Starting phenix.real_space_refine on Sun Aug 24 06:29:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dwb_8924/08_2025/6dwb_8924.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dwb_8924/08_2025/6dwb_8924.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6dwb_8924/08_2025/6dwb_8924.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dwb_8924/08_2025/6dwb_8924.map" model { file = "/net/cci-nas-00/data/ceres_data/6dwb_8924/08_2025/6dwb_8924.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dwb_8924/08_2025/6dwb_8924.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.026 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: 3 Type Number sf(0) Gaussians C 11610 2.51 5 N 3030 2.21 5 O 3720 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18360 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, a, b, c, d Time building chain proxies: 1.71, per 1000 atoms: 0.09 Number of scatterers: 18360 At special positions: 0 Unit cell: (93.15, 93.15, 202.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 3720 8.00 N 3030 7.00 C 11610 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: 1.58 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 715.3 nanoseconds 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4560 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 0 sheets defined 88.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 7 through 20 removed outlier: 3.806A pdb=" N PHE A 16 " --> pdb=" O VAL A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 37 removed outlier: 3.671A pdb=" N THR A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS A 37 " --> pdb=" O LYS A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 78 removed outlier: 3.834A pdb=" N ASN A 78 " --> pdb=" O ALA A 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 20 removed outlier: 3.807A pdb=" N PHE B 16 " --> pdb=" O VAL B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 37 removed outlier: 3.671A pdb=" N THR B 28 " --> pdb=" O GLN B 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS B 37 " --> pdb=" O LYS B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 78 removed outlier: 3.834A pdb=" N ASN B 78 " --> pdb=" O ALA B 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 20 removed outlier: 3.807A pdb=" N PHE C 16 " --> pdb=" O VAL C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 37 removed outlier: 3.672A pdb=" N THR C 28 " --> pdb=" O GLN C 24 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS C 37 " --> pdb=" O LYS C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 78 removed outlier: 3.834A pdb=" N ASN C 78 " --> pdb=" O ALA C 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 20 removed outlier: 3.806A pdb=" N PHE D 16 " --> pdb=" O VAL D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 37 removed outlier: 3.671A pdb=" N THR D 28 " --> pdb=" O GLN D 24 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS D 37 " --> pdb=" O LYS D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 78 removed outlier: 3.834A pdb=" N ASN D 78 " --> pdb=" O ALA D 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 20 removed outlier: 3.807A pdb=" N PHE E 16 " --> pdb=" O VAL E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 37 removed outlier: 3.670A pdb=" N THR E 28 " --> pdb=" O GLN E 24 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS E 37 " --> pdb=" O LYS E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 78 removed outlier: 3.834A pdb=" N ASN E 78 " --> pdb=" O ALA E 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 20 removed outlier: 3.807A pdb=" N PHE F 16 " --> pdb=" O VAL F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 37 removed outlier: 3.670A pdb=" N THR F 28 " --> pdb=" O GLN F 24 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS F 37 " --> pdb=" O LYS F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 78 removed outlier: 3.834A pdb=" N ASN F 78 " --> pdb=" O ALA F 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 20 removed outlier: 3.807A pdb=" N PHE G 16 " --> pdb=" O VAL G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 37 removed outlier: 3.672A pdb=" N THR G 28 " --> pdb=" O GLN G 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS G 37 " --> pdb=" O LYS G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 78 removed outlier: 3.835A pdb=" N ASN G 78 " --> pdb=" O ALA G 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 20 removed outlier: 3.806A pdb=" N PHE H 16 " --> pdb=" O VAL H 12 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 37 removed outlier: 3.670A pdb=" N THR H 28 " --> pdb=" O GLN H 24 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS H 37 " --> pdb=" O LYS H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 78 removed outlier: 3.834A pdb=" N ASN H 78 " --> pdb=" O ALA H 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 7 through 20 removed outlier: 3.807A pdb=" N PHE I 16 " --> pdb=" O VAL I 12 " (cutoff:3.500A) Processing helix chain 'I' and resid 22 through 37 removed outlier: 3.671A pdb=" N THR I 28 " --> pdb=" O GLN I 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS I 37 " --> pdb=" O LYS I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 78 removed outlier: 3.835A pdb=" N ASN I 78 " --> pdb=" O ALA I 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 20 removed outlier: 3.806A pdb=" N PHE J 16 " --> pdb=" O VAL J 12 " (cutoff:3.500A) Processing helix chain 'J' and resid 22 through 37 removed outlier: 3.671A pdb=" N THR J 28 " --> pdb=" O GLN J 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS J 37 " --> pdb=" O LYS J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 40 through 78 removed outlier: 3.835A pdb=" N ASN J 78 " --> pdb=" O ALA J 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 20 removed outlier: 3.806A pdb=" N PHE K 16 " --> pdb=" O VAL K 12 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 37 removed outlier: 3.670A pdb=" N THR K 28 " --> pdb=" O GLN K 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS K 37 " --> pdb=" O LYS K 33 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 78 removed outlier: 3.833A pdb=" N ASN K 78 " --> pdb=" O ALA K 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 7 through 20 removed outlier: 3.806A pdb=" N PHE L 16 " --> pdb=" O VAL L 12 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 37 removed outlier: 3.671A pdb=" N THR L 28 " --> pdb=" O GLN L 24 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS L 37 " --> pdb=" O LYS L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 40 through 78 removed outlier: 3.834A pdb=" N ASN L 78 " --> pdb=" O ALA L 74 " (cutoff:3.500A) Processing helix chain 'M' and resid 7 through 20 removed outlier: 3.806A pdb=" N PHE M 16 " --> pdb=" O VAL M 12 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 37 removed outlier: 3.670A pdb=" N THR M 28 " --> pdb=" O GLN M 24 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS M 37 " --> pdb=" O LYS M 33 " (cutoff:3.500A) Processing helix chain 'M' and resid 40 through 78 removed outlier: 3.833A pdb=" N ASN M 78 " --> pdb=" O ALA M 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 7 through 20 removed outlier: 3.806A pdb=" N PHE N 16 " --> pdb=" O VAL N 12 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 37 removed outlier: 3.671A pdb=" N THR N 28 " --> pdb=" O GLN N 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS N 37 " --> pdb=" O LYS N 33 " (cutoff:3.500A) Processing helix chain 'N' and resid 40 through 78 removed outlier: 3.834A pdb=" N ASN N 78 " --> pdb=" O ALA N 74 " (cutoff:3.500A) Processing helix chain 'O' and resid 7 through 20 removed outlier: 3.806A pdb=" N PHE O 16 " --> pdb=" O VAL O 12 " (cutoff:3.500A) Processing helix chain 'O' and resid 22 through 37 removed outlier: 3.671A pdb=" N THR O 28 " --> pdb=" O GLN O 24 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS O 37 " --> pdb=" O LYS O 33 " (cutoff:3.500A) Processing helix chain 'O' and resid 40 through 78 removed outlier: 3.834A pdb=" N ASN O 78 " --> pdb=" O ALA O 74 " (cutoff:3.500A) Processing helix chain 'P' and resid 7 through 20 removed outlier: 3.806A pdb=" N PHE P 16 " --> pdb=" O VAL P 12 " (cutoff:3.500A) Processing helix chain 'P' and resid 22 through 37 removed outlier: 3.672A pdb=" N THR P 28 " --> pdb=" O GLN P 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS P 37 " --> pdb=" O LYS P 33 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 78 removed outlier: 3.834A pdb=" N ASN P 78 " --> pdb=" O ALA P 74 " (cutoff:3.500A) Processing helix chain 'Q' and resid 7 through 20 removed outlier: 3.805A pdb=" N PHE Q 16 " --> pdb=" O VAL Q 12 " (cutoff:3.500A) Processing helix chain 'Q' and resid 22 through 37 removed outlier: 3.671A pdb=" N THR Q 28 " --> pdb=" O GLN Q 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS Q 37 " --> pdb=" O LYS Q 33 " (cutoff:3.500A) Processing helix chain 'Q' and resid 40 through 78 removed outlier: 3.833A pdb=" N ASN Q 78 " --> pdb=" O ALA Q 74 " (cutoff:3.500A) Processing helix chain 'R' and resid 7 through 20 removed outlier: 3.807A pdb=" N PHE R 16 " --> pdb=" O VAL R 12 " (cutoff:3.500A) Processing helix chain 'R' and resid 22 through 37 removed outlier: 3.671A pdb=" N THR R 28 " --> pdb=" O GLN R 24 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS R 37 " --> pdb=" O LYS R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 78 removed outlier: 3.834A pdb=" N ASN R 78 " --> pdb=" O ALA R 74 " (cutoff:3.500A) Processing helix chain 'S' and resid 7 through 20 removed outlier: 3.807A pdb=" N PHE S 16 " --> pdb=" O VAL S 12 " (cutoff:3.500A) Processing helix chain 'S' and resid 22 through 37 removed outlier: 3.670A pdb=" N THR S 28 " --> pdb=" O GLN S 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS S 37 " --> pdb=" O LYS S 33 " (cutoff:3.500A) Processing helix chain 'S' and resid 40 through 78 removed outlier: 3.834A pdb=" N ASN S 78 " --> pdb=" O ALA S 74 " (cutoff:3.500A) Processing helix chain 'T' and resid 7 through 20 removed outlier: 3.806A pdb=" N PHE T 16 " --> pdb=" O VAL T 12 " (cutoff:3.500A) Processing helix chain 'T' and resid 22 through 37 removed outlier: 3.671A pdb=" N THR T 28 " --> pdb=" O GLN T 24 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS T 37 " --> pdb=" O LYS T 33 " (cutoff:3.500A) Processing helix chain 'T' and resid 40 through 78 removed outlier: 3.834A pdb=" N ASN T 78 " --> pdb=" O ALA T 74 " (cutoff:3.500A) Processing helix chain 'U' and resid 7 through 20 removed outlier: 3.807A pdb=" N PHE U 16 " --> pdb=" O VAL U 12 " (cutoff:3.500A) Processing helix chain 'U' and resid 22 through 37 removed outlier: 3.670A pdb=" N THR U 28 " --> pdb=" O GLN U 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS U 37 " --> pdb=" O LYS U 33 " (cutoff:3.500A) Processing helix chain 'U' and resid 40 through 78 removed outlier: 3.834A pdb=" N ASN U 78 " --> pdb=" O ALA U 74 " (cutoff:3.500A) Processing helix chain 'V' and resid 7 through 20 removed outlier: 3.807A pdb=" N PHE V 16 " --> pdb=" O VAL V 12 " (cutoff:3.500A) Processing helix chain 'V' and resid 22 through 37 removed outlier: 3.671A pdb=" N THR V 28 " --> pdb=" O GLN V 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS V 37 " --> pdb=" O LYS V 33 " (cutoff:3.500A) Processing helix chain 'V' and resid 40 through 78 removed outlier: 3.834A pdb=" N ASN V 78 " --> pdb=" O ALA V 74 " (cutoff:3.500A) Processing helix chain 'W' and resid 7 through 20 removed outlier: 3.807A pdb=" N PHE W 16 " --> pdb=" O VAL W 12 " (cutoff:3.500A) Processing helix chain 'W' and resid 22 through 37 removed outlier: 3.670A pdb=" N THR W 28 " --> pdb=" O GLN W 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS W 37 " --> pdb=" O LYS W 33 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 78 removed outlier: 3.834A pdb=" N ASN W 78 " --> pdb=" O ALA W 74 " (cutoff:3.500A) Processing helix chain 'X' and resid 7 through 20 removed outlier: 3.807A pdb=" N PHE X 16 " --> pdb=" O VAL X 12 " (cutoff:3.500A) Processing helix chain 'X' and resid 22 through 37 removed outlier: 3.672A pdb=" N THR X 28 " --> pdb=" O GLN X 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS X 37 " --> pdb=" O LYS X 33 " (cutoff:3.500A) Processing helix chain 'X' and resid 40 through 78 removed outlier: 3.834A pdb=" N ASN X 78 " --> pdb=" O ALA X 74 " (cutoff:3.500A) Processing helix chain 'Y' and resid 7 through 20 removed outlier: 3.805A pdb=" N PHE Y 16 " --> pdb=" O VAL Y 12 " (cutoff:3.500A) Processing helix chain 'Y' and resid 22 through 37 removed outlier: 3.670A pdb=" N THR Y 28 " --> pdb=" O GLN Y 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS Y 37 " --> pdb=" O LYS Y 33 " (cutoff:3.500A) Processing helix chain 'Y' and resid 40 through 78 removed outlier: 3.834A pdb=" N ASN Y 78 " --> pdb=" O ALA Y 74 " (cutoff:3.500A) Processing helix chain 'Z' and resid 7 through 20 removed outlier: 3.806A pdb=" N PHE Z 16 " --> pdb=" O VAL Z 12 " (cutoff:3.500A) Processing helix chain 'Z' and resid 22 through 37 removed outlier: 3.671A pdb=" N THR Z 28 " --> pdb=" O GLN Z 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS Z 37 " --> pdb=" O LYS Z 33 " (cutoff:3.500A) Processing helix chain 'Z' and resid 40 through 78 removed outlier: 3.834A pdb=" N ASN Z 78 " --> pdb=" O ALA Z 74 " (cutoff:3.500A) Processing helix chain 'a' and resid 7 through 20 removed outlier: 3.805A pdb=" N PHE a 16 " --> pdb=" O VAL a 12 " (cutoff:3.500A) Processing helix chain 'a' and resid 22 through 37 removed outlier: 3.671A pdb=" N THR a 28 " --> pdb=" O GLN a 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS a 37 " --> pdb=" O LYS a 33 " (cutoff:3.500A) Processing helix chain 'a' and resid 40 through 78 removed outlier: 3.834A pdb=" N ASN a 78 " --> pdb=" O ALA a 74 " (cutoff:3.500A) Processing helix chain 'b' and resid 7 through 20 removed outlier: 3.806A pdb=" N PHE b 16 " --> pdb=" O VAL b 12 " (cutoff:3.500A) Processing helix chain 'b' and resid 22 through 37 removed outlier: 3.670A pdb=" N THR b 28 " --> pdb=" O GLN b 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS b 37 " --> pdb=" O LYS b 33 " (cutoff:3.500A) Processing helix chain 'b' and resid 40 through 78 removed outlier: 3.834A pdb=" N ASN b 78 " --> pdb=" O ALA b 74 " (cutoff:3.500A) Processing helix chain 'c' and resid 7 through 20 removed outlier: 3.806A pdb=" N PHE c 16 " --> pdb=" O VAL c 12 " (cutoff:3.500A) Processing helix chain 'c' and resid 22 through 37 removed outlier: 3.671A pdb=" N THR c 28 " --> pdb=" O GLN c 24 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS c 37 " --> pdb=" O LYS c 33 " (cutoff:3.500A) Processing helix chain 'c' and resid 40 through 78 removed outlier: 3.833A pdb=" N ASN c 78 " --> pdb=" O ALA c 74 " (cutoff:3.500A) Processing helix chain 'd' and resid 7 through 20 removed outlier: 3.806A pdb=" N PHE d 16 " --> pdb=" O VAL d 12 " (cutoff:3.500A) Processing helix chain 'd' and resid 22 through 37 removed outlier: 3.671A pdb=" N THR d 28 " --> pdb=" O GLN d 24 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS d 37 " --> pdb=" O LYS d 33 " (cutoff:3.500A) Processing helix chain 'd' and resid 40 through 78 removed outlier: 3.834A pdb=" N ASN d 78 " --> pdb=" O ALA d 74 " (cutoff:3.500A) 1590 hydrogen bonds defined for protein. 4770 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: 3.42 Time building geometry restraints manager: 2.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 3270 1.29 - 1.35: 2790 1.35 - 1.42: 1830 1.42 - 1.48: 2760 1.48 - 1.54: 8040 Bond restraints: 18690 Sorted by residual: bond pdb=" CB TRP Y 5 " pdb=" CG TRP Y 5 " ideal model delta sigma weight residual 1.498 1.466 0.032 3.10e-02 1.04e+03 1.08e+00 bond pdb=" CB TRP G 5 " pdb=" CG TRP G 5 " ideal model delta sigma weight residual 1.498 1.466 0.032 3.10e-02 1.04e+03 1.07e+00 bond pdb=" CB TRP M 5 " pdb=" CG TRP M 5 " ideal model delta sigma weight residual 1.498 1.466 0.032 3.10e-02 1.04e+03 1.07e+00 bond pdb=" CB TRP W 5 " pdb=" CG TRP W 5 " ideal model delta sigma weight residual 1.498 1.466 0.032 3.10e-02 1.04e+03 1.06e+00 bond pdb=" CB TRP a 5 " pdb=" CG TRP a 5 " ideal model delta sigma weight residual 1.498 1.466 0.032 3.10e-02 1.04e+03 1.06e+00 ... (remaining 18685 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.69: 20234 0.69 - 1.37: 3909 1.37 - 2.06: 973 2.06 - 2.75: 147 2.75 - 3.43: 177 Bond angle restraints: 25440 Sorted by residual: angle pdb=" N SER N 39 " pdb=" CA SER N 39 " pdb=" C SER N 39 " ideal model delta sigma weight residual 113.19 109.93 3.26 1.58e+00 4.01e-01 4.25e+00 angle pdb=" N SER M 39 " pdb=" CA SER M 39 " pdb=" C SER M 39 " ideal model delta sigma weight residual 113.19 109.93 3.26 1.58e+00 4.01e-01 4.25e+00 angle pdb=" N SER D 39 " pdb=" CA SER D 39 " pdb=" C SER D 39 " ideal model delta sigma weight residual 113.19 109.96 3.23 1.58e+00 4.01e-01 4.19e+00 angle pdb=" N SER E 39 " pdb=" CA SER E 39 " pdb=" C SER E 39 " ideal model delta sigma weight residual 113.19 109.96 3.23 1.58e+00 4.01e-01 4.18e+00 angle pdb=" N SER A 39 " pdb=" CA SER A 39 " pdb=" C SER A 39 " ideal model delta sigma weight residual 113.19 109.97 3.22 1.58e+00 4.01e-01 4.16e+00 ... (remaining 25435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 6.51: 9392 6.51 - 13.01: 1468 13.01 - 19.51: 360 19.51 - 26.02: 60 26.02 - 32.52: 60 Dihedral angle restraints: 11340 sinusoidal: 4350 harmonic: 6990 Sorted by residual: dihedral pdb=" CA ARG a 80 " pdb=" CB ARG a 80 " pdb=" CG ARG a 80 " pdb=" CD ARG a 80 " ideal model delta sinusoidal sigma weight residual -60.00 -92.52 32.52 3 1.50e+01 4.44e-03 5.37e+00 dihedral pdb=" CA ARG J 80 " pdb=" CB ARG J 80 " pdb=" CG ARG J 80 " pdb=" CD ARG J 80 " ideal model delta sinusoidal sigma weight residual -60.00 -92.50 32.50 3 1.50e+01 4.44e-03 5.36e+00 dihedral pdb=" CA ARG H 80 " pdb=" CB ARG H 80 " pdb=" CG ARG H 80 " pdb=" CD ARG H 80 " ideal model delta sinusoidal sigma weight residual -60.00 -92.48 32.48 3 1.50e+01 4.44e-03 5.35e+00 ... (remaining 11337 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.022: 1346 0.022 - 0.044: 912 0.044 - 0.066: 441 0.066 - 0.089: 152 0.089 - 0.111: 59 Chirality restraints: 2910 Sorted by residual: chirality pdb=" CA PRO H 41 " pdb=" N PRO H 41 " pdb=" C PRO H 41 " pdb=" CB PRO H 41 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.06e-01 chirality pdb=" CA PRO I 41 " pdb=" N PRO I 41 " pdb=" C PRO I 41 " pdb=" CB PRO I 41 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.91e-01 chirality pdb=" CA PRO c 41 " pdb=" N PRO c 41 " pdb=" C PRO c 41 " pdb=" CB PRO c 41 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.81e-01 ... (remaining 2907 not shown) Planarity restraints: 3330 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP N 40 " -0.020 5.00e-02 4.00e+02 3.07e-02 1.51e+00 pdb=" N PRO N 41 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO N 41 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO N 41 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP a 40 " -0.020 5.00e-02 4.00e+02 3.06e-02 1.50e+00 pdb=" N PRO a 41 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO a 41 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO a 41 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP U 40 " -0.020 5.00e-02 4.00e+02 3.04e-02 1.48e+00 pdb=" N PRO U 41 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO U 41 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO U 41 " -0.017 5.00e-02 4.00e+02 ... (remaining 3327 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 533 2.71 - 3.26: 19243 3.26 - 3.80: 29140 3.80 - 4.35: 37006 4.35 - 4.90: 63240 Nonbonded interactions: 149162 Sorted by model distance: nonbonded pdb=" OD1 ASP H 10 " pdb=" OG SER N 49 " model vdw 2.161 3.040 nonbonded pdb=" OD1 ASP S 10 " pdb=" OG SER Y 49 " model vdw 2.217 3.040 nonbonded pdb=" OD1 ASP R 10 " pdb=" OG SER X 49 " model vdw 2.222 3.040 nonbonded pdb=" OD1 ASP A 10 " pdb=" OG SER G 49 " model vdw 2.228 3.040 nonbonded pdb=" OD1 ASP M 10 " pdb=" OG SER S 49 " model vdw 2.239 3.040 ... (remaining 149157 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: 0.08 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' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 15.260 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 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 : 0.007 0.032 18690 Z= 0.311 Angle : 0.655 3.431 25440 Z= 0.419 Chirality : 0.036 0.111 2910 Planarity : 0.005 0.031 3330 Dihedral : 7.211 32.525 6780 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -6.22 (0.07), residues: 2280 helix: -3.61 (0.05), residues: 1980 sheet: None (None), residues: 0 loop : -5.46 (0.22), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG X 58 TYR 0.010 0.001 TYR E 57 PHE 0.013 0.002 PHE X 79 TRP 0.018 0.004 TRP I 5 Details of bonding type rmsd covalent geometry : bond 0.00701 (18690) covalent geometry : angle 0.65516 (25440) hydrogen bonds : bond 0.32114 ( 1590) hydrogen bonds : angle 8.12493 ( 4770) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 462 time to evaluate : 0.711 Fit side-chains revert: symmetry clash REVERT: A 72 ASP cc_start: 0.9080 (m-30) cc_final: 0.8798 (m-30) REVERT: B 15 LYS cc_start: 0.8215 (mttt) cc_final: 0.7963 (mtpp) REVERT: B 28 THR cc_start: 0.8594 (m) cc_final: 0.8330 (p) REVERT: B 77 GLN cc_start: 0.8108 (tt0) cc_final: 0.7855 (tp40) REVERT: C 28 THR cc_start: 0.8227 (m) cc_final: 0.7830 (p) REVERT: C 29 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7900 (mt-10) REVERT: C 37 LYS cc_start: 0.7550 (ttmt) cc_final: 0.6928 (tptt) REVERT: C 49 SER cc_start: 0.8374 (t) cc_final: 0.8046 (t) REVERT: C 57 TYR cc_start: 0.8222 (t80) cc_final: 0.7967 (t80) REVERT: D 11 ASP cc_start: 0.8395 (m-30) cc_final: 0.7988 (m-30) REVERT: D 37 LYS cc_start: 0.7488 (ttmt) cc_final: 0.6889 (tptt) REVERT: D 55 ASN cc_start: 0.8391 (t0) cc_final: 0.8131 (t0) REVERT: E 29 GLU cc_start: 0.8563 (mt-10) cc_final: 0.8234 (mt-10) REVERT: E 37 LYS cc_start: 0.7887 (ttmt) cc_final: 0.7096 (tptt) REVERT: F 6 SER cc_start: 0.8848 (m) cc_final: 0.8575 (p) REVERT: F 10 ASP cc_start: 0.8384 (m-30) cc_final: 0.7839 (m-30) REVERT: F 37 LYS cc_start: 0.8470 (ttmt) cc_final: 0.7272 (tptt) REVERT: G 6 SER cc_start: 0.8584 (m) cc_final: 0.8242 (p) REVERT: G 10 ASP cc_start: 0.8752 (m-30) cc_final: 0.8496 (m-30) REVERT: G 37 LYS cc_start: 0.8442 (ttmt) cc_final: 0.7204 (tptt) REVERT: H 24 GLN cc_start: 0.8151 (mp10) cc_final: 0.7685 (mp10) REVERT: H 37 LYS cc_start: 0.8084 (ttmt) cc_final: 0.6749 (tptt) REVERT: I 23 LEU cc_start: 0.7209 (tp) cc_final: 0.6697 (tp) REVERT: I 24 GLN cc_start: 0.8064 (mp10) cc_final: 0.7610 (mp10) REVERT: I 27 VAL cc_start: 0.8296 (t) cc_final: 0.8094 (t) REVERT: I 28 THR cc_start: 0.8525 (m) cc_final: 0.8093 (m) REVERT: I 32 ASP cc_start: 0.8186 (m-30) cc_final: 0.7860 (m-30) REVERT: I 37 LYS cc_start: 0.7526 (ttmt) cc_final: 0.6173 (tptt) REVERT: I 57 TYR cc_start: 0.7642 (t80) cc_final: 0.7115 (t80) REVERT: K 10 ASP cc_start: 0.8071 (m-30) cc_final: 0.7469 (m-30) REVERT: K 32 ASP cc_start: 0.8415 (m-30) cc_final: 0.8082 (m-30) REVERT: K 37 LYS cc_start: 0.8214 (ttmt) cc_final: 0.6583 (tptt) REVERT: N 21 ASP cc_start: 0.7674 (m-30) cc_final: 0.7434 (m-30) REVERT: Q 33 LYS cc_start: 0.8244 (mttt) cc_final: 0.8035 (mtpp) REVERT: R 37 LYS cc_start: 0.8343 (ttmt) cc_final: 0.8055 (ttmm) REVERT: R 49 SER cc_start: 0.8113 (t) cc_final: 0.7762 (p) REVERT: S 70 ASP cc_start: 0.7795 (m-30) cc_final: 0.7506 (m-30) REVERT: V 9 LEU cc_start: 0.4974 (mt) cc_final: 0.4648 (mt) REVERT: X 22 ASN cc_start: 0.7807 (p0) cc_final: 0.6934 (p0) REVERT: X 26 GLN cc_start: 0.7894 (mt0) cc_final: 0.6906 (mt0) REVERT: a 10 ASP cc_start: 0.6792 (m-30) cc_final: 0.6429 (m-30) outliers start: 0 outliers final: 0 residues processed: 462 average time/residue: 0.1495 time to fit residues: 104.4934 Evaluate side-chains 307 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 307 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 chunk 200 optimal weight: 0.8980 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 26 GLN D 63 ASN E 63 ASN P 61 GLN V 78 ASN Y 22 ASN c 77 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.117679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.097478 restraints weight = 25075.076| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.51 r_work: 0.3001 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 18690 Z= 0.157 Angle : 0.510 7.925 25440 Z= 0.296 Chirality : 0.033 0.110 2910 Planarity : 0.005 0.029 3330 Dihedral : 3.359 12.468 2520 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.91 % Allowed : 7.07 % Favored : 92.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.15), residues: 2280 helix: 1.18 (0.09), residues: 2040 sheet: None (None), residues: 0 loop : -4.86 (0.28), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG W 80 TYR 0.017 0.002 TYR G 57 PHE 0.012 0.002 PHE d 16 TRP 0.007 0.001 TRP S 5 Details of bonding type rmsd covalent geometry : bond 0.00279 (18690) covalent geometry : angle 0.51042 (25440) hydrogen bonds : bond 0.08052 ( 1590) hydrogen bonds : angle 3.30191 ( 4770) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 332 time to evaluate : 1.033 Fit side-chains revert: symmetry clash REVERT: A 59 ASN cc_start: 0.8655 (m110) cc_final: 0.8238 (m110) REVERT: C 11 ASP cc_start: 0.8672 (m-30) cc_final: 0.8405 (m-30) REVERT: C 25 THR cc_start: 0.8927 (OUTLIER) cc_final: 0.8470 (p) REVERT: C 37 LYS cc_start: 0.7319 (ttmt) cc_final: 0.6631 (tptt) REVERT: D 11 ASP cc_start: 0.8703 (m-30) cc_final: 0.8115 (m-30) REVERT: D 22 ASN cc_start: 0.7939 (p0) cc_final: 0.7550 (p0) REVERT: D 32 ASP cc_start: 0.8208 (m-30) cc_final: 0.7983 (m-30) REVERT: E 37 LYS cc_start: 0.8010 (ttmt) cc_final: 0.7320 (tptt) REVERT: E 53 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8423 (mm-30) REVERT: F 10 ASP cc_start: 0.9064 (m-30) cc_final: 0.8424 (m-30) REVERT: F 37 LYS cc_start: 0.8634 (ttmt) cc_final: 0.7581 (tptt) REVERT: F 53 GLU cc_start: 0.8489 (mm-30) cc_final: 0.7825 (mm-30) REVERT: G 10 ASP cc_start: 0.8931 (m-30) cc_final: 0.8725 (m-30) REVERT: G 32 ASP cc_start: 0.8225 (m-30) cc_final: 0.8007 (m-30) REVERT: G 37 LYS cc_start: 0.8136 (ttmt) cc_final: 0.6989 (tptt) REVERT: I 28 THR cc_start: 0.9094 (m) cc_final: 0.8686 (p) REVERT: K 10 ASP cc_start: 0.8709 (m-30) cc_final: 0.8405 (m-30) REVERT: L 33 LYS cc_start: 0.8968 (mtmm) cc_final: 0.8418 (mtpp) REVERT: N 15 LYS cc_start: 0.8633 (mttm) cc_final: 0.8341 (mtpp) REVERT: N 24 GLN cc_start: 0.8328 (mp10) cc_final: 0.8045 (mp10) REVERT: N 28 THR cc_start: 0.9167 (m) cc_final: 0.8675 (m) REVERT: P 32 ASP cc_start: 0.8288 (m-30) cc_final: 0.8087 (m-30) REVERT: U 10 ASP cc_start: 0.8229 (m-30) cc_final: 0.7808 (m-30) REVERT: W 57 TYR cc_start: 0.8839 (OUTLIER) cc_final: 0.8356 (t80) REVERT: X 24 GLN cc_start: 0.7839 (mp10) cc_final: 0.7471 (mp10) REVERT: b 69 LYS cc_start: 0.7224 (tttm) cc_final: 0.5898 (tptt) REVERT: c 49 SER cc_start: 0.7846 (t) cc_final: 0.7491 (p) REVERT: c 70 ASP cc_start: 0.7982 (OUTLIER) cc_final: 0.7753 (t0) REVERT: c 76 ILE cc_start: 0.7944 (mt) cc_final: 0.7472 (mm) REVERT: d 24 GLN cc_start: 0.7257 (mp10) cc_final: 0.6843 (mp10) outliers start: 18 outliers final: 9 residues processed: 342 average time/residue: 0.1464 time to fit residues: 76.5185 Evaluate side-chains 282 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 270 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain F residue 59 ASN Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain K residue 33 LYS Chi-restraints excluded: chain Q residue 49 SER Chi-restraints excluded: chain U residue 17 ASP Chi-restraints excluded: chain U residue 33 LYS Chi-restraints excluded: chain W residue 57 TYR Chi-restraints excluded: chain b residue 71 ILE Chi-restraints excluded: chain c residue 31 LEU Chi-restraints excluded: chain c residue 57 TYR Chi-restraints excluded: chain c residue 70 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 91 optimal weight: 10.0000 chunk 100 optimal weight: 0.9980 chunk 123 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 22 optimal weight: 0.0000 chunk 26 optimal weight: 6.9990 chunk 179 optimal weight: 0.9980 chunk 204 optimal weight: 5.9990 chunk 185 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN P 61 GLN V 61 GLN Z 61 GLN b 61 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.102450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.083103 restraints weight = 25833.743| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 1.52 r_work: 0.2781 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.5845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 18690 Z= 0.175 Angle : 0.541 9.044 25440 Z= 0.296 Chirality : 0.037 0.148 2910 Planarity : 0.003 0.024 3330 Dihedral : 3.790 24.798 2520 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.06 % Allowed : 9.60 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.12 (0.17), residues: 2280 helix: 2.79 (0.11), residues: 2040 sheet: None (None), residues: 0 loop : -5.14 (0.27), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG J 58 TYR 0.022 0.002 TYR T 54 PHE 0.015 0.002 PHE F 79 TRP 0.007 0.001 TRP C 5 Details of bonding type rmsd covalent geometry : bond 0.00379 (18690) covalent geometry : angle 0.54099 (25440) hydrogen bonds : bond 0.07028 ( 1590) hydrogen bonds : angle 3.00070 ( 4770) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 400 time to evaluate : 0.689 Fit side-chains revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8711 (tptp) cc_final: 0.6952 (mttm) REVERT: B 10 ASP cc_start: 0.9076 (m-30) cc_final: 0.8429 (m-30) REVERT: B 55 ASN cc_start: 0.7968 (t0) cc_final: 0.7447 (t0) REVERT: B 66 LYS cc_start: 0.8787 (tptp) cc_final: 0.7397 (ttmt) REVERT: C 27 VAL cc_start: 0.8626 (t) cc_final: 0.8190 (p) REVERT: C 66 LYS cc_start: 0.8900 (tptp) cc_final: 0.7366 (mttt) REVERT: D 32 ASP cc_start: 0.8227 (m-30) cc_final: 0.8020 (m-30) REVERT: D 37 LYS cc_start: 0.8044 (ttmt) cc_final: 0.7217 (tmtt) REVERT: D 66 LYS cc_start: 0.8887 (tptp) cc_final: 0.6967 (mttm) REVERT: E 20 VAL cc_start: 0.7836 (m) cc_final: 0.7614 (m) REVERT: E 37 LYS cc_start: 0.8279 (ttmt) cc_final: 0.7539 (tptt) REVERT: E 66 LYS cc_start: 0.8969 (tptp) cc_final: 0.7309 (ttmt) REVERT: F 37 LYS cc_start: 0.8702 (ttmt) cc_final: 0.7667 (tptt) REVERT: G 62 SER cc_start: 0.9019 (t) cc_final: 0.8583 (m) REVERT: H 53 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8187 (mm-30) REVERT: I 31 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8449 (tt) REVERT: L 21 ASP cc_start: 0.8652 (m-30) cc_final: 0.8437 (m-30) REVERT: N 15 LYS cc_start: 0.8879 (mttm) cc_final: 0.8678 (mtpp) REVERT: N 28 THR cc_start: 0.9101 (m) cc_final: 0.8595 (m) REVERT: N 32 ASP cc_start: 0.8654 (m-30) cc_final: 0.8303 (m-30) REVERT: N 53 GLU cc_start: 0.9113 (mm-30) cc_final: 0.8819 (mm-30) REVERT: P 80 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7298 (pmt100) REVERT: V 80 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.6271 (pmt100) REVERT: W 28 THR cc_start: 0.8959 (m) cc_final: 0.8650 (m) REVERT: X 33 LYS cc_start: 0.8896 (mtpp) cc_final: 0.8580 (mtmt) REVERT: Y 33 LYS cc_start: 0.8899 (mptt) cc_final: 0.8487 (mttm) REVERT: Z 66 LYS cc_start: 0.8854 (tptp) cc_final: 0.8409 (tptm) REVERT: a 69 LYS cc_start: 0.8203 (tttm) cc_final: 0.7341 (ttmt) REVERT: c 31 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8582 (tp) REVERT: c 61 GLN cc_start: 0.9045 (tt0) cc_final: 0.8563 (tt0) REVERT: c 71 ILE cc_start: 0.7680 (mm) cc_final: 0.7474 (mt) REVERT: d 29 GLU cc_start: 0.8295 (mm-30) cc_final: 0.8038 (mt-10) outliers start: 21 outliers final: 12 residues processed: 412 average time/residue: 0.1543 time to fit residues: 95.2058 Evaluate side-chains 327 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 311 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain G residue 59 ASN Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain K residue 33 LYS Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 80 ARG Chi-restraints excluded: chain U residue 33 LYS Chi-restraints excluded: chain V residue 18 THR Chi-restraints excluded: chain V residue 80 ARG Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain a residue 39 SER Chi-restraints excluded: chain c residue 31 LEU Chi-restraints excluded: chain c residue 75 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 157 optimal weight: 0.7980 chunk 133 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 129 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 chunk 42 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 170 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 137 optimal weight: 4.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN A 61 GLN U 78 ASN X 61 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.092235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.072685 restraints weight = 26405.486| |-----------------------------------------------------------------------------| r_work (start): 0.2715 rms_B_bonded: 1.48 r_work: 0.2609 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2490 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.6358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18690 Z= 0.184 Angle : 0.480 6.180 25440 Z= 0.268 Chirality : 0.035 0.117 2910 Planarity : 0.003 0.023 3330 Dihedral : 3.484 15.721 2520 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.52 % Allowed : 11.52 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.82 (0.17), residues: 2280 helix: 3.23 (0.10), residues: 2010 sheet: None (None), residues: 0 loop : -3.75 (0.32), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG a 58 TYR 0.019 0.002 TYR G 57 PHE 0.010 0.002 PHE U 16 TRP 0.006 0.001 TRP V 5 Details of bonding type rmsd covalent geometry : bond 0.00418 (18690) covalent geometry : angle 0.48012 (25440) hydrogen bonds : bond 0.07190 ( 1590) hydrogen bonds : angle 3.10245 ( 4770) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 309 time to evaluate : 0.427 Fit side-chains revert: symmetry clash REVERT: B 10 ASP cc_start: 0.9038 (m-30) cc_final: 0.8406 (m-30) REVERT: B 55 ASN cc_start: 0.8730 (t0) cc_final: 0.8358 (t0) REVERT: B 56 LEU cc_start: 0.9296 (mt) cc_final: 0.8870 (mp) REVERT: B 66 LYS cc_start: 0.8828 (tptp) cc_final: 0.6805 (mttt) REVERT: C 25 THR cc_start: 0.8831 (OUTLIER) cc_final: 0.8572 (p) REVERT: C 27 VAL cc_start: 0.8980 (t) cc_final: 0.8720 (p) REVERT: C 66 LYS cc_start: 0.9126 (tptp) cc_final: 0.7293 (mttt) REVERT: D 37 LYS cc_start: 0.8005 (ttmt) cc_final: 0.7128 (tmtt) REVERT: D 66 LYS cc_start: 0.8957 (tptp) cc_final: 0.6846 (mttm) REVERT: E 37 LYS cc_start: 0.8248 (ttmt) cc_final: 0.7374 (tptt) REVERT: E 66 LYS cc_start: 0.8963 (tptp) cc_final: 0.7450 (ttmt) REVERT: F 37 LYS cc_start: 0.8733 (ttmt) cc_final: 0.7673 (tptt) REVERT: G 32 ASP cc_start: 0.8181 (m-30) cc_final: 0.7857 (m-30) REVERT: I 72 ASP cc_start: 0.9263 (m-30) cc_final: 0.8963 (m-30) REVERT: J 80 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.6290 (pmt100) REVERT: K 80 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.6242 (pmt100) REVERT: L 21 ASP cc_start: 0.8636 (m-30) cc_final: 0.8376 (m-30) REVERT: M 53 GLU cc_start: 0.9136 (mm-30) cc_final: 0.8894 (mm-30) REVERT: N 15 LYS cc_start: 0.9005 (mttm) cc_final: 0.8796 (mtpp) REVERT: N 28 THR cc_start: 0.9137 (m) cc_final: 0.8321 (p) REVERT: N 32 ASP cc_start: 0.8562 (m-30) cc_final: 0.8207 (m-30) REVERT: O 32 ASP cc_start: 0.8589 (m-30) cc_final: 0.8286 (m-30) REVERT: O 80 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.6796 (pmt100) REVERT: Q 80 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.6127 (pmt100) REVERT: R 57 TYR cc_start: 0.9314 (OUTLIER) cc_final: 0.8447 (t80) REVERT: T 6 SER cc_start: 0.9183 (m) cc_final: 0.8967 (p) REVERT: U 10 ASP cc_start: 0.9034 (m-30) cc_final: 0.8614 (m-30) REVERT: U 80 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.5995 (pmt100) REVERT: V 80 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.6089 (pmt100) REVERT: X 33 LYS cc_start: 0.8870 (mtpp) cc_final: 0.8619 (mtmt) REVERT: Y 6 SER cc_start: 0.8937 (m) cc_final: 0.8533 (p) REVERT: Y 33 LYS cc_start: 0.8909 (mptt) cc_final: 0.8367 (mttt) REVERT: Z 66 LYS cc_start: 0.9108 (tptp) cc_final: 0.8820 (tptm) REVERT: a 78 ASN cc_start: 0.7689 (p0) cc_final: 0.7467 (p0) REVERT: c 75 ILE cc_start: 0.8089 (mm) cc_final: 0.7822 (mt) REVERT: c 77 GLN cc_start: 0.8794 (tp40) cc_final: 0.8387 (tp40) REVERT: d 29 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8255 (mt-10) outliers start: 30 outliers final: 18 residues processed: 330 average time/residue: 0.1422 time to fit residues: 70.7238 Evaluate side-chains 312 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 286 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain G residue 59 ASN Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain I residue 57 TYR Chi-restraints excluded: chain J residue 57 TYR Chi-restraints excluded: chain J residue 80 ARG Chi-restraints excluded: chain K residue 33 LYS Chi-restraints excluded: chain K residue 80 ARG Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 80 ARG Chi-restraints excluded: chain Q residue 80 ARG Chi-restraints excluded: chain R residue 6 SER Chi-restraints excluded: chain R residue 57 TYR Chi-restraints excluded: chain S residue 25 THR Chi-restraints excluded: chain U residue 33 LYS Chi-restraints excluded: chain U residue 80 ARG Chi-restraints excluded: chain V residue 18 THR Chi-restraints excluded: chain V residue 80 ARG Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain d residue 25 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 196 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 169 optimal weight: 5.9990 chunk 168 optimal weight: 10.0000 chunk 112 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 183 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 31 optimal weight: 0.0970 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.089950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.070620 restraints weight = 26527.575| |-----------------------------------------------------------------------------| r_work (start): 0.2672 rms_B_bonded: 1.47 r_work: 0.2565 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2448 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.6696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18690 Z= 0.188 Angle : 0.481 8.079 25440 Z= 0.265 Chirality : 0.036 0.113 2910 Planarity : 0.003 0.024 3330 Dihedral : 3.514 18.422 2520 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.17 % Allowed : 10.81 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.91 (0.17), residues: 2280 helix: 3.29 (0.10), residues: 2010 sheet: None (None), residues: 0 loop : -3.75 (0.32), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 58 TYR 0.018 0.002 TYR G 57 PHE 0.008 0.001 PHE U 16 TRP 0.005 0.001 TRP Y 5 Details of bonding type rmsd covalent geometry : bond 0.00433 (18690) covalent geometry : angle 0.48051 (25440) hydrogen bonds : bond 0.07237 ( 1590) hydrogen bonds : angle 3.05906 ( 4770) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 305 time to evaluate : 0.710 Fit side-chains revert: symmetry clash REVERT: B 10 ASP cc_start: 0.9028 (m-30) cc_final: 0.8395 (m-30) REVERT: B 55 ASN cc_start: 0.8922 (t0) cc_final: 0.8464 (t0) REVERT: B 66 LYS cc_start: 0.8856 (tptp) cc_final: 0.6878 (mttt) REVERT: C 27 VAL cc_start: 0.8906 (t) cc_final: 0.8555 (p) REVERT: C 66 LYS cc_start: 0.9150 (tptp) cc_final: 0.7292 (mttt) REVERT: D 37 LYS cc_start: 0.8055 (ttmt) cc_final: 0.7117 (tmtt) REVERT: D 66 LYS cc_start: 0.8970 (tptp) cc_final: 0.6886 (mttm) REVERT: E 37 LYS cc_start: 0.8271 (ttmt) cc_final: 0.7365 (tptt) REVERT: E 66 LYS cc_start: 0.9031 (tptp) cc_final: 0.7447 (ttmt) REVERT: F 37 LYS cc_start: 0.8526 (ttmt) cc_final: 0.7401 (tptt) REVERT: I 72 ASP cc_start: 0.9262 (m-30) cc_final: 0.8900 (m-30) REVERT: I 80 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7214 (ptt90) REVERT: J 28 THR cc_start: 0.9009 (m) cc_final: 0.8785 (m) REVERT: J 80 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.6356 (pmt100) REVERT: K 57 TYR cc_start: 0.9425 (OUTLIER) cc_final: 0.8464 (t80) REVERT: K 80 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.6325 (pmt100) REVERT: L 21 ASP cc_start: 0.8596 (m-30) cc_final: 0.8387 (m-30) REVERT: L 80 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.7967 (ptt90) REVERT: M 53 GLU cc_start: 0.9174 (mm-30) cc_final: 0.8892 (mm-30) REVERT: N 28 THR cc_start: 0.9125 (m) cc_final: 0.8193 (p) REVERT: N 32 ASP cc_start: 0.8585 (m-30) cc_final: 0.8233 (m-30) REVERT: N 57 TYR cc_start: 0.9421 (OUTLIER) cc_final: 0.8207 (t80) REVERT: N 80 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7705 (pmt100) REVERT: O 32 ASP cc_start: 0.8601 (m-30) cc_final: 0.8305 (m-30) REVERT: P 10 ASP cc_start: 0.8960 (m-30) cc_final: 0.8723 (m-30) REVERT: P 80 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.6476 (pmt100) REVERT: Q 80 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.6334 (pmt100) REVERT: R 57 TYR cc_start: 0.9279 (OUTLIER) cc_final: 0.8405 (t80) REVERT: T 32 ASP cc_start: 0.8752 (m-30) cc_final: 0.8188 (m-30) REVERT: U 10 ASP cc_start: 0.9004 (m-30) cc_final: 0.8589 (m-30) REVERT: U 39 SER cc_start: 0.8892 (OUTLIER) cc_final: 0.8617 (m) REVERT: U 80 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.5905 (pmt100) REVERT: V 33 LYS cc_start: 0.8925 (mtmt) cc_final: 0.8700 (mttp) REVERT: V 80 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.6158 (pmt100) REVERT: X 33 LYS cc_start: 0.8886 (mtpp) cc_final: 0.8667 (mtmt) REVERT: Y 6 SER cc_start: 0.8896 (m) cc_final: 0.8504 (p) REVERT: Y 33 LYS cc_start: 0.8873 (mptt) cc_final: 0.8396 (mttt) REVERT: Y 80 ARG cc_start: 0.7239 (OUTLIER) cc_final: 0.4497 (mtt-85) REVERT: Z 66 LYS cc_start: 0.9115 (tptp) cc_final: 0.8817 (tptm) REVERT: b 80 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.5172 (ptp90) REVERT: c 77 GLN cc_start: 0.8769 (tp40) cc_final: 0.8319 (tp40) outliers start: 43 outliers final: 20 residues processed: 340 average time/residue: 0.1640 time to fit residues: 81.3410 Evaluate side-chains 320 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 285 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain G residue 59 ASN Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain I residue 57 TYR Chi-restraints excluded: chain I residue 80 ARG Chi-restraints excluded: chain J residue 57 TYR Chi-restraints excluded: chain J residue 80 ARG Chi-restraints excluded: chain K residue 33 LYS Chi-restraints excluded: chain K residue 57 TYR Chi-restraints excluded: chain K residue 80 ARG Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 80 ARG Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain N residue 80 ARG Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain P residue 80 ARG Chi-restraints excluded: chain Q residue 80 ARG Chi-restraints excluded: chain R residue 57 TYR Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain U residue 33 LYS Chi-restraints excluded: chain U residue 39 SER Chi-restraints excluded: chain U residue 80 ARG Chi-restraints excluded: chain V residue 6 SER Chi-restraints excluded: chain V residue 18 THR Chi-restraints excluded: chain V residue 80 ARG Chi-restraints excluded: chain Y residue 80 ARG Chi-restraints excluded: chain a residue 17 ASP Chi-restraints excluded: chain a residue 39 SER Chi-restraints excluded: chain b residue 80 ARG Chi-restraints excluded: chain d residue 25 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 34 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 192 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 191 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 163 optimal weight: 5.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.092628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.073767 restraints weight = 26073.045| |-----------------------------------------------------------------------------| r_work (start): 0.2726 rms_B_bonded: 1.45 r_work: 0.2623 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2507 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.6879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 18690 Z= 0.135 Angle : 0.422 8.455 25440 Z= 0.234 Chirality : 0.033 0.106 2910 Planarity : 0.003 0.030 3330 Dihedral : 3.332 15.843 2520 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.92 % Allowed : 11.11 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.22 (0.17), residues: 2280 helix: 3.53 (0.10), residues: 2010 sheet: None (None), residues: 0 loop : -3.92 (0.30), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 80 TYR 0.017 0.001 TYR G 57 PHE 0.007 0.001 PHE K 16 TRP 0.005 0.001 TRP Y 5 Details of bonding type rmsd covalent geometry : bond 0.00280 (18690) covalent geometry : angle 0.42221 (25440) hydrogen bonds : bond 0.06206 ( 1590) hydrogen bonds : angle 2.90988 ( 4770) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 306 time to evaluate : 0.576 Fit side-chains revert: symmetry clash REVERT: A 80 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.7531 (ptt90) REVERT: B 10 ASP cc_start: 0.8974 (m-30) cc_final: 0.8359 (m-30) REVERT: B 55 ASN cc_start: 0.8687 (t0) cc_final: 0.8328 (t0) REVERT: B 66 LYS cc_start: 0.8853 (tptp) cc_final: 0.6879 (mttt) REVERT: B 80 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.7302 (pmt100) REVERT: C 27 VAL cc_start: 0.8928 (t) cc_final: 0.8607 (p) REVERT: C 57 TYR cc_start: 0.8947 (OUTLIER) cc_final: 0.8492 (t80) REVERT: C 66 LYS cc_start: 0.9129 (tptp) cc_final: 0.7273 (mttt) REVERT: D 37 LYS cc_start: 0.8058 (ttmt) cc_final: 0.7071 (tmtt) REVERT: D 66 LYS cc_start: 0.8949 (tptp) cc_final: 0.6817 (mttm) REVERT: E 37 LYS cc_start: 0.8205 (ttmt) cc_final: 0.7297 (tptt) REVERT: E 66 LYS cc_start: 0.9004 (tptp) cc_final: 0.7405 (ttmt) REVERT: F 37 LYS cc_start: 0.8430 (ttmt) cc_final: 0.7330 (tptt) REVERT: G 32 ASP cc_start: 0.8193 (m-30) cc_final: 0.7886 (m-30) REVERT: H 80 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7999 (pmt100) REVERT: I 72 ASP cc_start: 0.9034 (m-30) cc_final: 0.8820 (m-30) REVERT: J 28 THR cc_start: 0.8999 (m) cc_final: 0.8755 (m) REVERT: J 80 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.6214 (pmt100) REVERT: K 57 TYR cc_start: 0.9363 (OUTLIER) cc_final: 0.8381 (t80) REVERT: K 80 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.6761 (ptt90) REVERT: L 21 ASP cc_start: 0.8596 (m-30) cc_final: 0.8382 (m-30) REVERT: L 80 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7885 (ptt90) REVERT: N 28 THR cc_start: 0.9114 (m) cc_final: 0.8276 (p) REVERT: N 32 ASP cc_start: 0.8542 (m-30) cc_final: 0.8194 (m-30) REVERT: N 57 TYR cc_start: 0.9394 (OUTLIER) cc_final: 0.8303 (t80) REVERT: N 80 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7733 (pmt100) REVERT: O 32 ASP cc_start: 0.8567 (m-30) cc_final: 0.8269 (m-30) REVERT: O 80 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.6675 (pmt100) REVERT: P 80 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.6607 (pmt100) REVERT: R 53 GLU cc_start: 0.9136 (mm-30) cc_final: 0.8899 (mm-30) REVERT: R 57 TYR cc_start: 0.9271 (OUTLIER) cc_final: 0.8391 (t80) REVERT: T 32 ASP cc_start: 0.8733 (m-30) cc_final: 0.8140 (m-30) REVERT: T 53 GLU cc_start: 0.8994 (tp30) cc_final: 0.8660 (mm-30) REVERT: U 10 ASP cc_start: 0.9066 (m-30) cc_final: 0.8625 (m-30) REVERT: V 67 VAL cc_start: 0.9393 (t) cc_final: 0.9079 (t) REVERT: Y 6 SER cc_start: 0.8882 (m) cc_final: 0.8565 (p) REVERT: Y 33 LYS cc_start: 0.8884 (mptt) cc_final: 0.8391 (mttt) REVERT: Z 66 LYS cc_start: 0.9069 (tptp) cc_final: 0.8831 (tptm) REVERT: a 11 ASP cc_start: 0.8781 (m-30) cc_final: 0.8474 (m-30) REVERT: b 80 ARG cc_start: 0.7492 (OUTLIER) cc_final: 0.4955 (ptp90) REVERT: d 25 THR cc_start: 0.9167 (OUTLIER) cc_final: 0.8917 (p) outliers start: 38 outliers final: 15 residues processed: 335 average time/residue: 0.1414 time to fit residues: 70.7547 Evaluate side-chains 319 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 289 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain I residue 57 TYR Chi-restraints excluded: chain J residue 57 TYR Chi-restraints excluded: chain J residue 80 ARG Chi-restraints excluded: chain K residue 33 LYS Chi-restraints excluded: chain K residue 57 TYR Chi-restraints excluded: chain K residue 80 ARG Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 80 ARG Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain N residue 80 ARG Chi-restraints excluded: chain O residue 57 TYR Chi-restraints excluded: chain O residue 80 ARG Chi-restraints excluded: chain P residue 80 ARG Chi-restraints excluded: chain R residue 57 TYR Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain a residue 17 ASP Chi-restraints excluded: chain a residue 39 SER Chi-restraints excluded: chain b residue 80 ARG Chi-restraints excluded: chain d residue 25 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 121 optimal weight: 4.9990 chunk 102 optimal weight: 8.9990 chunk 133 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 209 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 chunk 3 optimal weight: 20.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 61 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.088272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.069143 restraints weight = 26876.514| |-----------------------------------------------------------------------------| r_work (start): 0.2647 rms_B_bonded: 1.47 r_work: 0.2541 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2423 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.6953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 18690 Z= 0.203 Angle : 0.491 7.951 25440 Z= 0.270 Chirality : 0.037 0.114 2910 Planarity : 0.003 0.029 3330 Dihedral : 3.697 30.500 2520 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.87 % Allowed : 11.41 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.01 (0.17), residues: 2280 helix: 3.37 (0.10), residues: 2010 sheet: None (None), residues: 0 loop : -3.79 (0.32), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 80 TYR 0.019 0.002 TYR G 57 PHE 0.008 0.001 PHE H 16 TRP 0.006 0.001 TRP Y 5 Details of bonding type rmsd covalent geometry : bond 0.00476 (18690) covalent geometry : angle 0.49092 (25440) hydrogen bonds : bond 0.07375 ( 1590) hydrogen bonds : angle 3.09031 ( 4770) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 291 time to evaluate : 0.764 Fit side-chains REVERT: A 80 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.7618 (ptt90) REVERT: B 10 ASP cc_start: 0.9031 (m-30) cc_final: 0.8420 (m-30) REVERT: B 55 ASN cc_start: 0.8944 (t0) cc_final: 0.8488 (t0) REVERT: B 66 LYS cc_start: 0.8914 (tptp) cc_final: 0.6978 (mttt) REVERT: C 66 LYS cc_start: 0.9147 (tptp) cc_final: 0.7275 (mttt) REVERT: D 37 LYS cc_start: 0.8302 (ttmt) cc_final: 0.7345 (tmtt) REVERT: D 66 LYS cc_start: 0.8962 (tptp) cc_final: 0.6852 (mttm) REVERT: E 37 LYS cc_start: 0.8297 (ttmt) cc_final: 0.7370 (tptt) REVERT: E 66 LYS cc_start: 0.9011 (tptp) cc_final: 0.7418 (ttmt) REVERT: F 37 LYS cc_start: 0.8474 (ttmt) cc_final: 0.7392 (tptt) REVERT: G 32 ASP cc_start: 0.8203 (m-30) cc_final: 0.7851 (m-30) REVERT: H 80 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.8061 (pmt100) REVERT: I 72 ASP cc_start: 0.9344 (m-30) cc_final: 0.8989 (m-30) REVERT: I 80 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.6952 (ptt90) REVERT: J 80 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.8098 (ptt90) REVERT: K 57 TYR cc_start: 0.9442 (OUTLIER) cc_final: 0.8569 (t80) REVERT: K 80 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.6320 (pmt100) REVERT: L 80 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7962 (ptt90) REVERT: M 53 GLU cc_start: 0.9169 (mm-30) cc_final: 0.8941 (mm-30) REVERT: N 28 THR cc_start: 0.9107 (m) cc_final: 0.8147 (p) REVERT: N 32 ASP cc_start: 0.8595 (m-30) cc_final: 0.8241 (m-30) REVERT: N 57 TYR cc_start: 0.9458 (OUTLIER) cc_final: 0.8147 (t80) REVERT: N 80 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7775 (pmt100) REVERT: O 32 ASP cc_start: 0.8620 (m-30) cc_final: 0.8333 (m-30) REVERT: O 80 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.6868 (pmt100) REVERT: P 53 GLU cc_start: 0.9373 (mm-30) cc_final: 0.9146 (mm-30) REVERT: Q 53 GLU cc_start: 0.9372 (mm-30) cc_final: 0.9112 (mm-30) REVERT: R 53 GLU cc_start: 0.9175 (mm-30) cc_final: 0.8974 (mm-30) REVERT: R 57 TYR cc_start: 0.9293 (OUTLIER) cc_final: 0.8412 (t80) REVERT: T 32 ASP cc_start: 0.8758 (m-30) cc_final: 0.8180 (m-30) REVERT: T 53 GLU cc_start: 0.9059 (tp30) cc_final: 0.8727 (mm-30) REVERT: U 10 ASP cc_start: 0.9030 (m-30) cc_final: 0.8546 (m-30) REVERT: Y 6 SER cc_start: 0.8901 (m) cc_final: 0.8589 (p) REVERT: Y 33 LYS cc_start: 0.8874 (mptt) cc_final: 0.8434 (mttt) REVERT: Y 80 ARG cc_start: 0.7387 (OUTLIER) cc_final: 0.4478 (ttm170) REVERT: Z 66 LYS cc_start: 0.9164 (tptp) cc_final: 0.8914 (tptm) REVERT: a 11 ASP cc_start: 0.8814 (m-30) cc_final: 0.8499 (m-30) REVERT: b 17 ASP cc_start: 0.8308 (m-30) cc_final: 0.7934 (m-30) REVERT: b 80 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.5566 (ptp90) REVERT: c 72 ASP cc_start: 0.7791 (m-30) cc_final: 0.7482 (m-30) REVERT: c 80 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.4600 (mmt90) REVERT: d 25 THR cc_start: 0.9196 (OUTLIER) cc_final: 0.8930 (p) outliers start: 37 outliers final: 17 residues processed: 323 average time/residue: 0.1495 time to fit residues: 70.9737 Evaluate side-chains 314 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 282 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain G residue 59 ASN Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain I residue 80 ARG Chi-restraints excluded: chain J residue 57 TYR Chi-restraints excluded: chain J residue 80 ARG Chi-restraints excluded: chain K residue 33 LYS Chi-restraints excluded: chain K residue 57 TYR Chi-restraints excluded: chain K residue 80 ARG Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 80 ARG Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain N residue 80 ARG Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 57 TYR Chi-restraints excluded: chain O residue 80 ARG Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain R residue 57 TYR Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain Y residue 80 ARG Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain a residue 17 ASP Chi-restraints excluded: chain a residue 39 SER Chi-restraints excluded: chain b residue 80 ARG Chi-restraints excluded: chain c residue 80 ARG Chi-restraints excluded: chain d residue 25 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 192 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 10 optimal weight: 40.0000 chunk 5 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 131 optimal weight: 0.9980 chunk 22 optimal weight: 10.0000 chunk 163 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 191 optimal weight: 6.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.086779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.067754 restraints weight = 26872.660| |-----------------------------------------------------------------------------| r_work (start): 0.2620 rms_B_bonded: 1.44 r_work: 0.2514 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2398 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.7062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 18690 Z= 0.224 Angle : 0.508 7.552 25440 Z= 0.279 Chirality : 0.038 0.117 2910 Planarity : 0.003 0.026 3330 Dihedral : 3.950 39.356 2520 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.32 % Allowed : 11.16 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.82 (0.17), residues: 2280 helix: 3.23 (0.10), residues: 2010 sheet: None (None), residues: 0 loop : -3.78 (0.32), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 80 TYR 0.020 0.002 TYR H 57 PHE 0.009 0.002 PHE H 16 TRP 0.007 0.001 TRP Y 5 Details of bonding type rmsd covalent geometry : bond 0.00534 (18690) covalent geometry : angle 0.50767 (25440) hydrogen bonds : bond 0.07732 ( 1590) hydrogen bonds : angle 3.18333 ( 4770) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 294 time to evaluate : 0.806 Fit side-chains REVERT: A 80 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.7584 (ptt90) REVERT: B 55 ASN cc_start: 0.8917 (t0) cc_final: 0.8458 (t0) REVERT: B 66 LYS cc_start: 0.8919 (tptp) cc_final: 0.6937 (mttt) REVERT: C 57 TYR cc_start: 0.9094 (OUTLIER) cc_final: 0.8548 (t80) REVERT: C 66 LYS cc_start: 0.9148 (tptp) cc_final: 0.7280 (mttt) REVERT: D 37 LYS cc_start: 0.8471 (ttmt) cc_final: 0.7518 (tmtt) REVERT: D 66 LYS cc_start: 0.9023 (tptp) cc_final: 0.6857 (mttm) REVERT: E 37 LYS cc_start: 0.8329 (ttmt) cc_final: 0.7391 (tptt) REVERT: E 66 LYS cc_start: 0.9033 (tptp) cc_final: 0.7451 (ttmt) REVERT: E 80 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7750 (ptt-90) REVERT: F 37 LYS cc_start: 0.8477 (ttmt) cc_final: 0.7426 (tptt) REVERT: H 80 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.8020 (pmt100) REVERT: I 32 ASP cc_start: 0.8231 (m-30) cc_final: 0.7782 (m-30) REVERT: I 72 ASP cc_start: 0.9328 (m-30) cc_final: 0.8907 (m-30) REVERT: I 80 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.6831 (ptt90) REVERT: J 80 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.8066 (ptt90) REVERT: K 57 TYR cc_start: 0.9450 (OUTLIER) cc_final: 0.8647 (t80) REVERT: K 80 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.6308 (pmt100) REVERT: M 53 GLU cc_start: 0.9189 (mm-30) cc_final: 0.8895 (mm-30) REVERT: N 28 THR cc_start: 0.9118 (m) cc_final: 0.8161 (p) REVERT: N 32 ASP cc_start: 0.8610 (m-30) cc_final: 0.8258 (m-30) REVERT: N 57 TYR cc_start: 0.9452 (OUTLIER) cc_final: 0.8177 (t80) REVERT: N 80 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7715 (pmt100) REVERT: O 32 ASP cc_start: 0.8609 (m-30) cc_final: 0.8321 (m-30) REVERT: O 80 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.6854 (pmt100) REVERT: P 53 GLU cc_start: 0.9347 (mm-30) cc_final: 0.8947 (mm-30) REVERT: R 57 TYR cc_start: 0.9327 (OUTLIER) cc_final: 0.8390 (t80) REVERT: T 32 ASP cc_start: 0.8741 (m-30) cc_final: 0.8130 (m-30) REVERT: T 53 GLU cc_start: 0.9060 (OUTLIER) cc_final: 0.8738 (mm-30) REVERT: U 10 ASP cc_start: 0.9060 (m-30) cc_final: 0.8539 (m-30) REVERT: W 24 GLN cc_start: 0.8461 (mp10) cc_final: 0.8145 (mp10) REVERT: W 57 TYR cc_start: 0.9345 (OUTLIER) cc_final: 0.8586 (t80) REVERT: W 75 ILE cc_start: 0.8771 (mm) cc_final: 0.8533 (mt) REVERT: Y 6 SER cc_start: 0.8872 (m) cc_final: 0.8637 (p) REVERT: Y 33 LYS cc_start: 0.8889 (mptt) cc_final: 0.8449 (mttt) REVERT: Y 80 ARG cc_start: 0.7502 (OUTLIER) cc_final: 0.4487 (ttm170) REVERT: Z 32 ASP cc_start: 0.9107 (m-30) cc_final: 0.8869 (m-30) REVERT: Z 66 LYS cc_start: 0.9177 (tptp) cc_final: 0.8934 (tptm) REVERT: b 17 ASP cc_start: 0.8483 (m-30) cc_final: 0.7970 (m-30) REVERT: b 80 ARG cc_start: 0.7601 (OUTLIER) cc_final: 0.4869 (mpt180) REVERT: c 80 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.4691 (mmt90) REVERT: d 25 THR cc_start: 0.9192 (OUTLIER) cc_final: 0.8939 (p) outliers start: 46 outliers final: 25 residues processed: 330 average time/residue: 0.1541 time to fit residues: 75.7732 Evaluate side-chains 326 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 283 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 80 ARG Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 57 TYR Chi-restraints excluded: chain G residue 59 ASN Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain I residue 80 ARG Chi-restraints excluded: chain J residue 57 TYR Chi-restraints excluded: chain J residue 80 ARG Chi-restraints excluded: chain K residue 33 LYS Chi-restraints excluded: chain K residue 57 TYR Chi-restraints excluded: chain K residue 80 ARG Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain N residue 80 ARG Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 57 TYR Chi-restraints excluded: chain O residue 80 ARG Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain Q residue 6 SER Chi-restraints excluded: chain R residue 57 TYR Chi-restraints excluded: chain R residue 79 PHE Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain S residue 25 THR Chi-restraints excluded: chain T residue 53 GLU Chi-restraints excluded: chain V residue 18 THR Chi-restraints excluded: chain W residue 57 TYR Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain Y residue 80 ARG Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain a residue 17 ASP Chi-restraints excluded: chain a residue 39 SER Chi-restraints excluded: chain b residue 80 ARG Chi-restraints excluded: chain c residue 80 ARG Chi-restraints excluded: chain d residue 25 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 171 optimal weight: 0.7980 chunk 155 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 189 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 129 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 78 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.086053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.066261 restraints weight = 26646.707| |-----------------------------------------------------------------------------| r_work (start): 0.2600 rms_B_bonded: 1.53 r_work: 0.2492 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2372 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.7103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 18690 Z= 0.232 Angle : 0.519 9.382 25440 Z= 0.284 Chirality : 0.038 0.116 2910 Planarity : 0.003 0.027 3330 Dihedral : 3.955 39.461 2520 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.47 % Allowed : 11.36 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.74 (0.17), residues: 2280 helix: 3.17 (0.10), residues: 2010 sheet: None (None), residues: 0 loop : -3.74 (0.33), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 80 TYR 0.019 0.002 TYR G 57 PHE 0.008 0.002 PHE A 68 TRP 0.007 0.001 TRP Y 5 Details of bonding type rmsd covalent geometry : bond 0.00554 (18690) covalent geometry : angle 0.51909 (25440) hydrogen bonds : bond 0.07800 ( 1590) hydrogen bonds : angle 3.19451 ( 4770) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 285 time to evaluate : 0.656 Fit side-chains REVERT: A 80 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.7617 (ptt90) REVERT: B 55 ASN cc_start: 0.8930 (t0) cc_final: 0.8459 (t0) REVERT: B 66 LYS cc_start: 0.8922 (tptp) cc_final: 0.6945 (mttt) REVERT: C 57 TYR cc_start: 0.9113 (OUTLIER) cc_final: 0.8566 (t80) REVERT: C 66 LYS cc_start: 0.9135 (tptp) cc_final: 0.7260 (mttt) REVERT: D 37 LYS cc_start: 0.8491 (ttmt) cc_final: 0.7534 (tmtt) REVERT: D 66 LYS cc_start: 0.8995 (tptp) cc_final: 0.6843 (mttm) REVERT: E 37 LYS cc_start: 0.8317 (ttmt) cc_final: 0.7376 (tptt) REVERT: E 53 GLU cc_start: 0.8940 (mm-30) cc_final: 0.8320 (mm-30) REVERT: E 66 LYS cc_start: 0.9020 (tptp) cc_final: 0.7432 (ttmt) REVERT: E 80 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7859 (ptt-90) REVERT: F 37 LYS cc_start: 0.8441 (ttmt) cc_final: 0.7404 (tptt) REVERT: H 80 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.8088 (pmt100) REVERT: I 32 ASP cc_start: 0.8335 (m-30) cc_final: 0.7836 (m-30) REVERT: I 72 ASP cc_start: 0.9353 (m-30) cc_final: 0.8936 (m-30) REVERT: I 80 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.6873 (ptt90) REVERT: J 80 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.8095 (ptt90) REVERT: K 57 TYR cc_start: 0.9446 (OUTLIER) cc_final: 0.8651 (t80) REVERT: K 80 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.6325 (pmt100) REVERT: L 80 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.6963 (pmt100) REVERT: M 53 GLU cc_start: 0.9235 (mm-30) cc_final: 0.8919 (mm-30) REVERT: N 28 THR cc_start: 0.9101 (m) cc_final: 0.8131 (p) REVERT: N 32 ASP cc_start: 0.8644 (m-30) cc_final: 0.8292 (m-30) REVERT: N 57 TYR cc_start: 0.9465 (OUTLIER) cc_final: 0.8191 (t80) REVERT: N 80 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7702 (pmt100) REVERT: O 32 ASP cc_start: 0.8636 (m-30) cc_final: 0.8360 (m-30) REVERT: O 80 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.6854 (pmt100) REVERT: P 53 GLU cc_start: 0.9356 (mm-30) cc_final: 0.9000 (mm-30) REVERT: Q 53 GLU cc_start: 0.9370 (mm-30) cc_final: 0.9125 (mm-30) REVERT: R 57 TYR cc_start: 0.9333 (OUTLIER) cc_final: 0.8376 (t80) REVERT: T 53 GLU cc_start: 0.9114 (OUTLIER) cc_final: 0.8781 (mm-30) REVERT: U 10 ASP cc_start: 0.9092 (m-30) cc_final: 0.8575 (m-30) REVERT: W 24 GLN cc_start: 0.8488 (mp10) cc_final: 0.8147 (mp10) REVERT: W 57 TYR cc_start: 0.9397 (OUTLIER) cc_final: 0.8601 (t80) REVERT: W 75 ILE cc_start: 0.8810 (mm) cc_final: 0.8581 (mt) REVERT: Y 33 LYS cc_start: 0.8865 (mptt) cc_final: 0.8432 (mttt) REVERT: Y 80 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.4498 (ttm170) REVERT: Z 32 ASP cc_start: 0.9161 (m-30) cc_final: 0.8903 (m-30) REVERT: Z 66 LYS cc_start: 0.9174 (tptp) cc_final: 0.8936 (tptm) REVERT: b 80 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.4878 (mpt180) REVERT: d 25 THR cc_start: 0.9180 (OUTLIER) cc_final: 0.8919 (p) outliers start: 49 outliers final: 28 residues processed: 322 average time/residue: 0.1466 time to fit residues: 69.9786 Evaluate side-chains 324 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 278 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 80 ARG Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 57 TYR Chi-restraints excluded: chain G residue 59 ASN Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain I residue 80 ARG Chi-restraints excluded: chain J residue 57 TYR Chi-restraints excluded: chain J residue 80 ARG Chi-restraints excluded: chain K residue 33 LYS Chi-restraints excluded: chain K residue 57 TYR Chi-restraints excluded: chain K residue 80 ARG Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 80 ARG Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain N residue 80 ARG Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 57 TYR Chi-restraints excluded: chain O residue 80 ARG Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain Q residue 6 SER Chi-restraints excluded: chain R residue 57 TYR Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain S residue 25 THR Chi-restraints excluded: chain T residue 53 GLU Chi-restraints excluded: chain U residue 33 LYS Chi-restraints excluded: chain U residue 57 TYR Chi-restraints excluded: chain V residue 18 THR Chi-restraints excluded: chain W residue 57 TYR Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain Y residue 17 ASP Chi-restraints excluded: chain Y residue 57 TYR Chi-restraints excluded: chain Y residue 80 ARG Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain a residue 17 ASP Chi-restraints excluded: chain a residue 39 SER Chi-restraints excluded: chain b residue 80 ARG Chi-restraints excluded: chain d residue 25 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 10 optimal weight: 4.9990 chunk 168 optimal weight: 10.0000 chunk 101 optimal weight: 0.9990 chunk 63 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 104 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 131 optimal weight: 0.9980 chunk 176 optimal weight: 3.9990 chunk 204 optimal weight: 7.9990 chunk 153 optimal weight: 2.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 78 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.092752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.073517 restraints weight = 26123.331| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 1.50 r_work: 0.2620 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2502 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.7271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 18690 Z= 0.125 Angle : 0.422 9.273 25440 Z= 0.232 Chirality : 0.033 0.116 2910 Planarity : 0.003 0.026 3330 Dihedral : 3.445 29.908 2520 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.67 % Allowed : 12.42 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.26 (0.17), residues: 2280 helix: 3.55 (0.10), residues: 2010 sheet: None (None), residues: 0 loop : -3.86 (0.31), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 80 TYR 0.016 0.001 TYR G 57 PHE 0.006 0.001 PHE O 79 TRP 0.006 0.000 TRP d 5 Details of bonding type rmsd covalent geometry : bond 0.00249 (18690) covalent geometry : angle 0.42209 (25440) hydrogen bonds : bond 0.05782 ( 1590) hydrogen bonds : angle 2.89462 ( 4770) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 300 time to evaluate : 0.700 Fit side-chains REVERT: B 10 ASP cc_start: 0.8994 (m-30) cc_final: 0.8338 (m-30) REVERT: B 55 ASN cc_start: 0.8791 (t0) cc_final: 0.8422 (t0) REVERT: B 66 LYS cc_start: 0.8847 (tptp) cc_final: 0.6787 (mttt) REVERT: C 57 TYR cc_start: 0.8967 (OUTLIER) cc_final: 0.8445 (t80) REVERT: C 66 LYS cc_start: 0.9106 (tptp) cc_final: 0.7253 (mttt) REVERT: D 37 LYS cc_start: 0.8384 (ttmt) cc_final: 0.7388 (tmtt) REVERT: D 66 LYS cc_start: 0.8887 (tptp) cc_final: 0.6818 (mttm) REVERT: E 37 LYS cc_start: 0.8189 (ttmt) cc_final: 0.7500 (tttp) REVERT: E 66 LYS cc_start: 0.8977 (tptp) cc_final: 0.7311 (ttmt) REVERT: F 37 LYS cc_start: 0.8373 (ttmt) cc_final: 0.7285 (tptt) REVERT: G 32 ASP cc_start: 0.8143 (m-30) cc_final: 0.7822 (m-30) REVERT: H 80 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.8269 (ptt90) REVERT: I 32 ASP cc_start: 0.8126 (m-30) cc_final: 0.7640 (m-30) REVERT: I 80 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.6900 (ptt90) REVERT: J 80 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.6062 (pmt100) REVERT: K 57 TYR cc_start: 0.9322 (OUTLIER) cc_final: 0.8509 (t80) REVERT: L 80 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.6711 (pmt100) REVERT: M 53 GLU cc_start: 0.9182 (mm-30) cc_final: 0.8904 (mm-30) REVERT: N 28 THR cc_start: 0.9093 (m) cc_final: 0.8244 (p) REVERT: N 32 ASP cc_start: 0.8530 (m-30) cc_final: 0.8166 (m-30) REVERT: N 57 TYR cc_start: 0.9376 (OUTLIER) cc_final: 0.8618 (t80) REVERT: N 80 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7026 (pmt100) REVERT: O 80 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.6622 (pmt100) REVERT: Q 53 GLU cc_start: 0.9317 (mm-30) cc_final: 0.9116 (mm-30) REVERT: R 57 TYR cc_start: 0.9240 (OUTLIER) cc_final: 0.8243 (t80) REVERT: T 32 ASP cc_start: 0.8828 (m-30) cc_final: 0.8237 (m-30) REVERT: T 53 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.8665 (mm-30) REVERT: U 10 ASP cc_start: 0.9089 (m-30) cc_final: 0.8659 (m-30) REVERT: V 67 VAL cc_start: 0.9366 (t) cc_final: 0.9038 (t) REVERT: W 57 TYR cc_start: 0.9284 (OUTLIER) cc_final: 0.8566 (t80) REVERT: Y 33 LYS cc_start: 0.8845 (mptt) cc_final: 0.8414 (mttt) REVERT: Y 80 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.4671 (mtt180) REVERT: Z 32 ASP cc_start: 0.9113 (m-30) cc_final: 0.8831 (m-30) REVERT: Z 66 LYS cc_start: 0.9159 (tptp) cc_final: 0.8937 (tptm) REVERT: b 80 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.4904 (mpt180) REVERT: c 61 GLN cc_start: 0.9400 (tt0) cc_final: 0.9190 (tt0) REVERT: d 21 ASP cc_start: 0.8571 (t0) cc_final: 0.8233 (t0) REVERT: d 59 ASN cc_start: 0.9168 (m-40) cc_final: 0.8936 (m-40) outliers start: 33 outliers final: 15 residues processed: 327 average time/residue: 0.1389 time to fit residues: 68.0723 Evaluate side-chains 310 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 281 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 57 TYR Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain I residue 80 ARG Chi-restraints excluded: chain J residue 57 TYR Chi-restraints excluded: chain J residue 80 ARG Chi-restraints excluded: chain K residue 33 LYS Chi-restraints excluded: chain K residue 57 TYR Chi-restraints excluded: chain L residue 80 ARG Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain N residue 80 ARG Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 57 TYR Chi-restraints excluded: chain O residue 80 ARG Chi-restraints excluded: chain Q residue 57 TYR Chi-restraints excluded: chain R residue 57 TYR Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain S residue 25 THR Chi-restraints excluded: chain T residue 53 GLU Chi-restraints excluded: chain W residue 57 TYR Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain Y residue 80 ARG Chi-restraints excluded: chain a residue 17 ASP Chi-restraints excluded: chain b residue 80 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 9 optimal weight: 8.9990 chunk 134 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 201 optimal weight: 0.8980 chunk 189 optimal weight: 10.0000 chunk 139 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 174 optimal weight: 10.0000 chunk 156 optimal weight: 7.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 78 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.093168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.074046 restraints weight = 26095.358| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 1.50 r_work: 0.2629 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2510 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.7306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 18690 Z= 0.122 Angle : 0.420 9.107 25440 Z= 0.231 Chirality : 0.033 0.107 2910 Planarity : 0.003 0.026 3330 Dihedral : 3.408 27.629 2520 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.52 % Allowed : 12.47 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.38 (0.17), residues: 2280 helix: 3.63 (0.10), residues: 2010 sheet: None (None), residues: 0 loop : -3.80 (0.31), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 80 TYR 0.017 0.001 TYR G 57 PHE 0.006 0.001 PHE K 16 TRP 0.005 0.001 TRP d 5 Details of bonding type rmsd covalent geometry : bond 0.00247 (18690) covalent geometry : angle 0.41975 (25440) hydrogen bonds : bond 0.05647 ( 1590) hydrogen bonds : angle 2.83092 ( 4770) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3973.06 seconds wall clock time: 69 minutes 22.98 seconds (4162.98 seconds total)