Processing helix chain 'K' and resid 366 through 402 removed outlier: 4.529A pdb=" N VAL K 372 " --> pdb=" O SER K 368 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 25 removed outlier: 4.895A pdb=" N GLY L 8 " --> pdb=" O GLN L 4 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 28 No H-bonds generated for 'chain 'L' and resid 26 through 28' Processing helix chain 'L' and resid 173 through 177 Processing helix chain 'L' and resid 366 through 402 removed outlier: 4.529A pdb=" N VAL L 372 " --> pdb=" O SER L 368 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 25 removed outlier: 4.894A pdb=" N GLY M 8 " --> pdb=" O GLN M 4 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 28 No H-bonds generated for 'chain 'M' and resid 26 through 28' Processing helix chain 'M' and resid 173 through 177 Processing helix chain 'M' and resid 366 through 402 removed outlier: 4.530A pdb=" N VAL M 372 " --> pdb=" O SER M 368 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 25 removed outlier: 4.895A pdb=" N GLY N 8 " --> pdb=" O GLN N 4 " (cutoff:3.500A) Processing helix chain 'N' and resid 26 through 28 No H-bonds generated for 'chain 'N' and resid 26 through 28' Processing helix chain 'N' and resid 173 through 177 Processing helix chain 'N' and resid 366 through 402 removed outlier: 4.530A pdb=" N VAL N 372 " --> pdb=" O SER N 368 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 25 removed outlier: 4.895A pdb=" N GLY O 8 " --> pdb=" O GLN O 4 " (cutoff:3.500A) Processing helix chain 'O' and resid 26 through 28 No H-bonds generated for 'chain 'O' and resid 26 through 28' Processing helix chain 'O' and resid 173 through 177 Processing helix chain 'O' and resid 366 through 402 removed outlier: 4.530A pdb=" N VAL O 372 " --> pdb=" O SER O 368 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 25 removed outlier: 4.895A pdb=" N GLY P 8 " --> pdb=" O GLN P 4 " (cutoff:3.500A) Processing helix chain 'P' and resid 26 through 28 No H-bonds generated for 'chain 'P' and resid 26 through 28' Processing helix chain 'P' and resid 173 through 177 Processing helix chain 'P' and resid 366 through 402 removed outlier: 4.530A pdb=" N VAL P 372 " --> pdb=" O SER P 368 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 25 removed outlier: 4.895A pdb=" N GLY Q 8 " --> pdb=" O GLN Q 4 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 28 No H-bonds generated for 'chain 'Q' and resid 26 through 28' Processing helix chain 'Q' and resid 173 through 177 Processing helix chain 'Q' and resid 366 through 402 removed outlier: 4.530A pdb=" N VAL Q 372 " --> pdb=" O SER Q 368 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 25 removed outlier: 4.895A pdb=" N GLY R 8 " --> pdb=" O GLN R 4 " (cutoff:3.500A) Processing helix chain 'R' and resid 26 through 28 No H-bonds generated for 'chain 'R' and resid 26 through 28' Processing helix chain 'R' and resid 173 through 177 Processing helix chain 'R' and resid 366 through 402 removed outlier: 4.530A pdb=" N VAL R 372 " --> pdb=" O SER R 368 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 25 removed outlier: 4.895A pdb=" N GLY S 8 " --> pdb=" O GLN S 4 " (cutoff:3.500A) Processing helix chain 'S' and resid 26 through 28 No H-bonds generated for 'chain 'S' and resid 26 through 28' Processing helix chain 'S' and resid 173 through 177 Processing helix chain 'S' and resid 366 through 402 removed outlier: 4.529A pdb=" N VAL S 372 " --> pdb=" O SER S 368 " (cutoff:3.500A) Processing helix chain 'T' and resid 2 through 25 removed outlier: 4.895A pdb=" N GLY T 8 " --> pdb=" O GLN T 4 " (cutoff:3.500A) Processing helix chain 'T' and resid 26 through 28 No H-bonds generated for 'chain 'T' and resid 26 through 28' Processing helix chain 'T' and resid 173 through 177 Processing helix chain 'T' and resid 366 through 402 removed outlier: 4.530A pdb=" N VAL T 372 " --> pdb=" O SER T 368 " (cutoff:3.500A) Processing helix chain 'U' and resid 2 through 25 removed outlier: 4.895A pdb=" N GLY U 8 " --> pdb=" O GLN U 4 " (cutoff:3.500A) Processing helix chain 'U' and resid 26 through 28 No H-bonds generated for 'chain 'U' and resid 26 through 28' Processing helix chain 'U' and resid 173 through 177 Processing helix chain 'U' and resid 366 through 402 removed outlier: 4.529A pdb=" N VAL U 372 " --> pdb=" O SER U 368 " (cutoff:3.500A) Processing helix chain 'V' and resid 2 through 25 removed outlier: 4.895A pdb=" N GLY V 8 " --> pdb=" O GLN V 4 " (cutoff:3.500A) Processing helix chain 'V' and resid 26 through 28 No H-bonds generated for 'chain 'V' and resid 26 through 28' Processing helix chain 'V' and resid 173 through 177 Processing helix chain 'V' and resid 366 through 402 removed outlier: 4.530A pdb=" N VAL V 372 " --> pdb=" O SER V 368 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 34 through 40 Processing sheet with id=2, first strand: chain 'A' and resid 90 through 94 removed outlier: 16.047A pdb=" N PHE A 81 " --> pdb=" O TYR A 118 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR A 118 " --> pdb=" O PHE A 81 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ARG A 83 " --> pdb=" O THR A 116 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N GLU A 308 " --> pdb=" O TYR A 303 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N TYR A 303 " --> pdb=" O GLU A 308 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL A 310 " --> pdb=" O GLY A 301 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLY A 301 " --> pdb=" O VAL A 310 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 134 through 135 removed outlier: 5.245A pdb=" N ARG A 83 " --> pdb=" O THR A 116 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR A 118 " --> pdb=" O PHE A 81 " (cutoff:3.500A) removed outlier: 16.047A pdb=" N PHE A 81 " --> pdb=" O TYR A 118 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'A' and resid 100 through 101 Processing sheet with id=5, first strand: chain 'A' and resid 120 through 121 Processing sheet with id=6, first strand: chain 'A' and resid 242 through 245 removed outlier: 6.726A pdb=" N ALA A 151 " --> pdb=" O SER A 261 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'A' and resid 242 through 245 removed outlier: 6.726A pdb=" N ALA A 151 " --> pdb=" O SER A 261 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N THR A 150 " --> pdb=" O GLN A 280 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N GLN A 280 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N SER A 152 " --> pdb=" O THR A 278 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR A 278 " --> pdb=" O SER A 152 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLN A 154 " --> pdb=" O VAL A 276 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'A' and resid 179 through 186 removed outlier: 6.852A pdb=" N GLU A 206 " --> pdb=" O THR A 202 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LYS A 230 " --> pdb=" O GLU A 238 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'A' and resid 326 through 328 Processing sheet with id=10, first strand: chain 'B' and resid 34 through 40 Processing sheet with id=11, first strand: chain 'B' and resid 90 through 94 removed outlier: 16.048A pdb=" N PHE B 81 " --> pdb=" O TYR B 118 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR B 118 " --> pdb=" O PHE B 81 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ARG B 83 " --> pdb=" O THR B 116 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N GLU B 308 " --> pdb=" O TYR B 303 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N TYR B 303 " --> pdb=" O GLU B 308 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N VAL B 310 " --> pdb=" O GLY B 301 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N GLY B 301 " --> pdb=" O VAL B 310 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'B' and resid 134 through 135 removed outlier: 5.245A pdb=" N ARG B 83 " --> pdb=" O THR B 116 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR B 118 " --> pdb=" O PHE B 81 " (cutoff:3.500A) removed outlier: 16.048A pdb=" N PHE B 81 " --> pdb=" O TYR B 118 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'B' and resid 100 through 101 Processing sheet with id=14, first strand: chain 'B' and resid 120 through 121 Processing sheet with id=15, first strand: chain 'B' and resid 242 through 245 removed outlier: 6.726A pdb=" N ALA B 151 " --> pdb=" O SER B 261 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'B' and resid 242 through 245 removed outlier: 6.726A pdb=" N ALA B 151 " --> pdb=" O SER B 261 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N THR B 150 " --> pdb=" O GLN B 280 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N GLN B 280 " --> pdb=" O THR B 150 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N SER B 152 " --> pdb=" O THR B 278 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR B 278 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLN B 154 " --> pdb=" O VAL B 276 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'B' and resid 179 through 186 removed outlier: 6.851A pdb=" N GLU B 206 " --> pdb=" O THR B 202 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LYS B 230 " --> pdb=" O GLU B 238 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'B' and resid 326 through 328 Processing sheet with id=19, first strand: chain 'C' and resid 34 through 40 Processing sheet with id=20, first strand: chain 'C' and resid 90 through 94 removed outlier: 16.047A pdb=" N PHE C 81 " --> pdb=" O TYR C 118 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR C 118 " --> pdb=" O PHE C 81 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ARG C 83 " --> pdb=" O THR C 116 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N GLU C 308 " --> pdb=" O TYR C 303 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N TYR C 303 " --> pdb=" O GLU C 308 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL C 310 " --> pdb=" O GLY C 301 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N GLY C 301 " --> pdb=" O VAL C 310 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'C' and resid 134 through 135 removed outlier: 5.245A pdb=" N ARG C 83 " --> pdb=" O THR C 116 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR C 118 " --> pdb=" O PHE C 81 " (cutoff:3.500A) removed outlier: 16.047A pdb=" N PHE C 81 " --> pdb=" O TYR C 118 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=23, first strand: chain 'C' and resid 120 through 121 Processing sheet with id=24, first strand: chain 'C' and resid 242 through 245 removed outlier: 6.725A pdb=" N ALA C 151 " --> pdb=" O SER C 261 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'C' and resid 242 through 245 removed outlier: 6.725A pdb=" N ALA C 151 " --> pdb=" O SER C 261 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N THR C 150 " --> pdb=" O GLN C 280 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N GLN C 280 " --> pdb=" O THR C 150 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N SER C 152 " --> pdb=" O THR C 278 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR C 278 " --> pdb=" O SER C 152 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N GLN C 154 " --> pdb=" O VAL C 276 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'C' and resid 179 through 186 removed outlier: 6.852A pdb=" N GLU C 206 " --> pdb=" O THR C 202 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LYS C 230 " --> pdb=" O GLU C 238 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'C' and resid 326 through 328 Processing sheet with id=28, first strand: chain 'D' and resid 34 through 40 Processing sheet with id=29, first strand: chain 'D' and resid 90 through 94 removed outlier: 16.047A pdb=" N PHE D 81 " --> pdb=" O TYR D 118 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR D 118 " --> pdb=" O PHE D 81 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ARG D 83 " --> pdb=" O THR D 116 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N GLU D 308 " --> pdb=" O TYR D 303 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N TYR D 303 " --> pdb=" O GLU D 308 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL D 310 " --> pdb=" O GLY D 301 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLY D 301 " --> pdb=" O VAL D 310 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'D' and resid 134 through 135 removed outlier: 5.245A pdb=" N ARG D 83 " --> pdb=" O THR D 116 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR D 118 " --> pdb=" O PHE D 81 " (cutoff:3.500A) removed outlier: 16.047A pdb=" N PHE D 81 " --> pdb=" O TYR D 118 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'D' and resid 100 through 101 Processing sheet with id=32, first strand: chain 'D' and resid 120 through 121 Processing sheet with id=33, first strand: chain 'D' and resid 242 through 245 removed outlier: 6.725A pdb=" N ALA D 151 " --> pdb=" O SER D 261 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'D' and resid 242 through 245 removed outlier: 6.725A pdb=" N ALA D 151 " --> pdb=" O SER D 261 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N THR D 150 " --> pdb=" O GLN D 280 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N GLN D 280 " --> pdb=" O THR D 150 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N SER D 152 " --> pdb=" O THR D 278 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR D 278 " --> pdb=" O SER D 152 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLN D 154 " --> pdb=" O VAL D 276 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'D' and resid 179 through 186 removed outlier: 6.852A pdb=" N GLU D 206 " --> pdb=" O THR D 202 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LYS D 230 " --> pdb=" O GLU D 238 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'D' and resid 326 through 328 Processing sheet with id=37, first strand: chain 'E' and resid 34 through 40 Processing sheet with id=38, first strand: chain 'E' and resid 90 through 94 removed outlier: 16.047A pdb=" N PHE E 81 " --> pdb=" O TYR E 118 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR E 118 " --> pdb=" O PHE E 81 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ARG E 83 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N GLU E 308 " --> pdb=" O TYR E 303 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N TYR E 303 " --> pdb=" O GLU E 308 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL E 310 " --> pdb=" O GLY E 301 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N GLY E 301 " --> pdb=" O VAL E 310 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'E' and resid 134 through 135 removed outlier: 5.245A pdb=" N ARG E 83 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR E 118 " --> pdb=" O PHE E 81 " (cutoff:3.500A) removed outlier: 16.047A pdb=" N PHE E 81 " --> pdb=" O TYR E 118 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'E' and resid 100 through 101 Processing sheet with id=41, first strand: chain 'E' and resid 120 through 121 Processing sheet with id=42, first strand: chain 'E' and resid 242 through 245 removed outlier: 6.725A pdb=" N ALA E 151 " --> pdb=" O SER E 261 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain 'E' and resid 242 through 245 removed outlier: 6.725A pdb=" N ALA E 151 " --> pdb=" O SER E 261 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N THR E 150 " --> pdb=" O GLN E 280 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N GLN E 280 " --> pdb=" O THR E 150 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N SER E 152 " --> pdb=" O THR E 278 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR E 278 " --> pdb=" O SER E 152 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLN E 154 " --> pdb=" O VAL E 276 " (cutoff:3.500A) Processing sheet with id=44, first strand: chain 'E' and resid 179 through 186 removed outlier: 6.852A pdb=" N GLU E 206 " --> pdb=" O THR E 202 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LYS E 230 " --> pdb=" O GLU E 238 " (cutoff:3.500A) Processing sheet with id=45, first strand: chain 'E' and resid 326 through 328 Processing sheet with id=46, first strand: chain 'F' and resid 34 through 40 Processing sheet with id=47, first strand: chain 'F' and resid 90 through 94 removed outlier: 16.047A pdb=" N PHE F 81 " --> pdb=" O TYR F 118 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR F 118 " --> pdb=" O PHE F 81 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N ARG F 83 " --> pdb=" O THR F 116 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N GLU F 308 " --> pdb=" O TYR F 303 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N TYR F 303 " --> pdb=" O GLU F 308 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL F 310 " --> pdb=" O GLY F 301 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N GLY F 301 " --> pdb=" O VAL F 310 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'F' and resid 134 through 135 removed outlier: 5.244A pdb=" N ARG F 83 " --> pdb=" O THR F 116 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR F 118 " --> pdb=" O PHE F 81 " (cutoff:3.500A) removed outlier: 16.047A pdb=" N PHE F 81 " --> pdb=" O TYR F 118 " (cutoff:3.500A) Processing sheet with id=49, first strand: chain 'F' and resid 100 through 101 Processing sheet with id=50, first strand: chain 'F' and resid 120 through 121 Processing sheet with id=51, first strand: chain 'F' and resid 242 through 245 removed outlier: 6.725A pdb=" N ALA F 151 " --> pdb=" O SER F 261 " (cutoff:3.500A) Processing sheet with id=52, first strand: chain 'F' and resid 242 through 245 removed outlier: 6.725A pdb=" N ALA F 151 " --> pdb=" O SER F 261 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N THR F 150 " --> pdb=" O GLN F 280 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N GLN F 280 " --> pdb=" O THR F 150 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N SER F 152 " --> pdb=" O THR F 278 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N THR F 278 " --> pdb=" O SER F 152 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N GLN F 154 " --> pdb=" O VAL F 276 " (cutoff:3.500A) Processing sheet with id=53, first strand: chain 'F' and resid 179 through 186 removed outlier: 6.851A pdb=" N GLU F 206 " --> pdb=" O THR F 202 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LYS F 230 " --> pdb=" O GLU F 238 " (cutoff:3.500A) Processing sheet with id=54, first strand: chain 'F' and resid 326 through 328 Processing sheet with id=55, first strand: chain 'G' and resid 34 through 40 Processing sheet with id=56, first strand: chain 'G' and resid 90 through 94 removed outlier: 16.047A pdb=" N PHE G 81 " --> pdb=" O TYR G 118 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR G 118 " --> pdb=" O PHE G 81 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N ARG G 83 " --> pdb=" O THR G 116 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N GLU G 308 " --> pdb=" O TYR G 303 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N TYR G 303 " --> pdb=" O GLU G 308 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL G 310 " --> pdb=" O GLY G 301 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLY G 301 " --> pdb=" O VAL G 310 " (cutoff:3.500A) Processing sheet with id=57, first strand: chain 'G' and resid 134 through 135 removed outlier: 5.244A pdb=" N ARG G 83 " --> pdb=" O THR G 116 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR G 118 " --> pdb=" O PHE G 81 " (cutoff:3.500A) removed outlier: 16.047A pdb=" N PHE G 81 " --> pdb=" O TYR G 118 " (cutoff:3.500A) Processing sheet with id=58, first strand: chain 'G' and resid 100 through 101 Processing sheet with id=59, first strand: chain 'G' and resid 120 through 121 Processing sheet with id=60, first strand: chain 'G' and resid 242 through 245 removed outlier: 6.725A pdb=" N ALA G 151 " --> pdb=" O SER G 261 " (cutoff:3.500A) Processing sheet with id=61, first strand: chain 'G' and resid 242 through 245 removed outlier: 6.725A pdb=" N ALA G 151 " --> pdb=" O SER G 261 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N THR G 150 " --> pdb=" O GLN G 280 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N GLN G 280 " --> pdb=" O THR G 150 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N SER G 152 " --> pdb=" O THR G 278 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR G 278 " --> pdb=" O SER G 152 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N GLN G 154 " --> pdb=" O VAL G 276 " (cutoff:3.500A) Processing sheet with id=62, first strand: chain 'G' and resid 179 through 186 removed outlier: 6.852A pdb=" N GLU G 206 " --> pdb=" O THR G 202 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LYS G 230 " --> pdb=" O GLU G 238 " (cutoff:3.500A) Processing sheet with id=63, first strand: chain 'G' and resid 326 through 328 Processing sheet with id=64, first strand: chain 'H' and resid 34 through 40 Processing sheet with id=65, first strand: chain 'H' and resid 90 through 94 removed outlier: 16.047A pdb=" N PHE H 81 " --> pdb=" O TYR H 118 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR H 118 " --> pdb=" O PHE H 81 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ARG H 83 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N GLU H 308 " --> pdb=" O TYR H 303 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N TYR H 303 " --> pdb=" O GLU H 308 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL H 310 " --> pdb=" O GLY H 301 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLY H 301 " --> pdb=" O VAL H 310 " (cutoff:3.500A) Processing sheet with id=66, first strand: chain 'H' and resid 134 through 135 removed outlier: 5.245A pdb=" N ARG H 83 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR H 118 " --> pdb=" O PHE H 81 " (cutoff:3.500A) removed outlier: 16.047A pdb=" N PHE H 81 " --> pdb=" O TYR H 118 " (cutoff:3.500A) Processing sheet with id=67, first strand: chain 'H' and resid 100 through 101 Processing sheet with id=68, first strand: chain 'H' and resid 120 through 121 Processing sheet with id=69, first strand: chain 'H' and resid 242 through 245 removed outlier: 6.725A pdb=" N ALA H 151 " --> pdb=" O SER H 261 " (cutoff:3.500A) Processing sheet with id=70, first strand: chain 'H' and resid 242 through 245 removed outlier: 6.725A pdb=" N ALA H 151 " --> pdb=" O SER H 261 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N THR H 150 " --> pdb=" O GLN H 280 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N GLN H 280 " --> pdb=" O THR H 150 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N SER H 152 " --> pdb=" O THR H 278 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR H 278 " --> pdb=" O SER H 152 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N GLN H 154 " --> pdb=" O VAL H 276 " (cutoff:3.500A) Processing sheet with id=71, first strand: chain 'H' and resid 179 through 186 removed outlier: 6.852A pdb=" N GLU H 206 " --> pdb=" O THR H 202 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LYS H 230 " --> pdb=" O GLU H 238 " (cutoff:3.500A) Processing sheet with id=72, first strand: chain 'H' and resid 326 through 328 Processing sheet with id=73, first strand: chain 'I' and resid 34 through 40 Processing sheet with id=74, first strand: chain 'I' and resid 90 through 94 removed outlier: 16.047A pdb=" N PHE I 81 " --> pdb=" O TYR I 118 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR I 118 " --> pdb=" O PHE I 81 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ARG I 83 " --> pdb=" O THR I 116 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N GLU I 308 " --> pdb=" O TYR I 303 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N TYR I 303 " --> pdb=" O GLU I 308 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL I 310 " --> pdb=" O GLY I 301 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N GLY I 301 " --> pdb=" O VAL I 310 " (cutoff:3.500A) Processing sheet with id=75, first strand: chain 'I' and resid 134 through 135 removed outlier: 5.245A pdb=" N ARG I 83 " --> pdb=" O THR I 116 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR I 118 " --> pdb=" O PHE I 81 " (cutoff:3.500A) removed outlier: 16.047A pdb=" N PHE I 81 " --> pdb=" O TYR I 118 " (cutoff:3.500A) Processing sheet with id=76, first strand: chain 'I' and resid 100 through 101 Processing sheet with id=77, first strand: chain 'I' and resid 120 through 121 Processing sheet with id=78, first strand: chain 'I' and resid 242 through 245 removed outlier: 6.726A pdb=" N ALA I 151 " --> pdb=" O SER I 261 " (cutoff:3.500A) Processing sheet with id=79, first strand: chain 'I' and resid 242 through 245 removed outlier: 6.726A pdb=" N ALA I 151 " --> pdb=" O SER I 261 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N THR I 150 " --> pdb=" O GLN I 280 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N GLN I 280 " --> pdb=" O THR I 150 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N SER I 152 " --> pdb=" O THR I 278 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR I 278 " --> pdb=" O SER I 152 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLN I 154 " --> pdb=" O VAL I 276 " (cutoff:3.500A) Processing sheet with id=80, first strand: chain 'I' and resid 179 through 186 removed outlier: 6.851A pdb=" N GLU I 206 " --> pdb=" O THR I 202 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LYS I 230 " --> pdb=" O GLU I 238 " (cutoff:3.500A) Processing sheet with id=81, first strand: chain 'I' and resid 326 through 328 Processing sheet with id=82, first strand: chain 'J' and resid 34 through 40 Processing sheet with id=83, first strand: chain 'J' and resid 90 through 94 removed outlier: 16.047A pdb=" N PHE J 81 " --> pdb=" O TYR J 118 " (cutoff:3.500A) removed outlier: 11.216A pdb=" N TYR J 118 " --> pdb=" O PHE J 81 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ARG J 83 " --> pdb=" O THR J 116 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N GLU J 308 " --> pdb=" O TYR J 303 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N TYR J 303 " --> pdb=" O GLU J 308 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL J 310 " --> pdb=" O GLY J 301 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLY J 301 " --> pdb=" O VAL J 310 " (cutoff:3.500A) Processing sheet with id=84, first strand: chain 'J' and resid 134 through 135 removed outlier: 5.245A pdb=" N ARG J 83 " --> pdb=" O THR J 116 " (cutoff:3.500A) removed outlier: 11.216A pdb=" N TYR J 118 " --> pdb=" O PHE J 81 " (cutoff:3.500A) removed outlier: 16.047A pdb=" N PHE J 81 " --> pdb=" O TYR J 118 " (cutoff:3.500A) Processing sheet with id=85, first strand: chain 'J' and resid 100 through 101 Processing sheet with id=86, first strand: chain 'J' and resid 120 through 121 Processing sheet with id=87, first strand: chain 'J' and resid 242 through 245 removed outlier: 6.726A pdb=" N ALA J 151 " --> pdb=" O SER J 261 " (cutoff:3.500A) Processing sheet with id=88, first strand: chain 'J' and resid 242 through 245 removed outlier: 6.726A pdb=" N ALA J 151 " --> pdb=" O SER J 261 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N THR J 150 " --> pdb=" O GLN J 280 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N GLN J 280 " --> pdb=" O THR J 150 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N SER J 152 " --> pdb=" O THR J 278 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR J 278 " --> pdb=" O SER J 152 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLN J 154 " --> pdb=" O VAL J 276 " (cutoff:3.500A) Processing sheet with id=89, first strand: chain 'J' and resid 179 through 186 removed outlier: 6.852A pdb=" N GLU J 206 " --> pdb=" O THR J 202 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LYS J 230 " --> pdb=" O GLU J 238 " (cutoff:3.500A) Processing sheet with id=90, first strand: chain 'J' and resid 326 through 328 Processing sheet with id=91, first strand: chain 'K' and resid 34 through 40 Processing sheet with id=92, first strand: chain 'K' and resid 90 through 94 removed outlier: 16.047A pdb=" N PHE K 81 " --> pdb=" O TYR K 118 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR K 118 " --> pdb=" O PHE K 81 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ARG K 83 " --> pdb=" O THR K 116 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N GLU K 308 " --> pdb=" O TYR K 303 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N TYR K 303 " --> pdb=" O GLU K 308 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL K 310 " --> pdb=" O GLY K 301 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLY K 301 " --> pdb=" O VAL K 310 " (cutoff:3.500A) Processing sheet with id=93, first strand: chain 'K' and resid 134 through 135 removed outlier: 5.245A pdb=" N ARG K 83 " --> pdb=" O THR K 116 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR K 118 " --> pdb=" O PHE K 81 " (cutoff:3.500A) removed outlier: 16.047A pdb=" N PHE K 81 " --> pdb=" O TYR K 118 " (cutoff:3.500A) Processing sheet with id=94, first strand: chain 'K' and resid 100 through 101 Processing sheet with id=95, first strand: chain 'K' and resid 120 through 121 Processing sheet with id=96, first strand: chain 'K' and resid 242 through 245 removed outlier: 6.726A pdb=" N ALA K 151 " --> pdb=" O SER K 261 " (cutoff:3.500A) Processing sheet with id=97, first strand: chain 'K' and resid 242 through 245 removed outlier: 6.726A pdb=" N ALA K 151 " --> pdb=" O SER K 261 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N THR K 150 " --> pdb=" O GLN K 280 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N GLN K 280 " --> pdb=" O THR K 150 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N SER K 152 " --> pdb=" O THR K 278 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR K 278 " --> pdb=" O SER K 152 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLN K 154 " --> pdb=" O VAL K 276 " (cutoff:3.500A) Processing sheet with id=98, first strand: chain 'K' and resid 179 through 186 removed outlier: 6.852A pdb=" N GLU K 206 " --> pdb=" O THR K 202 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LYS K 230 " --> pdb=" O GLU K 238 " (cutoff:3.500A) Processing sheet with id=99, first strand: chain 'K' and resid 326 through 328 Processing sheet with id=100, first strand: chain 'L' and resid 34 through 40 Processing sheet with id=101, first strand: chain 'L' and resid 90 through 94 removed outlier: 16.047A pdb=" N PHE L 81 " --> pdb=" O TYR L 118 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR L 118 " --> pdb=" O PHE L 81 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ARG L 83 " --> pdb=" O THR L 116 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N GLU L 308 " --> pdb=" O TYR L 303 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N TYR L 303 " --> pdb=" O GLU L 308 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N VAL L 310 " --> pdb=" O GLY L 301 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLY L 301 " --> pdb=" O VAL L 310 " (cutoff:3.500A) Processing sheet with id=102, first strand: chain 'L' and resid 134 through 135 removed outlier: 5.245A pdb=" N ARG L 83 " --> pdb=" O THR L 116 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR L 118 " --> pdb=" O PHE L 81 " (cutoff:3.500A) removed outlier: 16.047A pdb=" N PHE L 81 " --> pdb=" O TYR L 118 " (cutoff:3.500A) Processing sheet with id=103, first strand: chain 'L' and resid 100 through 101 Processing sheet with id=104, first strand: chain 'L' and resid 120 through 121 Processing sheet with id=105, first strand: chain 'L' and resid 242 through 245 removed outlier: 6.726A pdb=" N ALA L 151 " --> pdb=" O SER L 261 " (cutoff:3.500A) Processing sheet with id=106, first strand: chain 'L' and resid 242 through 245 removed outlier: 6.726A pdb=" N ALA L 151 " --> pdb=" O SER L 261 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N THR L 150 " --> pdb=" O GLN L 280 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N GLN L 280 " --> pdb=" O THR L 150 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N SER L 152 " --> pdb=" O THR L 278 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N THR L 278 " --> pdb=" O SER L 152 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLN L 154 " --> pdb=" O VAL L 276 " (cutoff:3.500A) Processing sheet with id=107, first strand: chain 'L' and resid 179 through 186 removed outlier: 6.851A pdb=" N GLU L 206 " --> pdb=" O THR L 202 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LYS L 230 " --> pdb=" O GLU L 238 " (cutoff:3.500A) Processing sheet with id=108, first strand: chain 'L' and resid 326 through 328 Processing sheet with id=109, first strand: chain 'M' and resid 34 through 40 Processing sheet with id=110, first strand: chain 'M' and resid 90 through 94 removed outlier: 16.048A pdb=" N PHE M 81 " --> pdb=" O TYR M 118 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR M 118 " --> pdb=" O PHE M 81 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ARG M 83 " --> pdb=" O THR M 116 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N GLU M 308 " --> pdb=" O TYR M 303 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N TYR M 303 " --> pdb=" O GLU M 308 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL M 310 " --> pdb=" O GLY M 301 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLY M 301 " --> pdb=" O VAL M 310 " (cutoff:3.500A) Processing sheet with id=111, first strand: chain 'M' and resid 134 through 135 removed outlier: 5.245A pdb=" N ARG M 83 " --> pdb=" O THR M 116 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR M 118 " --> pdb=" O PHE M 81 " (cutoff:3.500A) removed outlier: 16.048A pdb=" N PHE M 81 " --> pdb=" O TYR M 118 " (cutoff:3.500A) Processing sheet with id=112, first strand: chain 'M' and resid 100 through 101 Processing sheet with id=113, first strand: chain 'M' and resid 120 through 121 Processing sheet with id=114, first strand: chain 'M' and resid 242 through 245 removed outlier: 6.726A pdb=" N ALA M 151 " --> pdb=" O SER M 261 " (cutoff:3.500A) Processing sheet with id=115, first strand: chain 'M' and resid 242 through 245 removed outlier: 6.726A pdb=" N ALA M 151 " --> pdb=" O SER M 261 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N THR M 150 " --> pdb=" O GLN M 280 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N GLN M 280 " --> pdb=" O THR M 150 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N SER M 152 " --> pdb=" O THR M 278 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR M 278 " --> pdb=" O SER M 152 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N GLN M 154 " --> pdb=" O VAL M 276 " (cutoff:3.500A) Processing sheet with id=116, first strand: chain 'M' and resid 179 through 186 removed outlier: 6.852A pdb=" N GLU M 206 " --> pdb=" O THR M 202 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LYS M 230 " --> pdb=" O GLU M 238 " (cutoff:3.500A) Processing sheet with id=117, first strand: chain 'M' and resid 326 through 328 Processing sheet with id=118, first strand: chain 'N' and resid 34 through 40 Processing sheet with id=119, first strand: chain 'N' and resid 90 through 94 removed outlier: 16.047A pdb=" N PHE N 81 " --> pdb=" O TYR N 118 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR N 118 " --> pdb=" O PHE N 81 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N ARG N 83 " --> pdb=" O THR N 116 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N GLU N 308 " --> pdb=" O TYR N 303 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N TYR N 303 " --> pdb=" O GLU N 308 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL N 310 " --> pdb=" O GLY N 301 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLY N 301 " --> pdb=" O VAL N 310 " (cutoff:3.500A) Processing sheet with id=120, first strand: chain 'N' and resid 134 through 135 removed outlier: 5.246A pdb=" N ARG N 83 " --> pdb=" O THR N 116 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR N 118 " --> pdb=" O PHE N 81 " (cutoff:3.500A) removed outlier: 16.047A pdb=" N PHE N 81 " --> pdb=" O TYR N 118 " (cutoff:3.500A) Processing sheet with id=121, first strand: chain 'N' and resid 100 through 101 Processing sheet with id=122, first strand: chain 'N' and resid 120 through 121 Processing sheet with id=123, first strand: chain 'N' and resid 242 through 245 removed outlier: 6.726A pdb=" N ALA N 151 " --> pdb=" O SER N 261 " (cutoff:3.500A) Processing sheet with id=124, first strand: chain 'N' and resid 242 through 245 removed outlier: 6.726A pdb=" N ALA N 151 " --> pdb=" O SER N 261 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N THR N 150 " --> pdb=" O GLN N 280 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N GLN N 280 " --> pdb=" O THR N 150 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N SER N 152 " --> pdb=" O THR N 278 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR N 278 " --> pdb=" O SER N 152 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N GLN N 154 " --> pdb=" O VAL N 276 " (cutoff:3.500A) Processing sheet with id=125, first strand: chain 'N' and resid 179 through 186 removed outlier: 6.852A pdb=" N GLU N 206 " --> pdb=" O THR N 202 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LYS N 230 " --> pdb=" O GLU N 238 " (cutoff:3.500A) Processing sheet with id=126, first strand: chain 'N' and resid 326 through 328 Processing sheet with id=127, first strand: chain 'O' and resid 34 through 40 Processing sheet with id=128, first strand: chain 'O' and resid 90 through 94 removed outlier: 16.047A pdb=" N PHE O 81 " --> pdb=" O TYR O 118 " (cutoff:3.500A) removed outlier: 11.216A pdb=" N TYR O 118 " --> pdb=" O PHE O 81 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ARG O 83 " --> pdb=" O THR O 116 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N GLU O 308 " --> pdb=" O TYR O 303 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N TYR O 303 " --> pdb=" O GLU O 308 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL O 310 " --> pdb=" O GLY O 301 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N GLY O 301 " --> pdb=" O VAL O 310 " (cutoff:3.500A) Processing sheet with id=129, first strand: chain 'O' and resid 134 through 135 removed outlier: 5.245A pdb=" N ARG O 83 " --> pdb=" O THR O 116 " (cutoff:3.500A) removed outlier: 11.216A pdb=" N TYR O 118 " --> pdb=" O PHE O 81 " (cutoff:3.500A) removed outlier: 16.047A pdb=" N PHE O 81 " --> pdb=" O TYR O 118 " (cutoff:3.500A) Processing sheet with id=130, first strand: chain 'O' and resid 100 through 101 Processing sheet with id=131, first strand: chain 'O' and resid 120 through 121 Processing sheet with id=132, first strand: chain 'O' and resid 242 through 245 removed outlier: 6.725A pdb=" N ALA O 151 " --> pdb=" O SER O 261 " (cutoff:3.500A) Processing sheet with id=133, first strand: chain 'O' and resid 242 through 245 removed outlier: 6.725A pdb=" N ALA O 151 " --> pdb=" O SER O 261 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N THR O 150 " --> pdb=" O GLN O 280 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N GLN O 280 " --> pdb=" O THR O 150 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N SER O 152 " --> pdb=" O THR O 278 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR O 278 " --> pdb=" O SER O 152 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLN O 154 " --> pdb=" O VAL O 276 " (cutoff:3.500A) Processing sheet with id=134, first strand: chain 'O' and resid 179 through 186 removed outlier: 6.851A pdb=" N GLU O 206 " --> pdb=" O THR O 202 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LYS O 230 " --> pdb=" O GLU O 238 " (cutoff:3.500A) Processing sheet with id=135, first strand: chain 'O' and resid 326 through 328 Processing sheet with id=136, first strand: chain 'P' and resid 34 through 40 Processing sheet with id=137, first strand: chain 'P' and resid 90 through 94 removed outlier: 16.047A pdb=" N PHE P 81 " --> pdb=" O TYR P 118 " (cutoff:3.500A) removed outlier: 11.216A pdb=" N TYR P 118 " --> pdb=" O PHE P 81 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ARG P 83 " --> pdb=" O THR P 116 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N GLU P 308 " --> pdb=" O TYR P 303 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N TYR P 303 " --> pdb=" O GLU P 308 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N VAL P 310 " --> pdb=" O GLY P 301 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N GLY P 301 " --> pdb=" O VAL P 310 " (cutoff:3.500A) Processing sheet with id=138, first strand: chain 'P' and resid 134 through 135 removed outlier: 5.245A pdb=" N ARG P 83 " --> pdb=" O THR P 116 " (cutoff:3.500A) removed outlier: 11.216A pdb=" N TYR P 118 " --> pdb=" O PHE P 81 " (cutoff:3.500A) removed outlier: 16.047A pdb=" N PHE P 81 " --> pdb=" O TYR P 118 " (cutoff:3.500A) Processing sheet with id=139, first strand: chain 'P' and resid 100 through 101 Processing sheet with id=140, first strand: chain 'P' and resid 120 through 121 Processing sheet with id=141, first strand: chain 'P' and resid 242 through 245 removed outlier: 6.725A pdb=" N ALA P 151 " --> pdb=" O SER P 261 " (cutoff:3.500A) Processing sheet with id=142, first strand: chain 'P' and resid 242 through 245 removed outlier: 6.725A pdb=" N ALA P 151 " --> pdb=" O SER P 261 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N THR P 150 " --> pdb=" O GLN P 280 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N GLN P 280 " --> pdb=" O THR P 150 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N SER P 152 " --> pdb=" O THR P 278 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR P 278 " --> pdb=" O SER P 152 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLN P 154 " --> pdb=" O VAL P 276 " (cutoff:3.500A) Processing sheet with id=143, first strand: chain 'P' and resid 179 through 186 removed outlier: 6.852A pdb=" N GLU P 206 " --> pdb=" O THR P 202 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LYS P 230 " --> pdb=" O GLU P 238 " (cutoff:3.500A) Processing sheet with id=144, first strand: chain 'P' and resid 326 through 328 Processing sheet with id=145, first strand: chain 'Q' and resid 34 through 40 Processing sheet with id=146, first strand: chain 'Q' and resid 90 through 94 removed outlier: 16.047A pdb=" N PHE Q 81 " --> pdb=" O TYR Q 118 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR Q 118 " --> pdb=" O PHE Q 81 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ARG Q 83 " --> pdb=" O THR Q 116 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N GLU Q 308 " --> pdb=" O TYR Q 303 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N TYR Q 303 " --> pdb=" O GLU Q 308 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL Q 310 " --> pdb=" O GLY Q 301 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLY Q 301 " --> pdb=" O VAL Q 310 " (cutoff:3.500A) Processing sheet with id=147, first strand: chain 'Q' and resid 134 through 135 removed outlier: 5.245A pdb=" N ARG Q 83 " --> pdb=" O THR Q 116 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR Q 118 " --> pdb=" O PHE Q 81 " (cutoff:3.500A) removed outlier: 16.047A pdb=" N PHE Q 81 " --> pdb=" O TYR Q 118 " (cutoff:3.500A) Processing sheet with id=148, first strand: chain 'Q' and resid 100 through 101 Processing sheet with id=149, first strand: chain 'Q' and resid 120 through 121 Processing sheet with id=150, first strand: chain 'Q' and resid 242 through 245 removed outlier: 6.726A pdb=" N ALA Q 151 " --> pdb=" O SER Q 261 " (cutoff:3.500A) Processing sheet with id=151, first strand: chain 'Q' and resid 242 through 245 removed outlier: 6.726A pdb=" N ALA Q 151 " --> pdb=" O SER Q 261 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N THR Q 150 " --> pdb=" O GLN Q 280 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N GLN Q 280 " --> pdb=" O THR Q 150 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N SER Q 152 " --> pdb=" O THR Q 278 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR Q 278 " --> pdb=" O SER Q 152 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N GLN Q 154 " --> pdb=" O VAL Q 276 " (cutoff:3.500A) Processing sheet with id=152, first strand: chain 'Q' and resid 179 through 186 removed outlier: 6.852A pdb=" N GLU Q 206 " --> pdb=" O THR Q 202 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LYS Q 230 " --> pdb=" O GLU Q 238 " (cutoff:3.500A) Processing sheet with id=153, first strand: chain 'Q' and resid 326 through 328 Processing sheet with id=154, first strand: chain 'R' and resid 34 through 40 Processing sheet with id=155, first strand: chain 'R' and resid 90 through 94 removed outlier: 16.047A pdb=" N PHE R 81 " --> pdb=" O TYR R 118 " (cutoff:3.500A) removed outlier: 11.216A pdb=" N TYR R 118 " --> pdb=" O PHE R 81 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N ARG R 83 " --> pdb=" O THR R 116 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N GLU R 308 " --> pdb=" O TYR R 303 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N TYR R 303 " --> pdb=" O GLU R 308 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL R 310 " --> pdb=" O GLY R 301 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLY R 301 " --> pdb=" O VAL R 310 " (cutoff:3.500A) Processing sheet with id=156, first strand: chain 'R' and resid 134 through 135 removed outlier: 5.244A pdb=" N ARG R 83 " --> pdb=" O THR R 116 " (cutoff:3.500A) removed outlier: 11.216A pdb=" N TYR R 118 " --> pdb=" O PHE R 81 " (cutoff:3.500A) removed outlier: 16.047A pdb=" N PHE R 81 " --> pdb=" O TYR R 118 " (cutoff:3.500A) Processing sheet with id=157, first strand: chain 'R' and resid 100 through 101 Processing sheet with id=158, first strand: chain 'R' and resid 120 through 121 Processing sheet with id=159, first strand: chain 'R' and resid 242 through 245 removed outlier: 6.726A pdb=" N ALA R 151 " --> pdb=" O SER R 261 " (cutoff:3.500A) Processing sheet with id=160, first strand: chain 'R' and resid 242 through 245 removed outlier: 6.726A pdb=" N ALA R 151 " --> pdb=" O SER R 261 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N THR R 150 " --> pdb=" O GLN R 280 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N GLN R 280 " --> pdb=" O THR R 150 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N SER R 152 " --> pdb=" O THR R 278 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR R 278 " --> pdb=" O SER R 152 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLN R 154 " --> pdb=" O VAL R 276 " (cutoff:3.500A) Processing sheet with id=161, first strand: chain 'R' and resid 179 through 186 removed outlier: 6.851A pdb=" N GLU R 206 " --> pdb=" O THR R 202 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LYS R 230 " --> pdb=" O GLU R 238 " (cutoff:3.500A) Processing sheet with id=162, first strand: chain 'R' and resid 326 through 328 Processing sheet with id=163, first strand: chain 'S' and resid 34 through 40 Processing sheet with id=164, first strand: chain 'S' and resid 90 through 94 removed outlier: 16.047A pdb=" N PHE S 81 " --> pdb=" O TYR S 118 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR S 118 " --> pdb=" O PHE S 81 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ARG S 83 " --> pdb=" O THR S 116 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N GLU S 308 " --> pdb=" O TYR S 303 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N TYR S 303 " --> pdb=" O GLU S 308 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL S 310 " --> pdb=" O GLY S 301 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLY S 301 " --> pdb=" O VAL S 310 " (cutoff:3.500A) Processing sheet with id=165, first strand: chain 'S' and resid 134 through 135 removed outlier: 5.245A pdb=" N ARG S 83 " --> pdb=" O THR S 116 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR S 118 " --> pdb=" O PHE S 81 " (cutoff:3.500A) removed outlier: 16.047A pdb=" N PHE S 81 " --> pdb=" O TYR S 118 " (cutoff:3.500A) Processing sheet with id=166, first strand: chain 'S' and resid 100 through 101 Processing sheet with id=167, first strand: chain 'S' and resid 120 through 121 Processing sheet with id=168, first strand: chain 'S' and resid 242 through 245 removed outlier: 6.726A pdb=" N ALA S 151 " --> pdb=" O SER S 261 " (cutoff:3.500A) Processing sheet with id=169, first strand: chain 'S' and resid 242 through 245 removed outlier: 6.726A pdb=" N ALA S 151 " --> pdb=" O SER S 261 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N THR S 150 " --> pdb=" O GLN S 280 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N GLN S 280 " --> pdb=" O THR S 150 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N SER S 152 " --> pdb=" O THR S 278 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR S 278 " --> pdb=" O SER S 152 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N GLN S 154 " --> pdb=" O VAL S 276 " (cutoff:3.500A) Processing sheet with id=170, first strand: chain 'S' and resid 179 through 186 removed outlier: 6.852A pdb=" N GLU S 206 " --> pdb=" O THR S 202 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LYS S 230 " --> pdb=" O GLU S 238 " (cutoff:3.500A) Processing sheet with id=171, first strand: chain 'S' and resid 326 through 328 Processing sheet with id=172, first strand: chain 'T' and resid 34 through 40 Processing sheet with id=173, first strand: chain 'T' and resid 90 through 94 removed outlier: 16.047A pdb=" N PHE T 81 " --> pdb=" O TYR T 118 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR T 118 " --> pdb=" O PHE T 81 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N ARG T 83 " --> pdb=" O THR T 116 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N GLU T 308 " --> pdb=" O TYR T 303 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N TYR T 303 " --> pdb=" O GLU T 308 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL T 310 " --> pdb=" O GLY T 301 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLY T 301 " --> pdb=" O VAL T 310 " (cutoff:3.500A) Processing sheet with id=174, first strand: chain 'T' and resid 134 through 135 removed outlier: 5.244A pdb=" N ARG T 83 " --> pdb=" O THR T 116 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N TYR T 118 " --> pdb=" O PHE T 81 " (cutoff:3.500A) removed outlier: 16.047A pdb=" N PHE T 81 " --> pdb=" O TYR T 118 " (cutoff:3.500A) Processing sheet with id=175, first strand: chain 'T' and resid 100 through 101 Processing sheet with id=176, first strand: chain 'T' and resid 120 through 121 Processing sheet with id=177, first strand: chain 'T' and resid 242 through 245 removed outlier: 6.726A pdb=" N ALA T 151 " --> pdb=" O SER T 261 " (cutoff:3.500A) Processing sheet with id=178, first strand: chain 'T' and resid 242 through 245 removed outlier: 6.726A pdb=" N ALA T 151 " --> pdb=" O SER T 261 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N THR T 150 " --> pdb=" O GLN T 280 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N GLN T 280 " --> pdb=" O THR T 150 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N SER T 152 " --> pdb=" O THR T 278 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR T 278 " --> pdb=" O SER T 152 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N GLN T 154 " --> pdb=" O VAL T 276 " (cutoff:3.500A) Processing sheet with id=179, first strand: chain 'T' and resid 179 through 186 removed outlier: 6.851A pdb=" N GLU T 206 " --> pdb=" O THR T 202 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LYS T 230 " --> pdb=" O GLU T 238 " (cutoff:3.500A) Processing sheet with id=180, first strand: chain 'T' and resid 326 through 328 Processing sheet with id=181, first strand: chain 'U' and resid 34 through 40 Processing sheet with id=182, first strand: chain 'U' and resid 90 through 94 removed outlier: 16.047A pdb=" N PHE U 81 " --> pdb=" O TYR U 118 " (cutoff:3.500A) removed outlier: 11.216A pdb=" N TYR U 118 " --> pdb=" O PHE U 81 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ARG U 83 " --> pdb=" O THR U 116 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N GLU U 308 " --> pdb=" O TYR U 303 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N TYR U 303 " --> pdb=" O GLU U 308 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL U 310 " --> pdb=" O GLY U 301 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLY U 301 " --> pdb=" O VAL U 310 " (cutoff:3.500A) Processing sheet with id=183, first strand: chain 'U' and resid 134 through 135 removed outlier: 5.245A pdb=" N ARG U 83 " --> pdb=" O THR U 116 " (cutoff:3.500A) removed outlier: 11.216A pdb=" N TYR U 118 " --> pdb=" O PHE U 81 " (cutoff:3.500A) removed outlier: 16.047A pdb=" N PHE U 81 " --> pdb=" O TYR U 118 " (cutoff:3.500A) Processing sheet with id=184, first strand: chain 'U' and resid 100 through 101 Processing sheet with id=185, first strand: chain 'U' and resid 120 through 121 Processing sheet with id=186, first strand: chain 'U' and resid 242 through 245 removed outlier: 6.726A pdb=" N ALA U 151 " --> pdb=" O SER U 261 " (cutoff:3.500A) Processing sheet with id=187, first strand: chain 'U' and resid 242 through 245 removed outlier: 6.726A pdb=" N ALA U 151 " --> pdb=" O SER U 261 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N THR U 150 " --> pdb=" O GLN U 280 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N GLN U 280 " --> pdb=" O THR U 150 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N SER U 152 " --> pdb=" O THR U 278 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N THR U 278 " --> pdb=" O SER U 152 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLN U 154 " --> pdb=" O VAL U 276 " (cutoff:3.500A) Processing sheet with id=188, first strand: chain 'U' and resid 179 through 186 removed outlier: 6.852A pdb=" N GLU U 206 " --> pdb=" O THR U 202 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LYS U 230 " --> pdb=" O GLU U 238 " (cutoff:3.500A) Processing sheet with id=189, first strand: chain 'U' and resid 326 through 328 Processing sheet with id=190, first strand: chain 'V' and resid 34 through 40 Processing sheet with id=191, first strand: chain 'V' and resid 90 through 94 removed outlier: 16.047A pdb=" N PHE V 81 " --> pdb=" O TYR V 118 " (cutoff:3.500A) removed outlier: 11.216A pdb=" N TYR V 118 " --> pdb=" O PHE V 81 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ARG V 83 " --> pdb=" O THR V 116 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N GLU V 308 " --> pdb=" O TYR V 303 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N TYR V 303 " --> pdb=" O GLU V 308 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL V 310 " --> pdb=" O GLY V 301 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N GLY V 301 " --> pdb=" O VAL V 310 " (cutoff:3.500A) Processing sheet with id=192, first strand: chain 'V' and resid 134 through 135 removed outlier: 5.245A pdb=" N ARG V 83 " --> pdb=" O THR V 116 " (cutoff:3.500A) removed outlier: 11.216A pdb=" N TYR V 118 " --> pdb=" O PHE V 81 " (cutoff:3.500A) removed outlier: 16.047A pdb=" N PHE V 81 " --> pdb=" O TYR V 118 " (cutoff:3.500A) Processing sheet with id=193, first strand: chain 'V' and resid 100 through 101 Processing sheet with id=194, first strand: chain 'V' and resid 120 through 121 Processing sheet with id=195, first strand: chain 'V' and resid 242 through 245 removed outlier: 6.726A pdb=" N ALA V 151 " --> pdb=" O SER V 261 " (cutoff:3.500A) Processing sheet with id=196, first strand: chain 'V' and resid 242 through 245 removed outlier: 6.726A pdb=" N ALA V 151 " --> pdb=" O SER V 261 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N THR V 150 " --> pdb=" O GLN V 280 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N GLN V 280 " --> pdb=" O THR V 150 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N SER V 152 " --> pdb=" O THR V 278 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N THR V 278 " --> pdb=" O SER V 152 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N GLN V 154 " --> pdb=" O VAL V 276 " (cutoff:3.500A) Processing sheet with id=197, first strand: chain 'V' and resid 179 through 186 removed outlier: 6.851A pdb=" N GLU V 206 " --> pdb=" O THR V 202 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LYS V 230 " --> pdb=" O GLU V 238 " (cutoff:3.500A) Processing sheet with id=198, first strand: chain 'V' and resid 326 through 328 2838 hydrogen bonds defined for protein. 7260 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: 38.15 Time building geometry restraints manager: 15.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 16230 1.32 - 1.44: 14598 1.44 - 1.56: 34820 1.56 - 1.68: 44 1.68 - 1.81: 352 Bond restraints: 66044 Sorted by residual: bond pdb=" CA ASN F 305 " pdb=" CB ASN F 305 " ideal model delta sigma weight residual 1.528 1.447 0.081 1.37e-02 5.33e+03 3.50e+01 bond pdb=" CA ASN T 305 " pdb=" CB ASN T 305 " ideal model delta sigma weight residual 1.528 1.447 0.081 1.37e-02 5.33e+03 3.49e+01 bond pdb=" CA ASN S 305 " pdb=" CB ASN S 305 " ideal model delta sigma weight residual 1.528 1.447 0.081 1.37e-02 5.33e+03 3.49e+01 bond pdb=" CA ASN K 305 " pdb=" CB ASN K 305 " ideal model delta sigma weight residual 1.528 1.447 0.081 1.37e-02 5.33e+03 3.48e+01 bond pdb=" CA ASN P 305 " pdb=" CB ASN P 305 " ideal model delta sigma weight residual 1.528 1.448 0.081 1.37e-02 5.33e+03 3.47e+01 ... (remaining 66039 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.55: 89104 6.55 - 13.10: 788 13.10 - 19.65: 22 19.65 - 26.20: 22 26.20 - 32.75: 44 Bond angle restraints: 89980 Sorted by residual: angle pdb=" C GLY E 329 " pdb=" N ASP E 330 " pdb=" CA ASP E 330 " ideal model delta sigma weight residual 120.58 153.33 -32.75 1.71e+00 3.42e-01 3.67e+02 angle pdb=" C GLY L 329 " pdb=" N ASP L 330 " pdb=" CA ASP L 330 " ideal model delta sigma weight residual 120.58 153.32 -32.74 1.71e+00 3.42e-01 3.67e+02 angle pdb=" C GLY I 329 " pdb=" N ASP I 330 " pdb=" CA ASP I 330 " ideal model delta sigma weight residual 120.58 153.31 -32.73 1.71e+00 3.42e-01 3.66e+02 angle pdb=" C GLY O 329 " pdb=" N ASP O 330 " pdb=" CA ASP O 330 " ideal model delta sigma weight residual 120.58 153.31 -32.73 1.71e+00 3.42e-01 3.66e+02 angle pdb=" C GLY N 329 " pdb=" N ASP N 330 " pdb=" CA ASP N 330 " ideal model delta sigma weight residual 120.58 153.30 -32.72 1.71e+00 3.42e-01 3.66e+02 ... (remaining 89975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.70: 37444 16.70 - 33.39: 1056 33.39 - 50.09: 308 50.09 - 66.78: 154 66.78 - 83.48: 110 Dihedral angle restraints: 39072 sinusoidal: 14036 harmonic: 25036 Sorted by residual: dihedral pdb=" CA THR E 65 " pdb=" C THR E 65 " pdb=" N THR E 66 " pdb=" CA THR E 66 " ideal model delta harmonic sigma weight residual -180.00 -144.63 -35.37 0 5.00e+00 4.00e-02 5.00e+01 dihedral pdb=" CA THR M 65 " pdb=" C THR M 65 " pdb=" N THR M 66 " pdb=" CA THR M 66 " ideal model delta harmonic sigma weight residual 180.00 -144.63 -35.37 0 5.00e+00 4.00e-02 5.00e+01 dihedral pdb=" CA THR F 65 " pdb=" C THR F 65 " pdb=" N THR F 66 " pdb=" CA THR F 66 " ideal model delta harmonic sigma weight residual 180.00 -144.64 -35.36 0 5.00e+00 4.00e-02 5.00e+01 ... (remaining 39069 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 6544 0.067 - 0.134: 3118 0.134 - 0.201: 563 0.201 - 0.269: 269 0.269 - 0.336: 66 Chirality restraints: 10560 Sorted by residual: chirality pdb=" CA ASN E 400 " pdb=" N ASN E 400 " pdb=" C ASN E 400 " pdb=" CB ASN E 400 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CA ASN K 400 " pdb=" N ASN K 400 " pdb=" C ASN K 400 " pdb=" CB ASN K 400 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" CA TYR Q 303 " pdb=" N TYR Q 303 " pdb=" C TYR Q 303 " pdb=" CB TYR Q 303 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.80e+00 ... (remaining 10557 not shown) Planarity restraints: 12078 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 141 " 0.062 2.00e-02 2.50e+03 1.30e-01 1.68e+02 pdb=" C THR C 141 " -0.224 2.00e-02 2.50e+03 pdb=" O THR C 141 " 0.086 2.00e-02 2.50e+03 pdb=" N LEU C 142 " 0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR N 141 " 0.062 2.00e-02 2.50e+03 1.30e-01 1.68e+02 pdb=" C THR N 141 " -0.224 2.00e-02 2.50e+03 pdb=" O THR N 141 " 0.086 2.00e-02 2.50e+03 pdb=" N LEU N 142 " 0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 141 " 0.062 2.00e-02 2.50e+03 1.30e-01 1.68e+02 pdb=" C THR E 141 " -0.224 2.00e-02 2.50e+03 pdb=" O THR E 141 " 0.086 2.00e-02 2.50e+03 pdb=" N LEU E 142 " 0.076 2.00e-02 2.50e+03 ... (remaining 12075 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.13: 304 2.13 - 2.83: 25350 2.83 - 3.52: 100485 3.52 - 4.21: 173374 4.21 - 4.90: 282031 Nonbonded interactions: 581544 Sorted by model distance: nonbonded pdb=" CG2 THR J 65 " pdb=" CZ PHE T 42 " model vdw 1.444 3.760 nonbonded pdb=" CG2 THR D 65 " pdb=" CZ PHE N 42 " model vdw 1.444 3.760 nonbonded pdb=" CG2 THR K 65 " pdb=" CZ PHE U 42 " model vdw 1.444 3.760 nonbonded pdb=" CG2 THR I 65 " pdb=" CZ PHE S 42 " model vdw 1.444 3.760 nonbonded pdb=" CG2 THR L 65 " pdb=" CZ PHE V 42 " model vdw 1.444 3.760 ... (remaining 581539 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' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.920 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: 0.070 Extract box with map and model: 2.290 Check model and map are aligned: 0.400 Set scattering table: 0.500 Process input model: 117.580 Find NCS groups from input model: 1.990 Set up NCS constraints: 0.420 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: 0.030 Load rotamer database and sin/cos tables:2.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 129.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0635 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 : 0.015 0.090 66044 Z= 0.982 Angle : 1.991 32.750 89980 Z= 1.293 Chirality : 0.083 0.336 10560 Planarity : 0.011 0.130 12078 Dihedral : 10.936 83.477 23100 Min Nonbonded Distance : 1.444 Molprobity Statistics. All-atom Clashscore : 20.13 Ramachandran Plot: Outliers : 2.25 % Allowed : 8.25 % Favored : 89.50 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.51 % Twisted Proline : 0.00 % Twisted General : 0.77 % 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 (0.09), residues: 8800 helix: 1.29 (0.14), residues: 1276 sheet: -0.90 (0.10), residues: 2442 loop : -1.08 (0.08), residues: 5082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.009 TRP D 207 HIS 0.004 0.002 HIS Q 212 PHE 0.030 0.004 PHE V 169 TYR 0.050 0.008 TYR F 198 ARG 0.007 0.001 ARG C 95 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17600 Ramachandran restraints generated. 8800 Oldfield, 0 Emsley, 8800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17600 Ramachandran restraints generated. 8800 Oldfield, 0 Emsley, 8800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 863 residues out of total 7084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 863 time to evaluate : 4.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 195 MET cc_start: -0.1147 (mmp) cc_final: -0.1802 (tpt) REVERT: B 364 ASN cc_start: 0.4763 (p0) cc_final: 0.3988 (m-40) REVERT: C 113 MET cc_start: 0.0530 (mtt) cc_final: 0.0184 (mtp) REVERT: C 143 MET cc_start: -0.1473 (tpt) cc_final: -0.1963 (tpt) REVERT: C 195 MET cc_start: -0.0304 (mmp) cc_final: -0.0835 (tpt) REVERT: C 364 ASN cc_start: 0.4725 (p0) cc_final: 0.3914 (m-40) REVERT: D 143 MET cc_start: -0.1818 (tpt) cc_final: -0.2167 (tpt) REVERT: D 195 MET cc_start: -0.0715 (mmp) cc_final: -0.1243 (tpt) REVERT: E 143 MET cc_start: -0.1839 (tpt) cc_final: -0.2210 (tpt) REVERT: E 195 MET cc_start: -0.0407 (mmp) cc_final: -0.1116 (tpt) REVERT: E 266 MET cc_start: -0.1453 (mtm) cc_final: -0.1963 (mtt) REVERT: E 364 ASN cc_start: 0.4779 (p0) cc_final: 0.4095 (m-40) REVERT: F 113 MET cc_start: 0.0536 (mtt) cc_final: -0.0057 (mtp) REVERT: F 195 MET cc_start: -0.0563 (mmp) cc_final: -0.1133 (tpt) REVERT: F 266 MET cc_start: -0.1507 (mtm) cc_final: -0.1864 (mtt) REVERT: G 113 MET cc_start: 0.0374 (mtt) cc_final: 0.0048 (mtp) REVERT: G 143 MET cc_start: -0.1475 (tpt) cc_final: -0.1823 (tpt) REVERT: G 195 MET cc_start: -0.0184 (mmp) cc_final: -0.1171 (tpt) REVERT: H 41 MET cc_start: 0.1151 (mmm) cc_final: 0.0925 (mmm) REVERT: H 143 MET cc_start: -0.1866 (tpt) cc_final: -0.2282 (tpt) REVERT: H 195 MET cc_start: -0.0381 (mmp) cc_final: -0.0926 (tpt) REVERT: H 266 MET cc_start: -0.1552 (mtm) cc_final: -0.1932 (mtt) REVERT: I 41 MET cc_start: 0.0786 (mmm) cc_final: 0.0065 (mmm) REVERT: I 143 MET cc_start: -0.2140 (tpt) cc_final: -0.2407 (tpt) REVERT: I 195 MET cc_start: -0.0250 (mmp) cc_final: -0.0858 (tpt) REVERT: J 143 MET cc_start: -0.1913 (tpt) cc_final: -0.2291 (tpt) REVERT: J 195 MET cc_start: -0.0419 (mmp) cc_final: -0.1484 (tpt) REVERT: K 41 MET cc_start: 0.0981 (mmm) cc_final: 0.0226 (mmt) REVERT: K 113 MET cc_start: 0.0901 (mtt) cc_final: 0.0052 (mtp) REVERT: K 195 MET cc_start: -0.0833 (mmp) cc_final: -0.2111 (tpt) REVERT: K 266 MET cc_start: -0.1886 (mtm) cc_final: -0.2372 (mtt) REVERT: K 309 GLN cc_start: 0.4972 (pt0) cc_final: 0.4682 (pm20) REVERT: L 113 MET cc_start: 0.0573 (mtt) cc_final: -0.0023 (mtp) REVERT: L 195 MET cc_start: -0.1006 (mmp) cc_final: -0.1962 (tpt) REVERT: L 266 MET cc_start: -0.1933 (mtm) cc_final: -0.2421 (mtt) REVERT: L 295 ASN cc_start: 0.5048 (p0) cc_final: 0.3893 (m-40) REVERT: A 41 MET cc_start: 0.0904 (mmm) cc_final: 0.0558 (mmt) REVERT: A 195 MET cc_start: -0.0973 (mmp) cc_final: -0.1849 (tpt) REVERT: A 266 MET cc_start: -0.2135 (mtm) cc_final: -0.2540 (mtt) REVERT: A 309 GLN cc_start: 0.5027 (pt0) cc_final: 0.4652 (pm20) REVERT: M 41 MET cc_start: 0.1465 (mmm) cc_final: 0.1127 (mmt) REVERT: M 195 MET cc_start: -0.0962 (mmp) cc_final: -0.2267 (tpt) REVERT: N 195 MET cc_start: -0.1052 (mmp) cc_final: -0.2017 (tpt) REVERT: N 295 ASN cc_start: 0.5330 (p0) cc_final: 0.4319 (m-40) REVERT: O 41 MET cc_start: 0.1257 (mmm) cc_final: 0.0411 (mmt) REVERT: O 195 MET cc_start: -0.1460 (mmp) cc_final: -0.2046 (tpt) REVERT: O 295 ASN cc_start: 0.5379 (p0) cc_final: 0.4110 (m110) REVERT: P 41 MET cc_start: 0.1238 (mmm) cc_final: 0.0633 (mmm) REVERT: P 195 MET cc_start: -0.1503 (mmp) cc_final: -0.1878 (tpt) REVERT: P 295 ASN cc_start: 0.5106 (p0) cc_final: 0.4331 (m-40) REVERT: Q 41 MET cc_start: 0.1160 (mmm) cc_final: 0.0504 (mmt) REVERT: Q 195 MET cc_start: -0.0966 (mmp) cc_final: -0.1505 (tpt) REVERT: Q 204 ASP cc_start: 0.2712 (t0) cc_final: 0.2250 (m-30) REVERT: Q 295 ASN cc_start: 0.5358 (p0) cc_final: 0.4344 (m-40) REVERT: R 41 MET cc_start: 0.1398 (mmm) cc_final: 0.0485 (mmt) REVERT: R 143 MET cc_start: -0.1639 (tpt) cc_final: -0.1962 (tpt) REVERT: R 195 MET cc_start: -0.0685 (mmp) cc_final: -0.1437 (tpt) REVERT: R 295 ASN cc_start: 0.5249 (p0) cc_final: 0.4134 (m110) REVERT: S 41 MET cc_start: 0.1444 (mmm) cc_final: 0.0526 (mmt) REVERT: S 143 MET cc_start: -0.1964 (tpt) cc_final: -0.2199 (tpt) REVERT: S 195 MET cc_start: -0.0735 (mmp) cc_final: -0.1347 (tpt) REVERT: S 204 ASP cc_start: 0.2355 (t0) cc_final: 0.1963 (m-30) REVERT: T 41 MET cc_start: 0.1242 (mmm) cc_final: 0.0213 (mmt) REVERT: T 204 ASP cc_start: 0.2591 (t0) cc_final: 0.2200 (m-30) REVERT: T 309 GLN cc_start: 0.5020 (pt0) cc_final: 0.4639 (pt0) REVERT: U 204 ASP cc_start: 0.3361 (t0) cc_final: 0.2758 (m-30) REVERT: V 41 MET cc_start: 0.1320 (mmm) cc_final: 0.0316 (mmt) REVERT: V 204 ASP cc_start: 0.3242 (t0) cc_final: 0.2926 (m-30) REVERT: V 266 MET cc_start: -0.2253 (mtm) cc_final: -0.2465 (ttm) outliers start: 0 outliers final: 0 residues processed: 863 average time/residue: 0.5600 time to fit residues: 847.1616 Evaluate side-chains 531 residues out of total 7084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 531 time to evaluate : 4.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 880 random chunks: chunk 743 optimal weight: 4.9990 chunk 666 optimal weight: 5.9990 chunk 370 optimal weight: 4.9990 chunk 227 optimal weight: 7.9990 chunk 449 optimal weight: 1.9990 chunk 356 optimal weight: 2.9990 chunk 689 optimal weight: 6.9990 chunk 266 optimal weight: 3.9990 chunk 419 optimal weight: 7.9990 chunk 513 optimal weight: 5.9990 chunk 799 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 ASN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 ASN ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 GLN C 15 ASN ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 GLN C 191 ASN ** C 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 378 GLN D 15 ASN ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 ASN ** D 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 378 GLN E 15 ASN ** E 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 191 ASN ** E 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 292 GLN ** E 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 191 ASN ** F 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 GLN F 378 GLN G 15 ASN ** G 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 191 ASN ** G 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 322 ASN G 378 GLN H 15 ASN ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 269 ASN H 292 GLN ** H 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 313 GLN ** H 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 15 ASN ** I 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 313 GLN I 322 ASN J 15 ASN ** J 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 313 GLN J 322 ASN J 378 GLN ** K 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 ASN ** K 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 292 GLN ** K 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 309 GLN K 313 GLN K 322 ASN L 15 ASN ** L 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 322 ASN A 15 ASN ** A 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 ASN ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 GLN A 322 ASN ** M 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 15 ASN ** M 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 78 GLN ** M 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 191 ASN ** M 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 322 ASN ** N 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 15 ASN ** N 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 78 GLN ** N 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 313 GLN N 322 ASN N 378 GLN ** O 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 15 ASN ** O 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 78 GLN ** O 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 281 ASN ** O 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 378 GLN ** P 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 15 ASN ** P 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 78 GLN ** P 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 281 ASN ** P 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 378 GLN ** Q 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 15 ASN ** Q 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 78 GLN ** Q 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 281 ASN ** Q 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 313 GLN Q 322 ASN Q 378 GLN ** R 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 15 ASN R 78 GLN ** R 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 268 GLN ** R 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 313 GLN R 322 ASN ** S 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 15 ASN ** S 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 313 GLN S 322 ASN ** T 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 15 ASN ** T 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 268 GLN ** T 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 309 GLN T 313 GLN T 322 ASN ** U 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 15 ASN ** U 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 268 GLN U 281 ASN ** U 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 313 GLN ** U 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 15 ASN ** V 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 268 GLN V 281 ASN ** V 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 313 GLN ** V 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 87 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1076 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 66044 Z= 0.277 Angle : 0.910 13.984 89980 Z= 0.503 Chirality : 0.051 0.226 10560 Planarity : 0.005 0.055 12078 Dihedral : 5.939 25.588 9196 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 1.00 % Allowed : 5.99 % Favored : 93.01 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.51 % 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: -0.43 (0.09), residues: 8800 helix: 2.74 (0.13), residues: 1342 sheet: -0.99 (0.09), residues: 2486 loop : -0.72 (0.09), residues: 4972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP U 333 HIS 0.003 0.001 HIS B 193 PHE 0.031 0.003 PHE D 231 TYR 0.024 0.003 TYR J 303 ARG 0.006 0.001 ARG E 95 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17600 Ramachandran restraints generated. 8800 Oldfield, 0 Emsley, 8800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17600 Ramachandran restraints generated. 8800 Oldfield, 0 Emsley, 8800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 7084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 614 time to evaluate : 4.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 113 MET cc_start: 0.0429 (mtt) cc_final: 0.0034 (mtp) REVERT: B 143 MET cc_start: -0.1832 (ttt) cc_final: -0.2242 (ttt) REVERT: B 195 MET cc_start: -0.0573 (mmp) cc_final: -0.1042 (tpp) REVERT: B 364 ASN cc_start: 0.4638 (p0) cc_final: 0.3865 (m110) REVERT: C 110 MET cc_start: 0.2242 (tmm) cc_final: 0.0913 (ttt) REVERT: C 143 MET cc_start: -0.1793 (tpt) cc_final: -0.2399 (tpt) REVERT: D 143 MET cc_start: -0.2050 (tpt) cc_final: -0.2586 (tpt) REVERT: E 110 MET cc_start: 0.2411 (tmm) cc_final: 0.1424 (ttt) REVERT: E 143 MET cc_start: -0.2111 (tpt) cc_final: -0.2589 (tpt) REVERT: E 195 MET cc_start: 0.0130 (mmp) cc_final: -0.0397 (tpp) REVERT: F 110 MET cc_start: 0.2372 (tmm) cc_final: 0.0814 (ttt) REVERT: F 113 MET cc_start: 0.0555 (mtt) cc_final: 0.0123 (mtp) REVERT: G 113 MET cc_start: 0.0720 (mtt) cc_final: 0.0450 (mtp) REVERT: G 143 MET cc_start: -0.2046 (tpt) cc_final: -0.2633 (tpt) REVERT: H 143 MET cc_start: -0.1853 (tpt) cc_final: -0.2447 (tpt) REVERT: H 195 MET cc_start: 0.0152 (mmp) cc_final: -0.1016 (tpt) REVERT: H 266 MET cc_start: -0.1846 (mtm) cc_final: -0.2061 (mtm) REVERT: I 143 MET cc_start: -0.2339 (tpt) cc_final: -0.2851 (tpt) REVERT: I 195 MET cc_start: 0.0287 (mmp) cc_final: -0.0695 (tpt) REVERT: J 143 MET cc_start: -0.2137 (tpt) cc_final: -0.2774 (tpt) REVERT: J 266 MET cc_start: -0.1979 (mtm) cc_final: -0.2331 (mtm) REVERT: K 113 MET cc_start: 0.1136 (mtt) cc_final: 0.0295 (mtp) REVERT: K 143 MET cc_start: -0.1568 (ttt) cc_final: -0.2006 (ttt) REVERT: K 195 MET cc_start: -0.0368 (mmp) cc_final: -0.1907 (tpt) REVERT: L 143 MET cc_start: -0.1573 (ttt) cc_final: -0.2090 (ttt) REVERT: L 195 MET cc_start: -0.0445 (mmp) cc_final: -0.1625 (tpt) REVERT: L 295 ASN cc_start: 0.4803 (p0) cc_final: 0.4271 (m110) REVERT: A 41 MET cc_start: 0.1153 (mmm) cc_final: 0.0705 (mmm) REVERT: A 113 MET cc_start: 0.1080 (mtt) cc_final: 0.0840 (mtp) REVERT: A 143 MET cc_start: -0.1785 (ttt) cc_final: -0.2178 (ttt) REVERT: A 195 MET cc_start: -0.0479 (mmp) cc_final: -0.1874 (tpt) REVERT: M 195 MET cc_start: -0.0913 (mmp) cc_final: -0.1974 (tpt) REVERT: N 113 MET cc_start: 0.1059 (mtt) cc_final: 0.0805 (mtp) REVERT: N 195 MET cc_start: -0.0644 (mmp) cc_final: -0.1757 (tpt) REVERT: N 295 ASN cc_start: 0.5000 (p0) cc_final: 0.4366 (m-40) REVERT: O 113 MET cc_start: 0.0965 (mtt) cc_final: 0.0618 (mtp) REVERT: O 143 MET cc_start: -0.1870 (ttt) cc_final: -0.2289 (ttt) REVERT: O 195 MET cc_start: -0.1360 (mmp) cc_final: -0.1998 (tpt) REVERT: O 295 ASN cc_start: 0.5249 (p0) cc_final: 0.4250 (m110) REVERT: P 143 MET cc_start: -0.2070 (ttt) cc_final: -0.2456 (ttt) REVERT: P 195 MET cc_start: -0.1196 (mmp) cc_final: -0.2106 (tpt) REVERT: P 295 ASN cc_start: 0.5098 (p0) cc_final: 0.4358 (m-40) REVERT: Q 113 MET cc_start: -0.1263 (mtm) cc_final: -0.1706 (mtp) REVERT: Q 143 MET cc_start: -0.1673 (ttt) cc_final: -0.2994 (ttt) REVERT: Q 195 MET cc_start: -0.0578 (mmp) cc_final: -0.1453 (tpt) REVERT: Q 204 ASP cc_start: 0.2479 (t0) cc_final: 0.2261 (m-30) REVERT: Q 295 ASN cc_start: 0.5453 (p0) cc_final: 0.4655 (m-40) REVERT: R 143 MET cc_start: -0.2427 (tpt) cc_final: -0.2700 (tpt) REVERT: R 195 MET cc_start: -0.0376 (mmp) cc_final: -0.1219 (tpt) REVERT: R 266 MET cc_start: -0.2277 (mtm) cc_final: -0.2971 (ttm) REVERT: R 295 ASN cc_start: 0.5359 (p0) cc_final: 0.4398 (m110) REVERT: S 195 MET cc_start: -0.0472 (mmp) cc_final: -0.0948 (tpt) REVERT: T 143 MET cc_start: -0.1682 (ttt) cc_final: -0.2101 (ttt) REVERT: T 195 MET cc_start: 0.0588 (tpt) cc_final: 0.0253 (tpp) REVERT: T 266 MET cc_start: -0.2236 (mtm) cc_final: -0.2764 (ttm) REVERT: U 204 ASP cc_start: 0.3145 (t0) cc_final: 0.2858 (m-30) REVERT: V 266 MET cc_start: -0.2404 (mtm) cc_final: -0.3013 (ttm) outliers start: 0 outliers final: 0 residues processed: 614 average time/residue: 0.6076 time to fit residues: 654.0618 Evaluate side-chains 452 residues out of total 7084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 452 time to evaluate : 4.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 880 random chunks: chunk 444 optimal weight: 9.9990 chunk 248 optimal weight: 10.0000 chunk 665 optimal weight: 20.0000 chunk 544 optimal weight: 30.0000 chunk 220 optimal weight: 0.2980 chunk 800 optimal weight: 0.0970 chunk 864 optimal weight: 30.0000 chunk 712 optimal weight: 9.9990 chunk 793 optimal weight: 0.7980 chunk 272 optimal weight: 7.9990 chunk 642 optimal weight: 10.0000 overall best weight: 3.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 GLN B 307 GLN B 313 GLN B 380 ASN ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 GLN C 307 GLN C 313 GLN C 380 ASN ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 205 ASN D 212 HIS D 267 GLN D 307 GLN D 309 GLN D 313 GLN D 380 ASN ** E 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 196 ASN E 205 ASN E 212 HIS ** E 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 281 ASN ** E 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 313 GLN E 378 GLN E 380 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 196 ASN F 212 HIS F 267 GLN F 281 ASN F 313 GLN F 380 ASN ** G 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 205 ASN G 269 ASN G 281 ASN G 307 GLN G 309 GLN G 313 GLN ** G 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 205 ASN ** H 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 322 ASN H 378 GLN ** I 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 281 ASN ** I 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 378 GLN ** J 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 196 ASN J 267 GLN ** J 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 269 ASN K 307 GLN ** K 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 378 GLN ** L 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 267 GLN L 269 ASN L 313 GLN ** L 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 378 GLN ** A 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 ASN A 267 GLN A 307 GLN A 313 GLN ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 GLN ** M 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 313 GLN ** M 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 378 GLN ** N 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 269 ASN ** N 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 267 GLN ** O 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 313 GLN ** O 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 322 ASN ** P 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 189 GLN P 191 ASN P 267 GLN ** P 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 313 GLN ** P 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 322 ASN P 380 ASN ** Q 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 191 ASN ** Q 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 212 HIS R 307 GLN ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 212 HIS ** S 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 189 GLN T 191 ASN T 212 HIS T 251 ASN ** T 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 196 ASN U 212 HIS U 268 GLN ** U 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 322 ASN V 196 ASN V 212 HIS V 281 ASN ** V 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 322 ASN Total number of N/Q/H flips: 81 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1440 moved from start: 0.4841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 66044 Z= 0.272 Angle : 0.838 14.091 89980 Z= 0.461 Chirality : 0.048 0.197 10560 Planarity : 0.005 0.149 12078 Dihedral : 5.936 27.279 9196 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.75 % Allowed : 7.82 % Favored : 91.43 % Rotamer: Outliers : 0.07 % Allowed : 2.27 % Favored : 97.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.51 % 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: -0.37 (0.09), residues: 8800 helix: 2.69 (0.12), residues: 1210 sheet: -0.97 (0.10), residues: 2618 loop : -0.52 (0.09), residues: 4972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.005 TRP O 207 HIS 0.002 0.001 HIS C 212 PHE 0.022 0.003 PHE N 231 TYR 0.031 0.003 TYR N 177 ARG 0.020 0.001 ARG N 402 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17600 Ramachandran restraints generated. 8800 Oldfield, 0 Emsley, 8800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17600 Ramachandran restraints generated. 8800 Oldfield, 0 Emsley, 8800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 7084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 546 time to evaluate : 5.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 113 MET cc_start: 0.0221 (mtt) cc_final: -0.0016 (mtp) REVERT: B 143 MET cc_start: -0.2088 (ttt) cc_final: -0.2466 (ttt) REVERT: C 110 MET cc_start: 0.2342 (tmm) cc_final: 0.1390 (ttt) REVERT: C 143 MET cc_start: -0.2270 (tpt) cc_final: -0.2712 (tpt) REVERT: C 266 MET cc_start: -0.3201 (mtt) cc_final: -0.3782 (ttm) REVERT: D 143 MET cc_start: -0.2182 (tpt) cc_final: -0.2840 (tpt) REVERT: D 195 MET cc_start: -0.0095 (mmp) cc_final: -0.0772 (tpp) REVERT: D 266 MET cc_start: -0.2730 (mtt) cc_final: -0.3781 (ttm) REVERT: E 110 MET cc_start: 0.3039 (tmm) cc_final: 0.2323 (ttt) REVERT: E 143 MET cc_start: -0.2594 (tpt) cc_final: -0.3012 (tpt) REVERT: E 266 MET cc_start: -0.2953 (mtt) cc_final: -0.4061 (ttm) REVERT: F 110 MET cc_start: 0.2441 (tmm) cc_final: 0.1202 (ttt) REVERT: F 113 MET cc_start: 0.0293 (mtt) cc_final: 0.0035 (mtp) REVERT: G 113 MET cc_start: 0.0628 (mtt) cc_final: 0.0355 (mtp) REVERT: G 143 MET cc_start: -0.2493 (tpt) cc_final: -0.3017 (tpt) REVERT: G 266 MET cc_start: -0.1861 (mtm) cc_final: -0.2404 (mtt) REVERT: H 31 PHE cc_start: 0.5555 (t80) cc_final: 0.5122 (t80) REVERT: H 143 MET cc_start: -0.2174 (tpt) cc_final: -0.2618 (tpt) REVERT: I 143 MET cc_start: -0.2398 (tpt) cc_final: -0.2964 (tpt) REVERT: J 113 MET cc_start: -0.0505 (ttp) cc_final: -0.1214 (ttp) REVERT: J 143 MET cc_start: -0.2078 (tpt) cc_final: -0.2589 (tpt) REVERT: K 143 MET cc_start: -0.1952 (ttt) cc_final: -0.2307 (ttt) REVERT: K 195 MET cc_start: -0.0213 (mmp) cc_final: -0.2113 (tpt) REVERT: L 195 MET cc_start: -0.0535 (mmp) cc_final: -0.2052 (tpt) REVERT: L 266 MET cc_start: -0.3444 (mtt) cc_final: -0.4511 (ttm) REVERT: L 295 ASN cc_start: 0.4872 (p0) cc_final: 0.4310 (m-40) REVERT: A 40 ASP cc_start: 0.1218 (OUTLIER) cc_final: 0.0854 (m-30) REVERT: A 143 MET cc_start: -0.2087 (ttt) cc_final: -0.3544 (mpp) REVERT: A 266 MET cc_start: -0.3203 (mtt) cc_final: -0.4391 (ttm) REVERT: A 295 ASN cc_start: 0.5378 (p0) cc_final: 0.4095 (m110) REVERT: M 266 MET cc_start: -0.3115 (mtt) cc_final: -0.4225 (ttm) REVERT: M 295 ASN cc_start: 0.5301 (p0) cc_final: 0.4141 (m-40) REVERT: N 295 ASN cc_start: 0.5511 (p0) cc_final: 0.4249 (m-40) REVERT: O 143 MET cc_start: -0.2569 (ttt) cc_final: -0.4098 (mmt) REVERT: O 195 MET cc_start: -0.1199 (mmp) cc_final: -0.1953 (tpt) REVERT: P 143 MET cc_start: -0.2194 (ttt) cc_final: -0.2552 (ttt) REVERT: P 195 MET cc_start: -0.0955 (mmp) cc_final: -0.2156 (tpt) REVERT: P 295 ASN cc_start: 0.5227 (p0) cc_final: 0.4175 (m110) REVERT: Q 113 MET cc_start: -0.1418 (mtm) cc_final: -0.1816 (mtp) REVERT: Q 143 MET cc_start: -0.1837 (ttt) cc_final: -0.2874 (ttt) REVERT: Q 195 MET cc_start: -0.0287 (mmp) cc_final: -0.1497 (tpt) REVERT: Q 204 ASP cc_start: 0.2319 (t0) cc_final: 0.2009 (m-30) REVERT: Q 266 MET cc_start: -0.3062 (mtm) cc_final: -0.3515 (mtt) REVERT: Q 295 ASN cc_start: 0.5431 (p0) cc_final: 0.4600 (m110) REVERT: R 195 MET cc_start: 0.0057 (mmp) cc_final: -0.1089 (tpt) REVERT: R 292 GLN cc_start: 0.4125 (tp-100) cc_final: 0.3901 (tp-100) REVERT: R 295 ASN cc_start: 0.5352 (p0) cc_final: 0.4145 (m110) REVERT: S 195 MET cc_start: -0.0265 (mmp) cc_final: -0.1374 (tpt) REVERT: S 266 MET cc_start: -0.4121 (mtm) cc_final: -0.4617 (ttm) REVERT: S 295 ASN cc_start: 0.5799 (p0) cc_final: 0.4851 (m-40) REVERT: T 143 MET cc_start: -0.1947 (ttt) cc_final: -0.3139 (ttt) REVERT: T 292 GLN cc_start: 0.4105 (tp-100) cc_final: 0.3821 (tp-100) REVERT: U 204 ASP cc_start: 0.2815 (t0) cc_final: 0.2545 (m-30) outliers start: 5 outliers final: 2 residues processed: 550 average time/residue: 0.5987 time to fit residues: 571.0280 Evaluate side-chains 429 residues out of total 7084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 426 time to evaluate : 4.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 880 random chunks: chunk 790 optimal weight: 6.9990 chunk 601 optimal weight: 3.9990 chunk 415 optimal weight: 7.9990 chunk 88 optimal weight: 0.8980 chunk 382 optimal weight: 3.9990 chunk 537 optimal weight: 7.9990 chunk 803 optimal weight: 9.9990 chunk 850 optimal weight: 2.9990 chunk 419 optimal weight: 6.9990 chunk 761 optimal weight: 5.9990 chunk 229 optimal weight: 20.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** B 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 380 ASN C 25 ASN C 212 HIS ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 ASN ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 307 GLN ** E 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 212 HIS ** G 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 380 ASN H 25 ASN H 212 HIS H 281 ASN H 307 GLN ** H 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 212 HIS I 307 GLN I 309 GLN ** I 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 212 HIS ** J 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 309 GLN ** J 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 212 HIS K 292 GLN ** K 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 380 ASN ** L 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 212 HIS L 292 GLN ** L 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 307 GLN ** L 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 25 ASN A 212 HIS ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 189 GLN M 212 HIS M 307 GLN ** M 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 196 ASN N 212 HIS N 307 GLN ** N 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 196 ASN O 212 HIS O 268 GLN O 292 GLN O 307 GLN ** O 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 196 ASN P 212 HIS P 307 GLN ** P 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 25 ASN ** Q 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 292 GLN Q 307 GLN ** Q 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 380 ASN S 78 GLN ** S 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 307 GLN ** T 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 380 ASN ** U 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 78 GLN ** V 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1537 moved from start: 0.5610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 66044 Z= 0.238 Angle : 0.769 13.920 89980 Z= 0.417 Chirality : 0.046 0.226 10560 Planarity : 0.004 0.052 12078 Dihedral : 5.784 25.760 9196 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 1.00 % Allowed : 6.75 % Favored : 92.25 % Rotamer: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.51 % 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: -0.34 (0.09), residues: 8800 helix: 2.87 (0.13), residues: 1188 sheet: -0.89 (0.10), residues: 2574 loop : -0.58 (0.09), residues: 5038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP N 207 HIS 0.002 0.001 HIS E 212 PHE 0.021 0.002 PHE M 42 TYR 0.022 0.002 TYR F 303 ARG 0.009 0.001 ARG L 402 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17600 Ramachandran restraints generated. 8800 Oldfield, 0 Emsley, 8800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17600 Ramachandran restraints generated. 8800 Oldfield, 0 Emsley, 8800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 7084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 535 time to evaluate : 4.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 143 MET cc_start: -0.2013 (ttt) cc_final: -0.2455 (ttt) REVERT: B 195 MET cc_start: -0.0144 (mmp) cc_final: -0.0405 (tpp) REVERT: C 110 MET cc_start: 0.2475 (tmm) cc_final: 0.1586 (ttt) REVERT: C 143 MET cc_start: -0.2085 (tpt) cc_final: -0.2687 (tpt) REVERT: C 195 MET cc_start: 0.0511 (mmp) cc_final: -0.0738 (tpt) REVERT: C 266 MET cc_start: -0.3677 (mtt) cc_final: -0.4621 (ttm) REVERT: D 110 MET cc_start: 0.3159 (tmm) cc_final: 0.2723 (tmm) REVERT: D 143 MET cc_start: -0.2293 (tpt) cc_final: -0.2945 (tpt) REVERT: D 195 MET cc_start: 0.0068 (mmp) cc_final: -0.1334 (tpt) REVERT: E 110 MET cc_start: 0.3135 (tmm) cc_final: 0.2385 (ttt) REVERT: E 143 MET cc_start: -0.2646 (tpt) cc_final: -0.3199 (tpt) REVERT: E 195 MET cc_start: 0.0253 (mmp) cc_final: -0.1249 (tpt) REVERT: F 110 MET cc_start: 0.3073 (tmm) cc_final: 0.2635 (tmm) REVERT: G 143 MET cc_start: -0.2536 (tpt) cc_final: -0.3093 (tpt) REVERT: G 402 ARG cc_start: 0.2010 (mmp80) cc_final: 0.1667 (mtm110) REVERT: H 143 MET cc_start: -0.2181 (tpt) cc_final: -0.2661 (tpt) REVERT: H 195 MET cc_start: 0.0280 (mmp) cc_final: -0.0829 (tpt) REVERT: I 143 MET cc_start: -0.2437 (tpt) cc_final: -0.2968 (tpt) REVERT: I 295 ASN cc_start: 0.5373 (p0) cc_final: 0.4760 (m-40) REVERT: J 113 MET cc_start: -0.0411 (ttp) cc_final: -0.0888 (ttp) REVERT: J 143 MET cc_start: -0.2020 (tpt) cc_final: -0.2627 (tpt) REVERT: J 231 PHE cc_start: 0.0927 (m-80) cc_final: -0.0121 (m-80) REVERT: J 292 GLN cc_start: 0.4424 (tp-100) cc_final: 0.4217 (tp40) REVERT: K 143 MET cc_start: -0.2006 (ttt) cc_final: -0.2482 (ttt) REVERT: K 195 MET cc_start: -0.0380 (mmp) cc_final: -0.1480 (tpp) REVERT: L 143 MET cc_start: -0.1671 (ttp) cc_final: -0.2783 (mtt) REVERT: L 195 MET cc_start: -0.0220 (mmp) cc_final: -0.1808 (tpt) REVERT: L 295 ASN cc_start: 0.5063 (p0) cc_final: 0.4353 (m-40) REVERT: A 143 MET cc_start: -0.2115 (ttt) cc_final: -0.3706 (mmm) REVERT: A 195 MET cc_start: -0.0346 (mmp) cc_final: -0.1891 (tpt) REVERT: A 295 ASN cc_start: 0.5430 (p0) cc_final: 0.4116 (m110) REVERT: M 65 THR cc_start: 0.7021 (t) cc_final: 0.6631 (p) REVERT: M 195 MET cc_start: -0.0902 (mmp) cc_final: -0.1914 (mmm) REVERT: M 295 ASN cc_start: 0.5258 (p0) cc_final: 0.4093 (m-40) REVERT: N 143 MET cc_start: -0.2175 (ttt) cc_final: -0.3470 (ttt) REVERT: N 195 MET cc_start: -0.0774 (mmp) cc_final: -0.1932 (tpt) REVERT: N 295 ASN cc_start: 0.5673 (p0) cc_final: 0.4360 (m-40) REVERT: O 143 MET cc_start: -0.2450 (ttt) cc_final: -0.4069 (mmm) REVERT: O 292 GLN cc_start: 0.4172 (tp-100) cc_final: 0.3939 (tp-100) REVERT: P 143 MET cc_start: -0.2349 (ttt) cc_final: -0.2744 (ttt) REVERT: P 195 MET cc_start: -0.0847 (mmp) cc_final: -0.1488 (tpp) REVERT: P 295 ASN cc_start: 0.5214 (p0) cc_final: 0.4102 (m110) REVERT: Q 113 MET cc_start: -0.1401 (mtm) cc_final: -0.1835 (mtp) REVERT: Q 143 MET cc_start: -0.1757 (ttt) cc_final: -0.2923 (ttt) REVERT: Q 195 MET cc_start: -0.0309 (mmp) cc_final: -0.1482 (tpt) REVERT: Q 204 ASP cc_start: 0.2338 (t0) cc_final: 0.2074 (m-30) REVERT: Q 292 GLN cc_start: 0.4280 (tp-100) cc_final: 0.4020 (tp-100) REVERT: Q 295 ASN cc_start: 0.5563 (p0) cc_final: 0.4684 (m110) REVERT: R 195 MET cc_start: 0.0199 (mmp) cc_final: -0.1408 (tpt) REVERT: R 266 MET cc_start: -0.2065 (mtm) cc_final: -0.2512 (mtt) REVERT: R 295 ASN cc_start: 0.5460 (p0) cc_final: 0.4227 (m-40) REVERT: S 143 MET cc_start: -0.0735 (mmt) cc_final: -0.1241 (mmt) REVERT: S 195 MET cc_start: -0.0385 (mmp) cc_final: -0.1384 (tpt) REVERT: S 295 ASN cc_start: 0.5907 (p0) cc_final: 0.4916 (m-40) REVERT: T 143 MET cc_start: -0.2112 (ttt) cc_final: -0.3158 (ttt) REVERT: T 295 ASN cc_start: 0.5596 (p0) cc_final: 0.4421 (m-40) REVERT: U 204 ASP cc_start: 0.2894 (t0) cc_final: 0.2578 (m-30) REVERT: U 295 ASN cc_start: 0.5549 (p0) cc_final: 0.4405 (m-40) REVERT: U 364 ASN cc_start: 0.4973 (p0) cc_final: 0.4010 (m110) REVERT: V 266 MET cc_start: -0.2237 (mtm) cc_final: -0.2760 (mtt) outliers start: 0 outliers final: 0 residues processed: 535 average time/residue: 0.5855 time to fit residues: 541.5274 Evaluate side-chains 436 residues out of total 7084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 436 time to evaluate : 4.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 880 random chunks: chunk 708 optimal weight: 0.0980 chunk 482 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 chunk 633 optimal weight: 10.0000 chunk 350 optimal weight: 0.5980 chunk 725 optimal weight: 7.9990 chunk 587 optimal weight: 7.9990 chunk 1 optimal weight: 9.9990 chunk 434 optimal weight: 0.8980 chunk 763 optimal weight: 10.0000 chunk 214 optimal weight: 7.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 212 HIS B 267 GLN ** B 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 ASN C 267 GLN ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 382 GLN C 386 GLN ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 382 GLN ** E 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 267 GLN ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 386 GLN ** G 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 382 GLN ** H 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 382 GLN ** I 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 382 GLN J 267 GLN ** J 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 382 GLN ** K 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 267 GLN L 292 GLN ** L 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 382 GLN ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 382 GLN ** N 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 267 GLN ** O 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 267 GLN ** P 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 189 GLN Q 212 HIS Q 251 ASN ** Q 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 251 ASN ** R 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1523 moved from start: 0.6077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 66044 Z= 0.181 Angle : 0.693 13.230 89980 Z= 0.377 Chirality : 0.045 0.185 10560 Planarity : 0.004 0.048 12078 Dihedral : 5.275 25.892 9196 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 1.15 % Allowed : 6.30 % Favored : 92.56 % Rotamer: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.51 % 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: -0.12 (0.09), residues: 8800 helix: 3.26 (0.13), residues: 1210 sheet: -0.23 (0.11), residues: 2266 loop : -0.82 (0.08), residues: 5324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 207 HIS 0.002 0.001 HIS C 212 PHE 0.017 0.002 PHE S 231 TYR 0.030 0.002 TYR F 303 ARG 0.007 0.001 ARG S 402 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17600 Ramachandran restraints generated. 8800 Oldfield, 0 Emsley, 8800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17600 Ramachandran restraints generated. 8800 Oldfield, 0 Emsley, 8800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 7084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 510 time to evaluate : 4.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 143 MET cc_start: -0.2207 (ttt) cc_final: -0.2605 (ttt) REVERT: C 110 MET cc_start: 0.2608 (tmm) cc_final: 0.1792 (ttt) REVERT: C 195 MET cc_start: 0.0598 (mmp) cc_final: -0.0792 (tpt) REVERT: C 266 MET cc_start: -0.3654 (mtt) cc_final: -0.4522 (ttm) REVERT: D 110 MET cc_start: 0.2810 (tmm) cc_final: 0.2581 (tmm) REVERT: D 143 MET cc_start: -0.2278 (tpt) cc_final: -0.2960 (tpt) REVERT: D 195 MET cc_start: 0.0435 (mmp) cc_final: -0.1135 (tpt) REVERT: D 266 MET cc_start: -0.3003 (mtt) cc_final: -0.4184 (ttm) REVERT: E 110 MET cc_start: 0.3306 (tmm) cc_final: 0.2653 (ttt) REVERT: E 143 MET cc_start: -0.2417 (tpt) cc_final: -0.3084 (tpt) REVERT: E 195 MET cc_start: 0.0489 (mmp) cc_final: -0.1096 (tpt) REVERT: E 266 MET cc_start: -0.2879 (mtt) cc_final: -0.4145 (ttm) REVERT: F 110 MET cc_start: 0.2878 (tmm) cc_final: 0.2512 (tmm) REVERT: F 295 ASN cc_start: 0.5815 (p0) cc_final: 0.4691 (m-40) REVERT: G 143 MET cc_start: -0.2613 (tpt) cc_final: -0.3134 (tpt) REVERT: G 266 MET cc_start: -0.2954 (mtt) cc_final: -0.3380 (mtm) REVERT: G 295 ASN cc_start: 0.5532 (p0) cc_final: 0.4539 (m-40) REVERT: H 143 MET cc_start: -0.2204 (tpt) cc_final: -0.2806 (tpt) REVERT: H 195 MET cc_start: 0.0316 (mmp) cc_final: -0.0758 (tpt) REVERT: H 231 PHE cc_start: 0.1206 (m-80) cc_final: 0.0061 (m-80) REVERT: I 143 MET cc_start: -0.2456 (tpt) cc_final: -0.3018 (tpt) REVERT: I 292 GLN cc_start: 0.4599 (tp-100) cc_final: 0.4372 (tp-100) REVERT: I 295 ASN cc_start: 0.5315 (p0) cc_final: 0.4752 (m-40) REVERT: J 143 MET cc_start: -0.2139 (tpt) cc_final: -0.2682 (tpt) REVERT: K 143 MET cc_start: -0.1982 (ttt) cc_final: -0.2258 (ttt) REVERT: K 195 MET cc_start: -0.0366 (mmp) cc_final: -0.1435 (tpp) REVERT: L 143 MET cc_start: -0.1774 (ttp) cc_final: -0.2690 (mtt) REVERT: L 195 MET cc_start: -0.0224 (mmp) cc_final: -0.1067 (tpp) REVERT: L 266 MET cc_start: -0.3824 (mtt) cc_final: -0.4983 (ttm) REVERT: L 295 ASN cc_start: 0.4927 (p0) cc_final: 0.4296 (m-40) REVERT: A 65 THR cc_start: 0.7402 (t) cc_final: 0.6950 (p) REVERT: A 143 MET cc_start: -0.2254 (ttt) cc_final: -0.3388 (ttt) REVERT: A 195 MET cc_start: -0.0362 (mmp) cc_final: -0.1686 (tpt) REVERT: A 295 ASN cc_start: 0.5408 (p0) cc_final: 0.4136 (m110) REVERT: M 65 THR cc_start: 0.7190 (t) cc_final: 0.6676 (p) REVERT: M 113 MET cc_start: 0.0008 (mtm) cc_final: -0.0722 (mtp) REVERT: M 143 MET cc_start: -0.1984 (ttt) cc_final: -0.3369 (ttt) REVERT: M 195 MET cc_start: -0.0893 (mmp) cc_final: -0.1884 (mmm) REVERT: M 295 ASN cc_start: 0.5357 (p0) cc_final: 0.4206 (m-40) REVERT: N 65 THR cc_start: 0.7175 (t) cc_final: 0.6746 (p) REVERT: N 110 MET cc_start: 0.1585 (ttt) cc_final: 0.1364 (tmm) REVERT: N 143 MET cc_start: -0.2407 (ttt) cc_final: -0.2994 (ppp) REVERT: N 195 MET cc_start: -0.0801 (mmp) cc_final: -0.2319 (ttt) REVERT: N 295 ASN cc_start: 0.5566 (p0) cc_final: 0.4366 (m110) REVERT: O 143 MET cc_start: -0.2928 (ttt) cc_final: -0.3936 (ttt) REVERT: O 292 GLN cc_start: 0.4033 (tp-100) cc_final: 0.3769 (tp-100) REVERT: P 65 THR cc_start: 0.7711 (t) cc_final: 0.7253 (p) REVERT: P 143 MET cc_start: -0.2454 (ttt) cc_final: -0.3624 (ttt) REVERT: P 195 MET cc_start: -0.0894 (mmp) cc_final: -0.1446 (tpp) REVERT: P 295 ASN cc_start: 0.5119 (p0) cc_final: 0.4062 (m110) REVERT: Q 113 MET cc_start: -0.1369 (mtm) cc_final: -0.1897 (mtp) REVERT: Q 143 MET cc_start: -0.2036 (ttt) cc_final: -0.3030 (ttt) REVERT: Q 195 MET cc_start: -0.0308 (mmp) cc_final: -0.1608 (tpt) REVERT: Q 292 GLN cc_start: 0.4396 (tp-100) cc_final: 0.4092 (tp-100) REVERT: Q 295 ASN cc_start: 0.5529 (p0) cc_final: 0.4667 (m110) REVERT: R 65 THR cc_start: 0.7172 (t) cc_final: 0.6719 (p) REVERT: R 195 MET cc_start: 0.0222 (mmp) cc_final: -0.0976 (tpt) REVERT: R 266 MET cc_start: -0.2257 (mtm) cc_final: -0.2691 (mtt) REVERT: R 295 ASN cc_start: 0.5451 (p0) cc_final: 0.4384 (m-40) REVERT: S 65 THR cc_start: 0.7285 (t) cc_final: 0.6896 (p) REVERT: S 143 MET cc_start: -0.1023 (mmt) cc_final: -0.1256 (mmt) REVERT: S 195 MET cc_start: -0.0390 (mmp) cc_final: -0.0647 (tpt) REVERT: S 295 ASN cc_start: 0.5857 (p0) cc_final: 0.4905 (m-40) REVERT: T 143 MET cc_start: -0.2450 (ttt) cc_final: -0.3369 (ttt) REVERT: T 295 ASN cc_start: 0.5581 (p0) cc_final: 0.4455 (m-40) REVERT: U 295 ASN cc_start: 0.5495 (p0) cc_final: 0.4476 (m-40) REVERT: U 364 ASN cc_start: 0.4967 (p0) cc_final: 0.4120 (m-40) REVERT: V 266 MET cc_start: -0.2281 (mtm) cc_final: -0.2818 (ttm) REVERT: V 364 ASN cc_start: 0.4894 (p0) cc_final: 0.3803 (m-40) outliers start: 0 outliers final: 0 residues processed: 510 average time/residue: 0.5690 time to fit residues: 507.9609 Evaluate side-chains 420 residues out of total 7084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 420 time to evaluate : 4.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 880 random chunks: chunk 286 optimal weight: 20.0000 chunk 766 optimal weight: 8.9990 chunk 168 optimal weight: 10.0000 chunk 499 optimal weight: 30.0000 chunk 209 optimal weight: 6.9990 chunk 851 optimal weight: 6.9990 chunk 706 optimal weight: 8.9990 chunk 394 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 281 optimal weight: 3.9990 chunk 446 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 4 GLN B 280 GLN ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 322 ASN B 382 GLN B 386 GLN C 4 GLN C 25 ASN ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 322 ASN ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 322 ASN D 386 GLN ** E 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 322 ASN E 386 GLN ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 322 ASN F 382 GLN ** G 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 4 GLN ** H 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 25 ASN H 281 ASN ** H 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 380 ASN ** I 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 380 ASN I 386 GLN ** J 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 292 GLN ** J 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 380 ASN ** K 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 382 GLN ** L 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 292 GLN ** L 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 GLN ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 280 GLN ** N 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 382 GLN ** N 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 268 GLN ** O 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 380 ASN O 382 GLN ** P 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 280 GLN ** P 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 382 GLN ** Q 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 251 ASN ** Q 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 328 GLN ** R 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 251 ASN ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 251 ASN ** T 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1873 moved from start: 0.7287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 66044 Z= 0.266 Angle : 0.808 13.059 89980 Z= 0.432 Chirality : 0.048 0.248 10560 Planarity : 0.004 0.056 12078 Dihedral : 5.756 31.994 9196 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 1.24 % Allowed : 7.51 % Favored : 91.25 % Rotamer: Outliers : 0.04 % Allowed : 1.57 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.51 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.65 (0.09), residues: 8800 helix: 2.40 (0.14), residues: 1188 sheet: -0.53 (0.10), residues: 2332 loop : -1.07 (0.08), residues: 5280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP T 333 HIS 0.002 0.001 HIS A 193 PHE 0.028 0.002 PHE J 42 TYR 0.028 0.002 TYR F 303 ARG 0.006 0.001 ARG R 83 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17600 Ramachandran restraints generated. 8800 Oldfield, 0 Emsley, 8800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17600 Ramachandran restraints generated. 8800 Oldfield, 0 Emsley, 8800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 7084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 489 time to evaluate : 5.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 143 MET cc_start: -0.2062 (ttt) cc_final: -0.2500 (ttt) REVERT: B 195 MET cc_start: 0.0258 (mmp) cc_final: -0.0092 (tpp) REVERT: B 231 PHE cc_start: 0.1568 (m-80) cc_final: 0.0506 (m-80) REVERT: C 143 MET cc_start: -0.1569 (ttt) cc_final: -0.2438 (ttt) REVERT: C 266 MET cc_start: -0.3519 (mtt) cc_final: -0.4556 (ttm) REVERT: C 295 ASN cc_start: 0.5832 (p0) cc_final: 0.4647 (m-40) REVERT: D 110 MET cc_start: 0.3104 (tmm) cc_final: 0.2575 (tmm) REVERT: D 143 MET cc_start: -0.2107 (tpt) cc_final: -0.2933 (tpt) REVERT: E 110 MET cc_start: 0.3359 (tmm) cc_final: 0.2822 (ttt) REVERT: E 143 MET cc_start: -0.2199 (tpt) cc_final: -0.2983 (tpt) REVERT: E 195 MET cc_start: 0.0653 (mmp) cc_final: -0.1001 (tpt) REVERT: E 295 ASN cc_start: 0.5644 (p0) cc_final: 0.4412 (m-40) REVERT: F 110 MET cc_start: 0.3350 (tmm) cc_final: 0.2761 (tmm) REVERT: F 195 MET cc_start: 0.0312 (mmp) cc_final: -0.0935 (tpt) REVERT: F 295 ASN cc_start: 0.5940 (p0) cc_final: 0.4596 (m-40) REVERT: G 195 MET cc_start: 0.0870 (mmp) cc_final: -0.0642 (tpt) REVERT: G 266 MET cc_start: -0.3101 (mtt) cc_final: -0.3324 (mmt) REVERT: G 295 ASN cc_start: 0.5786 (p0) cc_final: 0.4516 (m-40) REVERT: H 195 MET cc_start: 0.0755 (mmp) cc_final: -0.0628 (tpt) REVERT: H 295 ASN cc_start: 0.5574 (p0) cc_final: 0.4333 (m-40) REVERT: I 143 MET cc_start: -0.2518 (tpt) cc_final: -0.3313 (tpt) REVERT: I 295 ASN cc_start: 0.5315 (p0) cc_final: 0.4264 (m-40) REVERT: J 143 MET cc_start: -0.2136 (tpt) cc_final: -0.2989 (tpt) REVERT: J 292 GLN cc_start: 0.4573 (tp-100) cc_final: 0.4364 (tp40) REVERT: J 295 ASN cc_start: 0.5532 (p0) cc_final: 0.4394 (m110) REVERT: K 143 MET cc_start: -0.2105 (ttt) cc_final: -0.2577 (ttt) REVERT: K 195 MET cc_start: -0.0180 (mmp) cc_final: -0.1320 (tpp) REVERT: K 295 ASN cc_start: 0.5055 (p0) cc_final: 0.4155 (m-40) REVERT: L 46 LYS cc_start: 0.4620 (mttt) cc_final: 0.4329 (mtmm) REVERT: L 143 MET cc_start: -0.2391 (ttp) cc_final: -0.3229 (mtt) REVERT: L 195 MET cc_start: 0.0109 (mmp) cc_final: -0.1484 (tpt) REVERT: L 266 MET cc_start: -0.3714 (mtt) cc_final: -0.5128 (ttm) REVERT: A 65 THR cc_start: 0.7732 (t) cc_final: 0.7190 (p) REVERT: A 143 MET cc_start: -0.2147 (ttt) cc_final: -0.3291 (ttt) REVERT: A 195 MET cc_start: -0.0032 (mmp) cc_final: -0.1443 (tpt) REVERT: M 65 THR cc_start: 0.7433 (t) cc_final: 0.6857 (p) REVERT: M 113 MET cc_start: 0.0035 (mtm) cc_final: -0.0267 (mtp) REVERT: M 195 MET cc_start: -0.0607 (mmp) cc_final: -0.1724 (mmm) REVERT: N 65 THR cc_start: 0.7397 (t) cc_final: 0.6917 (p) REVERT: N 195 MET cc_start: -0.0701 (mmp) cc_final: -0.1721 (tpp) REVERT: N 295 ASN cc_start: 0.5768 (p0) cc_final: 0.4235 (m110) REVERT: O 65 THR cc_start: 0.7603 (t) cc_final: 0.7017 (p) REVERT: O 143 MET cc_start: -0.2705 (ttt) cc_final: -0.3057 (ttt) REVERT: O 292 GLN cc_start: 0.4484 (tp-100) cc_final: 0.4197 (tp-100) REVERT: P 65 THR cc_start: 0.7792 (t) cc_final: 0.7243 (p) REVERT: P 143 MET cc_start: -0.2312 (ttt) cc_final: -0.2613 (ttt) REVERT: P 195 MET cc_start: -0.0805 (mmp) cc_final: -0.1263 (tpp) REVERT: Q 113 MET cc_start: -0.1203 (mtm) cc_final: -0.1532 (mtp) REVERT: Q 143 MET cc_start: -0.2107 (ttt) cc_final: -0.3126 (ttt) REVERT: Q 195 MET cc_start: 0.0122 (mmp) cc_final: -0.0526 (tpt) REVERT: Q 295 ASN cc_start: 0.5797 (p0) cc_final: 0.4783 (m-40) REVERT: R 65 THR cc_start: 0.7427 (t) cc_final: 0.6901 (p) REVERT: R 195 MET cc_start: 0.0184 (mmp) cc_final: -0.0835 (tpt) REVERT: R 266 MET cc_start: -0.2173 (mtm) cc_final: -0.2561 (mtt) REVERT: R 295 ASN cc_start: 0.5337 (p0) cc_final: 0.4150 (m110) REVERT: S 65 THR cc_start: 0.7670 (t) cc_final: 0.7189 (p) REVERT: S 195 MET cc_start: -0.0117 (mmp) cc_final: -0.0475 (tpt) REVERT: S 295 ASN cc_start: 0.6085 (p0) cc_final: 0.4838 (m-40) REVERT: T 266 MET cc_start: -0.2248 (mtm) cc_final: -0.2637 (mtt) REVERT: V 266 MET cc_start: -0.2467 (mtm) cc_final: -0.3170 (ttm) outliers start: 3 outliers final: 2 residues processed: 492 average time/residue: 0.5682 time to fit residues: 491.6803 Evaluate side-chains 419 residues out of total 7084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 417 time to evaluate : 4.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 880 random chunks: chunk 820 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 485 optimal weight: 2.9990 chunk 621 optimal weight: 0.0270 chunk 481 optimal weight: 5.9990 chunk 716 optimal weight: 20.0000 chunk 475 optimal weight: 6.9990 chunk 848 optimal weight: 8.9990 chunk 530 optimal weight: 0.9990 chunk 517 optimal weight: 3.9990 chunk 391 optimal weight: 1.9990 overall best weight: 2.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 ASN ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 ASN ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 328 GLN ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 GLN ** J 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 292 GLN ** K 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 292 GLN ** L 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 380 ASN ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 25 ASN A 267 GLN ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 189 GLN ** M 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 380 ASN N 280 GLN ** N 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 189 GLN P 191 ASN ** P 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 25 ASN ** Q 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 292 GLN ** Q 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 380 ASN T 189 GLN T 191 ASN ** T 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 268 GLN V 292 GLN ** V 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1760 moved from start: 0.7458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 66044 Z= 0.181 Angle : 0.687 12.126 89980 Z= 0.369 Chirality : 0.045 0.226 10560 Planarity : 0.004 0.053 12078 Dihedral : 5.283 31.934 9196 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 1.16 % Allowed : 6.19 % Favored : 92.65 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.51 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.33 (0.09), residues: 8800 helix: 2.98 (0.13), residues: 1188 sheet: -0.14 (0.10), residues: 2354 loop : -1.05 (0.08), residues: 5258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP V 333 HIS 0.003 0.001 HIS I 193 PHE 0.014 0.002 PHE E 42 TYR 0.022 0.002 TYR F 303 ARG 0.005 0.001 ARG R 95 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17600 Ramachandran restraints generated. 8800 Oldfield, 0 Emsley, 8800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17600 Ramachandran restraints generated. 8800 Oldfield, 0 Emsley, 8800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 7084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 496 time to evaluate : 4.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 143 MET cc_start: -0.1956 (ttt) cc_final: -0.2322 (ttt) REVERT: B 195 MET cc_start: 0.0372 (mmp) cc_final: 0.0020 (tpp) REVERT: B 231 PHE cc_start: 0.1566 (m-80) cc_final: 0.0432 (m-80) REVERT: C 143 MET cc_start: -0.1548 (ttt) cc_final: -0.2404 (ttt) REVERT: C 266 MET cc_start: -0.3530 (mtt) cc_final: -0.4563 (ttm) REVERT: D 110 MET cc_start: 0.3040 (tmm) cc_final: 0.2674 (tmm) REVERT: D 143 MET cc_start: -0.2372 (tpt) cc_final: -0.3058 (tpt) REVERT: D 195 MET cc_start: 0.0690 (mmp) cc_final: -0.0322 (tpp) REVERT: E 110 MET cc_start: 0.3206 (tmm) cc_final: 0.2731 (ttt) REVERT: E 195 MET cc_start: 0.0658 (mmp) cc_final: -0.0978 (tpt) REVERT: E 295 ASN cc_start: 0.5534 (p0) cc_final: 0.4456 (m-40) REVERT: F 110 MET cc_start: 0.3402 (tmm) cc_final: 0.2957 (tmm) REVERT: F 195 MET cc_start: 0.0420 (mmp) cc_final: -0.0974 (tpt) REVERT: F 295 ASN cc_start: 0.5817 (p0) cc_final: 0.4638 (m-40) REVERT: G 143 MET cc_start: -0.2140 (ttt) cc_final: -0.3442 (ttt) REVERT: G 195 MET cc_start: 0.0807 (mmp) cc_final: -0.0808 (tpt) REVERT: G 266 MET cc_start: -0.3069 (mtt) cc_final: -0.3336 (mmt) REVERT: G 295 ASN cc_start: 0.5510 (p0) cc_final: 0.4507 (m-40) REVERT: H 195 MET cc_start: 0.0732 (mmp) cc_final: -0.0655 (tpt) REVERT: H 231 PHE cc_start: 0.1410 (m-80) cc_final: 0.0094 (m-80) REVERT: H 295 ASN cc_start: 0.5312 (p0) cc_final: 0.4314 (m-40) REVERT: I 110 MET cc_start: 0.2381 (tmm) cc_final: 0.1380 (ttt) REVERT: I 143 MET cc_start: -0.2878 (tpt) cc_final: -0.3529 (tpt) REVERT: I 295 ASN cc_start: 0.5147 (p0) cc_final: 0.4249 (m-40) REVERT: J 143 MET cc_start: -0.2047 (tpt) cc_final: -0.2848 (tpt) REVERT: J 231 PHE cc_start: 0.1204 (m-80) cc_final: -0.0192 (m-80) REVERT: J 292 GLN cc_start: 0.4061 (tp-100) cc_final: 0.3856 (tp40) REVERT: J 295 ASN cc_start: 0.5363 (p0) cc_final: 0.4411 (m110) REVERT: K 143 MET cc_start: -0.2113 (ttt) cc_final: -0.2482 (ttt) REVERT: K 195 MET cc_start: -0.0130 (mmp) cc_final: -0.1148 (tpp) REVERT: K 295 ASN cc_start: 0.5070 (p0) cc_final: 0.4299 (m-40) REVERT: L 143 MET cc_start: -0.2261 (ttp) cc_final: -0.2891 (mtt) REVERT: L 177 TYR cc_start: 0.3365 (p90) cc_final: 0.3150 (p90) REVERT: L 195 MET cc_start: 0.0107 (mmp) cc_final: -0.1285 (tpt) REVERT: L 266 MET cc_start: -0.3805 (mtt) cc_final: -0.5241 (ttm) REVERT: A 65 THR cc_start: 0.7767 (t) cc_final: 0.7186 (p) REVERT: A 143 MET cc_start: -0.2246 (ttt) cc_final: -0.3388 (ttt) REVERT: A 195 MET cc_start: 0.0039 (mmp) cc_final: -0.1529 (tpt) REVERT: M 195 MET cc_start: -0.0623 (mmp) cc_final: -0.1671 (mmm) REVERT: N 65 THR cc_start: 0.7527 (t) cc_final: 0.6989 (p) REVERT: N 110 MET cc_start: 0.1575 (ttt) cc_final: 0.1361 (tmm) REVERT: N 143 MET cc_start: -0.2149 (ttt) cc_final: -0.3451 (ttt) REVERT: N 195 MET cc_start: -0.0804 (mmp) cc_final: -0.1783 (tpp) REVERT: N 295 ASN cc_start: 0.5603 (p0) cc_final: 0.4272 (m110) REVERT: O 143 MET cc_start: -0.3000 (ttt) cc_final: -0.4133 (ttt) REVERT: O 292 GLN cc_start: 0.4309 (tp-100) cc_final: 0.4023 (tp-100) REVERT: P 65 THR cc_start: 0.7892 (t) cc_final: 0.7312 (p) REVERT: P 143 MET cc_start: -0.2478 (ttt) cc_final: -0.3740 (ttt) REVERT: P 195 MET cc_start: -0.0737 (mmp) cc_final: -0.1303 (tpp) REVERT: P 295 ASN cc_start: 0.5219 (p0) cc_final: 0.4020 (m-40) REVERT: Q 113 MET cc_start: -0.1265 (mtm) cc_final: -0.1613 (mtp) REVERT: Q 143 MET cc_start: -0.2221 (ttt) cc_final: -0.3222 (ttt) REVERT: Q 195 MET cc_start: 0.0006 (mmp) cc_final: -0.0621 (tpt) REVERT: Q 292 GLN cc_start: 0.4332 (tp-100) cc_final: 0.4113 (tp-100) REVERT: Q 295 ASN cc_start: 0.5685 (p0) cc_final: 0.4810 (m-40) REVERT: R 65 THR cc_start: 0.7577 (t) cc_final: 0.6998 (p) REVERT: R 143 MET cc_start: -0.2588 (ttt) cc_final: -0.2823 (pmm) REVERT: R 195 MET cc_start: 0.0401 (mmp) cc_final: -0.1451 (tpt) REVERT: R 266 MET cc_start: -0.2244 (mtm) cc_final: -0.2549 (mtt) REVERT: R 295 ASN cc_start: 0.5280 (p0) cc_final: 0.4231 (m110) REVERT: S 65 THR cc_start: 0.7727 (t) cc_final: 0.7231 (p) REVERT: S 143 MET cc_start: -0.1842 (mmt) cc_final: -0.2208 (mmt) REVERT: S 195 MET cc_start: 0.0268 (mmp) cc_final: -0.0390 (tpt) REVERT: S 295 ASN cc_start: 0.5998 (p0) cc_final: 0.4892 (m-40) REVERT: T 143 MET cc_start: -0.2702 (ttt) cc_final: -0.3689 (ttt) REVERT: T 266 MET cc_start: -0.2283 (mtm) cc_final: -0.2598 (mtt) REVERT: U 364 ASN cc_start: 0.4543 (p0) cc_final: 0.4152 (m-40) REVERT: V 266 MET cc_start: -0.2386 (mtm) cc_final: -0.2719 (mtt) REVERT: V 364 ASN cc_start: 0.4696 (p0) cc_final: 0.4048 (m-40) outliers start: 0 outliers final: 0 residues processed: 496 average time/residue: 0.5581 time to fit residues: 487.9689 Evaluate side-chains 416 residues out of total 7084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 416 time to evaluate : 4.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 880 random chunks: chunk 524 optimal weight: 5.9990 chunk 338 optimal weight: 50.0000 chunk 506 optimal weight: 1.9990 chunk 255 optimal weight: 9.9990 chunk 166 optimal weight: 0.8980 chunk 164 optimal weight: 0.0970 chunk 539 optimal weight: 10.0000 chunk 577 optimal weight: 10.0000 chunk 419 optimal weight: 10.0000 chunk 79 optimal weight: 8.9990 chunk 666 optimal weight: 20.0000 overall best weight: 3.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 GLN ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 378 GLN ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 GLN ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 GLN ** E 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 328 GLN ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 GLN ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 280 GLN ** G 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 GLN J 280 GLN ** J 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 292 GLN ** L 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 GLN A 309 GLN ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 ASN A 382 GLN ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 380 ASN ** N 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 154 GLN ** N 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 380 ASN ** O 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 280 GLN ** O 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 380 ASN ** Q 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 251 ASN ** Q 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 380 ASN R 15 ASN ** R 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 15 ASN ** S 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 380 ASN T 15 ASN ** T 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 380 ASN V 58 GLN ** V 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1982 moved from start: 0.8212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 66044 Z= 0.233 Angle : 0.752 12.769 89980 Z= 0.403 Chirality : 0.046 0.230 10560 Planarity : 0.004 0.059 12078 Dihedral : 5.526 32.421 9196 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 1.00 % Allowed : 7.77 % Favored : 91.23 % Rotamer: Outliers : 0.10 % Allowed : 0.93 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.51 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.68 (0.09), residues: 8800 helix: 2.46 (0.13), residues: 1254 sheet: -0.89 (0.10), residues: 2310 loop : -0.97 (0.08), residues: 5236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP V 333 HIS 0.005 0.001 HIS J 193 PHE 0.018 0.002 PHE M 31 TYR 0.026 0.002 TYR F 303 ARG 0.007 0.001 ARG I 95 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17600 Ramachandran restraints generated. 8800 Oldfield, 0 Emsley, 8800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17600 Ramachandran restraints generated. 8800 Oldfield, 0 Emsley, 8800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 7084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 532 time to evaluate : 4.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 143 MET cc_start: -0.2005 (ttt) cc_final: -0.2402 (ttt) REVERT: C 110 MET cc_start: 0.2795 (tmm) cc_final: 0.1730 (ttt) REVERT: C 143 MET cc_start: -0.1828 (ttt) cc_final: -0.2484 (ttt) REVERT: C 266 MET cc_start: -0.3452 (mtt) cc_final: -0.4548 (ttm) REVERT: D 195 MET cc_start: 0.1004 (mmp) cc_final: -0.0674 (tpt) REVERT: D 231 PHE cc_start: 0.2185 (m-80) cc_final: 0.0583 (m-80) REVERT: E 110 MET cc_start: 0.3321 (tmm) cc_final: 0.2843 (ttt) REVERT: E 195 MET cc_start: 0.0988 (mmp) cc_final: -0.0836 (tpt) REVERT: E 295 ASN cc_start: 0.5735 (p0) cc_final: 0.4473 (m-40) REVERT: F 110 MET cc_start: 0.3512 (tmm) cc_final: 0.3093 (tmm) REVERT: F 195 MET cc_start: 0.0604 (mmp) cc_final: -0.0745 (tpt) REVERT: G 143 MET cc_start: -0.2239 (ttt) cc_final: -0.3407 (ttt) REVERT: G 195 MET cc_start: 0.0948 (mmp) cc_final: -0.0628 (tpt) REVERT: G 266 MET cc_start: -0.3139 (mtt) cc_final: -0.3372 (mmt) REVERT: G 295 ASN cc_start: 0.5526 (p0) cc_final: 0.4252 (m-40) REVERT: H 143 MET cc_start: -0.2313 (ttt) cc_final: -0.3523 (ttt) REVERT: H 195 MET cc_start: 0.0897 (mmp) cc_final: -0.0503 (tpt) REVERT: I 143 MET cc_start: -0.2574 (tpt) cc_final: -0.3376 (tpt) REVERT: I 195 MET cc_start: 0.1332 (mmp) cc_final: -0.0434 (tpt) REVERT: I 295 ASN cc_start: 0.5304 (p0) cc_final: 0.4230 (m-40) REVERT: J 292 GLN cc_start: 0.4220 (tp-100) cc_final: 0.4004 (tp40) REVERT: J 295 ASN cc_start: 0.5454 (p0) cc_final: 0.4460 (m110) REVERT: K 143 MET cc_start: -0.2300 (ttt) cc_final: -0.2715 (ttt) REVERT: K 195 MET cc_start: 0.0009 (mmp) cc_final: -0.1485 (tpt) REVERT: K 295 ASN cc_start: 0.5070 (p0) cc_final: 0.3887 (m-40) REVERT: L 143 MET cc_start: -0.2365 (ttp) cc_final: -0.3058 (mtt) REVERT: L 195 MET cc_start: 0.0343 (mmp) cc_final: -0.1105 (tpt) REVERT: A 65 THR cc_start: 0.7883 (t) cc_final: 0.7277 (p) REVERT: A 74 VAL cc_start: 0.4653 (m) cc_final: 0.3851 (t) REVERT: A 143 MET cc_start: -0.2118 (ttt) cc_final: -0.3321 (ttt) REVERT: M 65 THR cc_start: 0.7937 (t) cc_final: 0.7301 (p) REVERT: M 195 MET cc_start: -0.0523 (mmp) cc_final: -0.1590 (mmm) REVERT: N 65 THR cc_start: 0.7755 (t) cc_final: 0.7191 (p) REVERT: N 195 MET cc_start: -0.0706 (mmp) cc_final: -0.1861 (tpt) REVERT: N 295 ASN cc_start: 0.5657 (p0) cc_final: 0.4184 (m110) REVERT: O 29 TYR cc_start: 0.4947 (m-80) cc_final: 0.3840 (m-80) REVERT: O 143 MET cc_start: -0.2968 (ttt) cc_final: -0.3284 (ttt) REVERT: O 266 MET cc_start: -0.2060 (ttp) cc_final: -0.4930 (mtt) REVERT: O 292 GLN cc_start: 0.4353 (tp-100) cc_final: 0.4104 (tp-100) REVERT: P 143 MET cc_start: -0.2549 (ttt) cc_final: -0.3477 (mmt) REVERT: P 195 MET cc_start: -0.0789 (mmp) cc_final: -0.1243 (tpt) REVERT: Q 143 MET cc_start: -0.2341 (ttt) cc_final: -0.3332 (mmt) REVERT: Q 195 MET cc_start: -0.0054 (mmp) cc_final: -0.0541 (tpt) REVERT: Q 295 ASN cc_start: 0.5818 (p0) cc_final: 0.4771 (m-40) REVERT: Q 379 ARG cc_start: 0.3204 (mmp80) cc_final: 0.2860 (ttt180) REVERT: R 65 THR cc_start: 0.7803 (t) cc_final: 0.7199 (p) REVERT: R 143 MET cc_start: -0.2894 (ttt) cc_final: -0.4016 (ttt) REVERT: R 195 MET cc_start: 0.0247 (mmp) cc_final: -0.0867 (tpt) REVERT: R 266 MET cc_start: -0.2358 (mtm) cc_final: -0.2595 (mtt) REVERT: R 379 ARG cc_start: 0.2977 (mmp80) cc_final: 0.2646 (ttt180) REVERT: S 65 THR cc_start: 0.7940 (t) cc_final: 0.7376 (p) REVERT: S 143 MET cc_start: -0.1510 (mmt) cc_final: -0.1943 (mmt) REVERT: S 195 MET cc_start: -0.0058 (mmp) cc_final: -0.0423 (tpt) REVERT: S 379 ARG cc_start: 0.2687 (mmp80) cc_final: 0.2369 (ttt180) REVERT: T 266 MET cc_start: -0.2427 (mtm) cc_final: -0.2766 (mtt) REVERT: T 346 THR cc_start: 0.0936 (m) cc_final: 0.0718 (p) REVERT: U 346 THR cc_start: 0.1233 (m) cc_final: 0.1014 (p) REVERT: U 364 ASN cc_start: 0.4872 (p0) cc_final: 0.4602 (m-40) REVERT: V 266 MET cc_start: -0.2339 (mtm) cc_final: -0.2623 (mtt) REVERT: V 364 ASN cc_start: 0.4708 (p0) cc_final: 0.4268 (m-40) outliers start: 7 outliers final: 3 residues processed: 539 average time/residue: 0.5786 time to fit residues: 542.9712 Evaluate side-chains 448 residues out of total 7084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 445 time to evaluate : 4.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 880 random chunks: chunk 771 optimal weight: 0.0970 chunk 812 optimal weight: 3.9990 chunk 741 optimal weight: 20.0000 chunk 790 optimal weight: 3.9990 chunk 475 optimal weight: 9.9990 chunk 344 optimal weight: 8.9990 chunk 620 optimal weight: 7.9990 chunk 242 optimal weight: 7.9990 chunk 714 optimal weight: 30.0000 chunk 747 optimal weight: 0.0970 chunk 787 optimal weight: 8.9990 overall best weight: 3.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 GLN ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 378 GLN D 386 GLN ** E 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 328 GLN ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 154 GLN ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 378 GLN ** G 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 378 GLN H 280 GLN ** H 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 378 GLN ** H 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 280 GLN ** I 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 378 GLN ** K 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 292 GLN ** K 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 292 GLN ** L 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 GLN ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 378 GLN ** O 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 307 GLN ** Q 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 378 GLN ** R 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 307 GLN ** T 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 15 ASN ** U 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 292 GLN ** V 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1998 moved from start: 0.8594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 66044 Z= 0.211 Angle : 0.729 16.882 89980 Z= 0.390 Chirality : 0.046 0.241 10560 Planarity : 0.004 0.059 12078 Dihedral : 5.461 32.043 9196 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.92 % Allowed : 6.68 % Favored : 92.40 % Rotamer: Outliers : 0.04 % Allowed : 0.62 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.51 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.75 (0.09), residues: 8800 helix: 2.50 (0.13), residues: 1254 sheet: -0.97 (0.10), residues: 2332 loop : -1.03 (0.08), residues: 5214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 333 HIS 0.008 0.001 HIS C 193 PHE 0.030 0.002 PHE S 42 TYR 0.027 0.002 TYR N 303 ARG 0.009 0.001 ARG N 95 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17600 Ramachandran restraints generated. 8800 Oldfield, 0 Emsley, 8800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17600 Ramachandran restraints generated. 8800 Oldfield, 0 Emsley, 8800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 7084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 520 time to evaluate : 6.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 143 MET cc_start: -0.2292 (ttt) cc_final: -0.2595 (ttt) REVERT: B 231 PHE cc_start: 0.1739 (m-80) cc_final: 0.0489 (m-80) REVERT: C 110 MET cc_start: 0.3093 (tmm) cc_final: 0.2157 (ttt) REVERT: C 143 MET cc_start: -0.1847 (ttt) cc_final: -0.2420 (ttt) REVERT: C 177 TYR cc_start: 0.2559 (p90) cc_final: 0.2314 (p90) REVERT: C 266 MET cc_start: -0.3548 (mtt) cc_final: -0.4622 (ttm) REVERT: D 110 MET cc_start: 0.2414 (tmm) cc_final: 0.0862 (ttt) REVERT: D 380 ASN cc_start: 0.6273 (m-40) cc_final: 0.5961 (m-40) REVERT: E 110 MET cc_start: 0.3504 (tmm) cc_final: 0.3183 (ttt) REVERT: E 143 MET cc_start: -0.2301 (ttt) cc_final: -0.3279 (ttt) REVERT: E 195 MET cc_start: 0.1007 (mmp) cc_final: -0.0773 (tpt) REVERT: E 231 PHE cc_start: 0.1806 (m-80) cc_final: 0.0640 (m-80) REVERT: E 295 ASN cc_start: 0.5800 (p0) cc_final: 0.4619 (m-40) REVERT: F 110 MET cc_start: 0.3184 (tmm) cc_final: 0.2840 (tmm) REVERT: F 195 MET cc_start: 0.0594 (mmp) cc_final: -0.0753 (tpt) REVERT: G 143 MET cc_start: -0.2370 (ttt) cc_final: -0.3508 (ttt) REVERT: G 195 MET cc_start: 0.1106 (mmp) cc_final: -0.0523 (tpt) REVERT: G 266 MET cc_start: -0.3115 (mtt) cc_final: -0.3400 (mmt) REVERT: G 295 ASN cc_start: 0.5493 (p0) cc_final: 0.4230 (m-40) REVERT: H 41 MET cc_start: 0.1371 (mmm) cc_final: -0.1286 (tpp) REVERT: H 143 MET cc_start: -0.2410 (ttt) cc_final: -0.3687 (ttt) REVERT: H 195 MET cc_start: 0.1051 (mmp) cc_final: -0.0526 (tpt) REVERT: I 110 MET cc_start: 0.2679 (tmm) cc_final: 0.1816 (ttt) REVERT: I 143 MET cc_start: -0.2628 (tpt) cc_final: -0.3449 (tpt) REVERT: I 195 MET cc_start: 0.1367 (mmp) cc_final: -0.0466 (tpt) REVERT: I 295 ASN cc_start: 0.5276 (p0) cc_final: 0.4250 (m-40) REVERT: J 295 ASN cc_start: 0.5374 (p0) cc_final: 0.4484 (m110) REVERT: K 143 MET cc_start: -0.2193 (ttt) cc_final: -0.2584 (ttt) REVERT: K 195 MET cc_start: -0.0182 (mmp) cc_final: -0.0846 (tpp) REVERT: K 295 ASN cc_start: 0.5120 (p0) cc_final: 0.3911 (m-40) REVERT: L 143 MET cc_start: -0.2242 (ttp) cc_final: -0.2860 (mtt) REVERT: L 195 MET cc_start: 0.0569 (mmp) cc_final: -0.0895 (tpt) REVERT: A 65 THR cc_start: 0.7994 (t) cc_final: 0.7357 (p) REVERT: A 74 VAL cc_start: 0.4643 (m) cc_final: 0.3854 (t) REVERT: A 143 MET cc_start: -0.2161 (ttt) cc_final: -0.3394 (ttt) REVERT: A 195 MET cc_start: -0.0252 (mmp) cc_final: -0.2005 (tpt) REVERT: M 195 MET cc_start: -0.0355 (mmp) cc_final: -0.1623 (tpt) REVERT: N 65 THR cc_start: 0.7908 (t) cc_final: 0.7277 (p) REVERT: N 143 MET cc_start: -0.2484 (ttt) cc_final: -0.2885 (ppp) REVERT: N 195 MET cc_start: -0.0575 (mmp) cc_final: -0.1744 (tpt) REVERT: N 295 ASN cc_start: 0.5652 (p0) cc_final: 0.4211 (m110) REVERT: O 143 MET cc_start: -0.2489 (ttt) cc_final: -0.2993 (ttt) REVERT: P 143 MET cc_start: -0.2391 (ttt) cc_final: -0.3653 (mmt) REVERT: P 195 MET cc_start: -0.0639 (mmp) cc_final: -0.1108 (tpt) REVERT: Q 110 MET cc_start: 0.3195 (tmm) cc_final: 0.2552 (ttt) REVERT: Q 143 MET cc_start: -0.2386 (ttt) cc_final: -0.3678 (mmt) REVERT: Q 195 MET cc_start: -0.0099 (mmp) cc_final: -0.0671 (tpt) REVERT: Q 295 ASN cc_start: 0.5909 (p0) cc_final: 0.4805 (m-40) REVERT: Q 379 ARG cc_start: 0.3674 (mmp80) cc_final: 0.3123 (ttt180) REVERT: Q 398 LEU cc_start: 0.5793 (tp) cc_final: 0.5500 (mm) REVERT: R 65 THR cc_start: 0.7924 (t) cc_final: 0.7265 (p) REVERT: R 143 MET cc_start: -0.2845 (ttt) cc_final: -0.3204 (pmm) REVERT: R 195 MET cc_start: 0.0258 (mmp) cc_final: -0.0776 (tpt) REVERT: R 379 ARG cc_start: 0.3072 (mmp80) cc_final: 0.2771 (ttt180) REVERT: S 65 THR cc_start: 0.8032 (t) cc_final: 0.7421 (p) REVERT: S 143 MET cc_start: -0.1570 (mmt) cc_final: -0.1981 (mmt) REVERT: S 195 MET cc_start: 0.0251 (mmp) cc_final: -0.0317 (tpt) REVERT: S 379 ARG cc_start: 0.2875 (mmp80) cc_final: 0.2400 (ttt180) REVERT: T 143 MET cc_start: 0.0399 (pmm) cc_final: 0.0069 (mtt) REVERT: T 266 MET cc_start: -0.2333 (mtm) cc_final: -0.2681 (mtt) REVERT: T 379 ARG cc_start: 0.3309 (mmp80) cc_final: 0.2653 (ttt180) REVERT: U 266 MET cc_start: -0.3324 (ttm) cc_final: -0.5897 (mtt) REVERT: V 266 MET cc_start: -0.2263 (mtm) cc_final: -0.2525 (mtt) REVERT: V 364 ASN cc_start: 0.4693 (p0) cc_final: 0.4282 (m-40) outliers start: 3 outliers final: 0 residues processed: 523 average time/residue: 0.6073 time to fit residues: 549.7234 Evaluate side-chains 446 residues out of total 7084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 446 time to evaluate : 5.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 880 random chunks: chunk 519 optimal weight: 2.9990 chunk 835 optimal weight: 20.0000 chunk 510 optimal weight: 0.0060 chunk 396 optimal weight: 9.9990 chunk 581 optimal weight: 40.0000 chunk 876 optimal weight: 30.0000 chunk 806 optimal weight: 8.9990 chunk 698 optimal weight: 9.9990 chunk 72 optimal weight: 6.9990 chunk 539 optimal weight: 10.0000 chunk 428 optimal weight: 9.9990 overall best weight: 5.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 ASN ** B 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 GLN ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 GLN C 15 ASN ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 GLN ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 GLN E 196 ASN ** E 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 328 GLN E 378 GLN ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 154 GLN G 280 GLN ** G 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 154 GLN ** H 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 154 GLN ** I 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 382 GLN ** J 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 154 GLN ** J 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 ASN ** K 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 154 GLN K 280 GLN ** K 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 154 GLN L 280 GLN L 292 GLN ** L 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 15 ASN ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 GLN A 280 GLN ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 154 GLN ** M 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 280 GLN ** M 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 154 GLN ** N 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 382 GLN ** O 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 154 GLN ** O 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 154 GLN ** P 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 251 ASN Q 280 GLN Q 292 GLN ** Q 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 280 GLN ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 78 GLN ** S 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 280 GLN ** S 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 280 GLN T 302 ASN T 307 GLN ** T 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 280 GLN ** U 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 15 ASN ** V 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 268 GLN V 280 GLN ** V 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2365 moved from start: 0.9871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 66044 Z= 0.336 Angle : 0.933 17.700 89980 Z= 0.500 Chirality : 0.053 0.382 10560 Planarity : 0.005 0.091 12078 Dihedral : 6.431 33.315 9196 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 21.26 Ramachandran Plot: Outliers : 0.89 % Allowed : 8.86 % Favored : 90.25 % Rotamer: Outliers : 0.16 % Allowed : 0.55 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.51 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.51 (0.08), residues: 8800 helix: 1.14 (0.13), residues: 1254 sheet: -1.29 (0.11), residues: 1958 loop : -1.45 (0.08), residues: 5588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.004 TRP R 333 HIS 0.010 0.001 HIS I 193 PHE 0.036 0.003 PHE M 60 TYR 0.023 0.002 TYR O 198 ARG 0.014 0.002 ARG O 95 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17600 Ramachandran restraints generated. 8800 Oldfield, 0 Emsley, 8800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17600 Ramachandran restraints generated. 8800 Oldfield, 0 Emsley, 8800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 7084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 578 time to evaluate : 4.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 143 MET cc_start: -0.1999 (ttt) cc_final: -0.2386 (ttt) REVERT: B 231 PHE cc_start: 0.2244 (m-80) cc_final: 0.0877 (m-80) REVERT: C 110 MET cc_start: 0.3310 (tmm) cc_final: 0.2507 (ttt) REVERT: C 143 MET cc_start: -0.1607 (ttt) cc_final: -0.2066 (ttt) REVERT: C 391 GLN cc_start: 0.6126 (mt0) cc_final: 0.5126 (mm110) REVERT: D 110 MET cc_start: 0.2780 (tmm) cc_final: 0.1149 (ttt) REVERT: D 143 MET cc_start: -0.1853 (ttt) cc_final: -0.3289 (ttt) REVERT: D 195 MET cc_start: 0.1603 (mmp) cc_final: -0.0463 (tpt) REVERT: D 231 PHE cc_start: 0.2490 (m-80) cc_final: 0.0954 (m-80) REVERT: D 374 MET cc_start: 0.2037 (ptt) cc_final: 0.0652 (mtt) REVERT: E 110 MET cc_start: 0.3649 (tmm) cc_final: 0.3402 (ttt) REVERT: E 143 MET cc_start: -0.1877 (ttt) cc_final: -0.3006 (ttt) REVERT: E 231 PHE cc_start: 0.2271 (m-80) cc_final: 0.0812 (m-80) REVERT: F 110 MET cc_start: 0.3592 (tmm) cc_final: 0.3366 (ttt) REVERT: G 143 MET cc_start: -0.2243 (ttt) cc_final: -0.3630 (ttt) REVERT: G 195 MET cc_start: 0.1809 (mmp) cc_final: -0.0054 (tpt) REVERT: H 143 MET cc_start: -0.2212 (ttt) cc_final: -0.3754 (ttt) REVERT: H 195 MET cc_start: 0.1182 (mmp) cc_final: -0.0421 (tpt) REVERT: I 41 MET cc_start: 0.0578 (mmp) cc_final: 0.0337 (mmm) REVERT: I 110 MET cc_start: 0.2679 (tmm) cc_final: 0.2030 (ttt) REVERT: I 374 MET cc_start: 0.2900 (ptt) cc_final: 0.1111 (mmt) REVERT: I 380 ASN cc_start: 0.6657 (m-40) cc_final: 0.5865 (t0) REVERT: I 387 THR cc_start: 0.5782 (m) cc_final: 0.5320 (m) REVERT: J 32 LYS cc_start: 0.6466 (mmtt) cc_final: 0.6220 (mmpt) REVERT: J 143 MET cc_start: -0.2825 (ttt) cc_final: -0.3424 (ttt) REVERT: K 143 MET cc_start: -0.2165 (ttt) cc_final: -0.2633 (ttt) REVERT: K 280 GLN cc_start: 0.1950 (OUTLIER) cc_final: 0.1714 (mm-40) REVERT: K 380 ASN cc_start: 0.5777 (m-40) cc_final: 0.5108 (t0) REVERT: L 143 MET cc_start: -0.2095 (ttp) cc_final: -0.2885 (mtt) REVERT: L 195 MET cc_start: 0.1070 (mmp) cc_final: -0.0524 (tpt) REVERT: A 143 MET cc_start: -0.1959 (ttt) cc_final: -0.2340 (ttt) REVERT: A 195 MET cc_start: 0.0390 (mmp) cc_final: -0.1576 (tpt) REVERT: M 195 MET cc_start: 0.0058 (mmp) cc_final: -0.1262 (tpt) REVERT: N 65 THR cc_start: 0.7925 (t) cc_final: 0.7305 (p) REVERT: N 110 MET cc_start: 0.3083 (tmm) cc_final: 0.2374 (ttt) REVERT: N 143 MET cc_start: -0.2646 (ttt) cc_final: -0.2890 (ttt) REVERT: N 195 MET cc_start: -0.0134 (mmp) cc_final: -0.0874 (tpt) REVERT: O 110 MET cc_start: 0.2743 (tmm) cc_final: 0.2433 (ttt) REVERT: O 143 MET cc_start: -0.2708 (ttt) cc_final: -0.2937 (ttt) REVERT: O 195 MET cc_start: -0.0251 (tmm) cc_final: -0.0502 (tmm) REVERT: O 266 MET cc_start: -0.2476 (ttp) cc_final: -0.5363 (mtt) REVERT: P 143 MET cc_start: -0.2016 (ttt) cc_final: -0.2319 (ttt) REVERT: P 177 TYR cc_start: 0.3359 (p90) cc_final: 0.3154 (p90) REVERT: P 195 MET cc_start: -0.0342 (mmp) cc_final: -0.0748 (tpt) REVERT: Q 110 MET cc_start: 0.3372 (tmm) cc_final: 0.3049 (ttt) REVERT: Q 143 MET cc_start: -0.1952 (ttt) cc_final: -0.3109 (ttt) REVERT: Q 195 MET cc_start: 0.0453 (mmp) cc_final: -0.0097 (tpt) REVERT: Q 280 GLN cc_start: 0.2988 (OUTLIER) cc_final: 0.2760 (mm-40) REVERT: Q 374 MET cc_start: 0.3697 (ptt) cc_final: 0.1899 (mmt) REVERT: Q 391 GLN cc_start: 0.6153 (mt0) cc_final: 0.5301 (mp10) REVERT: R 143 MET cc_start: -0.2679 (ttt) cc_final: -0.3305 (pmm) REVERT: R 195 MET cc_start: 0.0349 (mmp) cc_final: -0.0211 (tpt) REVERT: S 143 MET cc_start: -0.1319 (mmt) cc_final: -0.1779 (mmt) REVERT: S 195 MET cc_start: 0.0430 (mmp) cc_final: -0.0185 (tpt) REVERT: S 379 ARG cc_start: 0.4386 (mmp80) cc_final: 0.3262 (ttt180) REVERT: T 309 GLN cc_start: 0.6084 (pm20) cc_final: 0.4024 (pt0) REVERT: T 380 ASN cc_start: 0.7072 (m-40) cc_final: 0.6337 (t0) REVERT: U 379 ARG cc_start: 0.4414 (mmp80) cc_final: 0.3399 (ttt180) REVERT: V 380 ASN cc_start: 0.6597 (m-40) cc_final: 0.6373 (m-40) REVERT: V 391 GLN cc_start: 0.6235 (mt0) cc_final: 0.5292 (mm110) outliers start: 11 outliers final: 2 residues processed: 588 average time/residue: 0.5864 time to fit residues: 605.5518 Evaluate side-chains 481 residues out of total 7084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 477 time to evaluate : 5.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 880 random chunks: chunk 554 optimal weight: 20.0000 chunk 743 optimal weight: 4.9990 chunk 213 optimal weight: 0.8980 chunk 643 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 194 optimal weight: 7.9990 chunk 699 optimal weight: 6.9990 chunk 292 optimal weight: 0.9980 chunk 718 optimal weight: 20.0000 chunk 88 optimal weight: 0.9990 chunk 128 optimal weight: 5.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 4 GLN ** B 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 GLN ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 4 GLN ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 GLN ** E 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 328 GLN ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 154 GLN F 292 GLN ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 154 GLN ** H 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 391 GLN ** I 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 154 GLN I 280 GLN ** I 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 378 GLN J 154 GLN ** J 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 391 GLN ** K 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 391 GLN ** L 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 292 GLN ** L 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 391 GLN ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 GLN ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 ASN A 391 GLN ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 280 GLN ** M 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 337 GLN M 391 GLN ** N 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 154 GLN ** N 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 380 ASN ** O 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 292 GLN ** Q 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 380 ASN ** R 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 268 GLN ** S 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 292 GLN ** U 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 364 ASN ** V 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 380 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5436 r_free = 0.5436 target = 0.328164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.5260 r_free = 0.5260 target = 0.314339 restraints weight = 1131687.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.5317 r_free = 0.5317 target = 0.319650 restraints weight = 710005.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.5299 r_free = 0.5299 target = 0.317610 restraints weight = 630293.900| |-----------------------------------------------------------------------------| r_work (final): 0.5297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2757 moved from start: 0.9938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 66044 Z= 0.205 Angle : 0.735 11.998 89980 Z= 0.399 Chirality : 0.047 0.237 10560 Planarity : 0.004 0.055 12078 Dihedral : 5.785 30.277 9196 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.80 % Allowed : 6.89 % Favored : 92.32 % Rotamer: Outliers : 0.01 % Allowed : 0.24 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.51 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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 (0.09), residues: 8800 helix: 1.91 (0.14), residues: 1276 sheet: -0.96 (0.10), residues: 2398 loop : -1.46 (0.08), residues: 5126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 333 HIS 0.005 0.001 HIS G 193 PHE 0.021 0.002 PHE J 31 TYR 0.020 0.002 TYR F 303 ARG 0.017 0.001 ARG B 379 =============================================================================== Job complete usr+sys time: 11934.64 seconds wall clock time: 212 minutes 1.87 seconds (12721.87 seconds total)