Starting phenix.real_space_refine on Sun Jul 5 12:15:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9moq_48478/07_2026/9moq_48478_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9moq_48478/07_2026/9moq_48478.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9moq_48478/07_2026/9moq_48478_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9moq_48478/07_2026/9moq_48478_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9moq_48478/07_2026/9moq_48478.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9moq_48478/07_2026/9moq_48478.map" } resolution = 3.5 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= 0.002 sd= 0.031 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: 5 Type Number sf(0) Gaussians P 50 5.49 5 S 250 5.16 5 C 17250 2.51 5 N 3700 2.21 5 O 4550 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25800 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 476 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'X41': 1} Classifications: {'undetermined': 1} 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, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, a, b, c, d, e, f, g, h, i, j, k, l, m, n Residues with excluded nonbonded symmetry interactions: 50 residue: pdb=" C1 X41 A 101 " occ=0.30 ... (38 atoms not shown) pdb=" P1 X41 A 101 " occ=0.30 residue: pdb=" C1 X41 B 101 " occ=0.30 ... (38 atoms not shown) pdb=" P1 X41 B 101 " occ=0.30 residue: pdb=" C1 X41 C 101 " occ=0.30 ... (38 atoms not shown) pdb=" P1 X41 C 101 " occ=0.30 residue: pdb=" C1 X41 D 101 " occ=0.30 ... (38 atoms not shown) pdb=" P1 X41 D 101 " occ=0.30 residue: pdb=" C1 X41 E 101 " occ=0.30 ... (38 atoms not shown) pdb=" P1 X41 E 101 " occ=0.30 residue: pdb=" C1 X41 F 101 " occ=0.30 ... (38 atoms not shown) pdb=" P1 X41 F 101 " occ=0.30 residue: pdb=" C1 X41 G 101 " occ=0.30 ... (38 atoms not shown) pdb=" P1 X41 G 101 " occ=0.30 residue: pdb=" C1 X41 H 101 " occ=0.30 ... (38 atoms not shown) pdb=" P1 X41 H 101 " occ=0.30 residue: pdb=" C1 X41 I 101 " occ=0.30 ... (38 atoms not shown) pdb=" P1 X41 I 101 " occ=0.30 residue: pdb=" C1 X41 J 101 " occ=0.30 ... (38 atoms not shown) pdb=" P1 X41 J 101 " occ=0.30 residue: pdb=" C1 X41 K 101 " occ=0.30 ... (38 atoms not shown) pdb=" P1 X41 K 101 " occ=0.30 residue: pdb=" C1 X41 L 101 " occ=0.30 ... (38 atoms not shown) pdb=" P1 X41 L 101 " occ=0.30 ... (remaining 38 not shown) Time building chain proxies: 2.22, per 1000 atoms: 0.09 Number of scatterers: 25800 At special positions: 0 Unit cell: (97.79, 97.79, 187.11, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 250 16.00 P 50 15.00 O 4550 8.00 N 3700 7.00 C 17250 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: 1.76 Conformation dependent library (CDL) restraints added in 853.7 milliseconds 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5900 Finding SS restraints... Secondary structure from input PDB file: 250 helices and 0 sheets defined 89.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 9 through 11 No H-bonds generated for 'chain 'A' and resid 9 through 11' Processing helix chain 'A' and resid 12 through 20 Processing helix chain 'A' and resid 24 through 46 removed outlier: 3.787A pdb=" N LYS A 28 " --> pdb=" O SER A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 51 removed outlier: 3.512A pdb=" N PHE A 50 " --> pdb=" O ASN A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 69 removed outlier: 3.753A pdb=" N VAL A 67 " --> pdb=" O VAL A 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 11 No H-bonds generated for 'chain 'B' and resid 9 through 11' Processing helix chain 'B' and resid 12 through 20 Processing helix chain 'B' and resid 24 through 46 removed outlier: 3.787A pdb=" N LYS B 28 " --> pdb=" O SER B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 51 removed outlier: 3.512A pdb=" N PHE B 50 " --> pdb=" O ASN B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 69 removed outlier: 3.753A pdb=" N VAL B 67 " --> pdb=" O VAL B 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 11 No H-bonds generated for 'chain 'C' and resid 9 through 11' Processing helix chain 'C' and resid 12 through 20 Processing helix chain 'C' and resid 24 through 46 removed outlier: 3.787A pdb=" N LYS C 28 " --> pdb=" O SER C 24 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N MET C 44 " --> pdb=" O VAL C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 51 removed outlier: 3.512A pdb=" N PHE C 50 " --> pdb=" O ASN C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 69 removed outlier: 3.753A pdb=" N VAL C 67 " --> pdb=" O VAL C 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 11 No H-bonds generated for 'chain 'D' and resid 9 through 11' Processing helix chain 'D' and resid 12 through 20 Processing helix chain 'D' and resid 24 through 46 removed outlier: 3.787A pdb=" N LYS D 28 " --> pdb=" O SER D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 51 removed outlier: 3.512A pdb=" N PHE D 50 " --> pdb=" O ASN D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 69 removed outlier: 3.753A pdb=" N VAL D 67 " --> pdb=" O VAL D 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 11 No H-bonds generated for 'chain 'E' and resid 9 through 11' Processing helix chain 'E' and resid 12 through 20 Processing helix chain 'E' and resid 24 through 46 removed outlier: 3.787A pdb=" N LYS E 28 " --> pdb=" O SER E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 51 removed outlier: 3.512A pdb=" N PHE E 50 " --> pdb=" O ASN E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 69 removed outlier: 3.753A pdb=" N VAL E 67 " --> pdb=" O VAL E 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 11 No H-bonds generated for 'chain 'F' and resid 9 through 11' Processing helix chain 'F' and resid 12 through 20 Processing helix chain 'F' and resid 24 through 46 removed outlier: 3.787A pdb=" N LYS F 28 " --> pdb=" O SER F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 51 removed outlier: 3.512A pdb=" N PHE F 50 " --> pdb=" O ASN F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 69 removed outlier: 3.753A pdb=" N VAL F 67 " --> pdb=" O VAL F 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 11 No H-bonds generated for 'chain 'G' and resid 9 through 11' Processing helix chain 'G' and resid 12 through 20 Processing helix chain 'G' and resid 24 through 46 removed outlier: 3.787A pdb=" N LYS G 28 " --> pdb=" O SER G 24 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N MET G 44 " --> pdb=" O VAL G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 51 removed outlier: 3.512A pdb=" N PHE G 50 " --> pdb=" O ASN G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 52 through 69 removed outlier: 3.753A pdb=" N VAL G 67 " --> pdb=" O VAL G 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 11 No H-bonds generated for 'chain 'H' and resid 9 through 11' Processing helix chain 'H' and resid 12 through 20 Processing helix chain 'H' and resid 24 through 46 removed outlier: 3.787A pdb=" N LYS H 28 " --> pdb=" O SER H 24 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 51 removed outlier: 3.512A pdb=" N PHE H 50 " --> pdb=" O ASN H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 69 removed outlier: 3.753A pdb=" N VAL H 67 " --> pdb=" O VAL H 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 11 No H-bonds generated for 'chain 'I' and resid 9 through 11' Processing helix chain 'I' and resid 12 through 20 Processing helix chain 'I' and resid 24 through 46 removed outlier: 3.787A pdb=" N LYS I 28 " --> pdb=" O SER I 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 51 removed outlier: 3.512A pdb=" N PHE I 50 " --> pdb=" O ASN I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 52 through 69 removed outlier: 3.753A pdb=" N VAL I 67 " --> pdb=" O VAL I 63 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 11 No H-bonds generated for 'chain 'J' and resid 9 through 11' Processing helix chain 'J' and resid 12 through 20 Processing helix chain 'J' and resid 24 through 46 removed outlier: 3.787A pdb=" N LYS J 28 " --> pdb=" O SER J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 51 removed outlier: 3.512A pdb=" N PHE J 50 " --> pdb=" O ASN J 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 52 through 69 removed outlier: 3.753A pdb=" N VAL J 67 " --> pdb=" O VAL J 63 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 11 No H-bonds generated for 'chain 'K' and resid 9 through 11' Processing helix chain 'K' and resid 12 through 20 Processing helix chain 'K' and resid 24 through 46 removed outlier: 3.787A pdb=" N LYS K 28 " --> pdb=" O SER K 24 " (cutoff:3.500A) Processing helix chain 'K' and resid 47 through 51 removed outlier: 3.512A pdb=" N PHE K 50 " --> pdb=" O ASN K 47 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 69 removed outlier: 3.753A pdb=" N VAL K 67 " --> pdb=" O VAL K 63 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 11 No H-bonds generated for 'chain 'L' and resid 9 through 11' Processing helix chain 'L' and resid 12 through 20 Processing helix chain 'L' and resid 24 through 46 removed outlier: 3.787A pdb=" N LYS L 28 " --> pdb=" O SER L 24 " (cutoff:3.500A) Processing helix chain 'L' and resid 47 through 51 removed outlier: 3.511A pdb=" N PHE L 50 " --> pdb=" O ASN L 47 " (cutoff:3.500A) Processing helix chain 'L' and resid 52 through 69 removed outlier: 3.753A pdb=" N VAL L 67 " --> pdb=" O VAL L 63 " (cutoff:3.500A) Processing helix chain 'M' and resid 9 through 11 No H-bonds generated for 'chain 'M' and resid 9 through 11' Processing helix chain 'M' and resid 12 through 20 Processing helix chain 'M' and resid 24 through 46 removed outlier: 3.787A pdb=" N LYS M 28 " --> pdb=" O SER M 24 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N MET M 44 " --> pdb=" O VAL M 40 " (cutoff:3.500A) Processing helix chain 'M' and resid 47 through 51 removed outlier: 3.512A pdb=" N PHE M 50 " --> pdb=" O ASN M 47 " (cutoff:3.500A) Processing helix chain 'M' and resid 52 through 69 removed outlier: 3.753A pdb=" N VAL M 67 " --> pdb=" O VAL M 63 " (cutoff:3.500A) Processing helix chain 'N' and resid 9 through 11 No H-bonds generated for 'chain 'N' and resid 9 through 11' Processing helix chain 'N' and resid 12 through 20 Processing helix chain 'N' and resid 24 through 46 removed outlier: 3.787A pdb=" N LYS N 28 " --> pdb=" O SER N 24 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N MET N 44 " --> pdb=" O VAL N 40 " (cutoff:3.500A) Processing helix chain 'N' and resid 47 through 51 removed outlier: 3.512A pdb=" N PHE N 50 " --> pdb=" O ASN N 47 " (cutoff:3.500A) Processing helix chain 'N' and resid 52 through 69 removed outlier: 3.753A pdb=" N VAL N 67 " --> pdb=" O VAL N 63 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 11 No H-bonds generated for 'chain 'O' and resid 9 through 11' Processing helix chain 'O' and resid 12 through 20 Processing helix chain 'O' and resid 24 through 46 removed outlier: 3.787A pdb=" N LYS O 28 " --> pdb=" O SER O 24 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N MET O 44 " --> pdb=" O VAL O 40 " (cutoff:3.500A) Processing helix chain 'O' and resid 47 through 51 removed outlier: 3.512A pdb=" N PHE O 50 " --> pdb=" O ASN O 47 " (cutoff:3.500A) Processing helix chain 'O' and resid 52 through 69 removed outlier: 3.753A pdb=" N VAL O 67 " --> pdb=" O VAL O 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 9 through 11 No H-bonds generated for 'chain 'P' and resid 9 through 11' Processing helix chain 'P' and resid 12 through 20 Processing helix chain 'P' and resid 24 through 46 removed outlier: 3.787A pdb=" N LYS P 28 " --> pdb=" O SER P 24 " (cutoff:3.500A) Processing helix chain 'P' and resid 47 through 51 removed outlier: 3.512A pdb=" N PHE P 50 " --> pdb=" O ASN P 47 " (cutoff:3.500A) Processing helix chain 'P' and resid 52 through 69 removed outlier: 3.754A pdb=" N VAL P 67 " --> pdb=" O VAL P 63 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 11 No H-bonds generated for 'chain 'Q' and resid 9 through 11' Processing helix chain 'Q' and resid 12 through 20 Processing helix chain 'Q' and resid 24 through 46 removed outlier: 3.787A pdb=" N LYS Q 28 " --> pdb=" O SER Q 24 " (cutoff:3.500A) Processing helix chain 'Q' and resid 47 through 51 removed outlier: 3.512A pdb=" N PHE Q 50 " --> pdb=" O ASN Q 47 " (cutoff:3.500A) Processing helix chain 'Q' and resid 52 through 69 removed outlier: 3.753A pdb=" N VAL Q 67 " --> pdb=" O VAL Q 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 9 through 11 No H-bonds generated for 'chain 'R' and resid 9 through 11' Processing helix chain 'R' and resid 12 through 20 Processing helix chain 'R' and resid 24 through 46 removed outlier: 3.787A pdb=" N LYS R 28 " --> pdb=" O SER R 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 47 through 51 removed outlier: 3.512A pdb=" N PHE R 50 " --> pdb=" O ASN R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 52 through 69 removed outlier: 3.753A pdb=" N VAL R 67 " --> pdb=" O VAL R 63 " (cutoff:3.500A) Processing helix chain 'S' and resid 9 through 11 No H-bonds generated for 'chain 'S' and resid 9 through 11' Processing helix chain 'S' and resid 12 through 20 Processing helix chain 'S' and resid 24 through 46 removed outlier: 3.787A pdb=" N LYS S 28 " --> pdb=" O SER S 24 " (cutoff:3.500A) Processing helix chain 'S' and resid 47 through 51 removed outlier: 3.511A pdb=" N PHE S 50 " --> pdb=" O ASN S 47 " (cutoff:3.500A) Processing helix chain 'S' and resid 52 through 69 removed outlier: 3.754A pdb=" N VAL S 67 " --> pdb=" O VAL S 63 " (cutoff:3.500A) Processing helix chain 'T' and resid 9 through 11 No H-bonds generated for 'chain 'T' and resid 9 through 11' Processing helix chain 'T' and resid 12 through 20 Processing helix chain 'T' and resid 24 through 46 removed outlier: 3.787A pdb=" N LYS T 28 " --> pdb=" O SER T 24 " (cutoff:3.500A) Processing helix chain 'T' and resid 47 through 51 removed outlier: 3.512A pdb=" N PHE T 50 " --> pdb=" O ASN T 47 " (cutoff:3.500A) Processing helix chain 'T' and resid 52 through 69 removed outlier: 3.753A pdb=" N VAL T 67 " --> pdb=" O VAL T 63 " (cutoff:3.500A) Processing helix chain 'U' and resid 9 through 11 No H-bonds generated for 'chain 'U' and resid 9 through 11' Processing helix chain 'U' and resid 12 through 20 Processing helix chain 'U' and resid 24 through 46 removed outlier: 3.787A pdb=" N LYS U 28 " --> pdb=" O SER U 24 " (cutoff:3.500A) Processing helix chain 'U' and resid 47 through 51 removed outlier: 3.512A pdb=" N PHE U 50 " --> pdb=" O ASN U 47 " (cutoff:3.500A) Processing helix chain 'U' and resid 52 through 69 removed outlier: 3.753A pdb=" N VAL U 67 " --> pdb=" O VAL U 63 " (cutoff:3.500A) Processing helix chain 'V' and resid 9 through 11 No H-bonds generated for 'chain 'V' and resid 9 through 11' Processing helix chain 'V' and resid 12 through 20 Processing helix chain 'V' and resid 24 through 46 removed outlier: 3.787A pdb=" N LYS V 28 " --> pdb=" O SER V 24 " (cutoff:3.500A) Processing helix chain 'V' and resid 47 through 51 removed outlier: 3.512A pdb=" N PHE V 50 " --> pdb=" O ASN V 47 " (cutoff:3.500A) Processing helix chain 'V' and resid 52 through 69 removed outlier: 3.753A pdb=" N VAL V 67 " --> pdb=" O VAL V 63 " (cutoff:3.500A) Processing helix chain 'W' and resid 9 through 11 No H-bonds generated for 'chain 'W' and resid 9 through 11' Processing helix chain 'W' and resid 12 through 20 Processing helix chain 'W' and resid 24 through 46 removed outlier: 3.787A pdb=" N LYS W 28 " --> pdb=" O SER W 24 " (cutoff:3.500A) Processing helix chain 'W' and resid 47 through 51 removed outlier: 3.512A pdb=" N PHE W 50 " --> pdb=" O ASN W 47 " (cutoff:3.500A) Processing helix chain 'W' and resid 52 through 69 removed outlier: 3.753A pdb=" N VAL W 67 " --> pdb=" O VAL W 63 " (cutoff:3.500A) Processing helix chain 'X' and resid 9 through 11 No H-bonds generated for 'chain 'X' and resid 9 through 11' Processing helix chain 'X' and resid 12 through 20 Processing helix chain 'X' and resid 24 through 46 removed outlier: 3.787A pdb=" N LYS X 28 " --> pdb=" O SER X 24 " (cutoff:3.500A) Processing helix chain 'X' and resid 47 through 51 removed outlier: 3.512A pdb=" N PHE X 50 " --> pdb=" O ASN X 47 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 69 removed outlier: 3.753A pdb=" N VAL X 67 " --> pdb=" O VAL X 63 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 11 No H-bonds generated for 'chain 'Y' and resid 9 through 11' Processing helix chain 'Y' and resid 12 through 20 Processing helix chain 'Y' and resid 24 through 46 removed outlier: 3.788A pdb=" N LYS Y 28 " --> pdb=" O SER Y 24 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N MET Y 44 " --> pdb=" O VAL Y 40 " (cutoff:3.500A) Processing helix chain 'Y' and resid 47 through 51 removed outlier: 3.512A pdb=" N PHE Y 50 " --> pdb=" O ASN Y 47 " (cutoff:3.500A) Processing helix chain 'Y' and resid 52 through 69 removed outlier: 3.753A pdb=" N VAL Y 67 " --> pdb=" O VAL Y 63 " (cutoff:3.500A) Processing helix chain 'Z' and resid 9 through 11 No H-bonds generated for 'chain 'Z' and resid 9 through 11' Processing helix chain 'Z' and resid 12 through 20 Processing helix chain 'Z' and resid 24 through 46 removed outlier: 3.787A pdb=" N LYS Z 28 " --> pdb=" O SER Z 24 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N MET Z 44 " --> pdb=" O VAL Z 40 " (cutoff:3.500A) Processing helix chain 'Z' and resid 47 through 51 removed outlier: 3.511A pdb=" N PHE Z 50 " --> pdb=" O ASN Z 47 " (cutoff:3.500A) Processing helix chain 'Z' and resid 52 through 69 removed outlier: 3.753A pdb=" N VAL Z 67 " --> pdb=" O VAL Z 63 " (cutoff:3.500A) Processing helix chain '0' and resid 9 through 11 No H-bonds generated for 'chain '0' and resid 9 through 11' Processing helix chain '0' and resid 12 through 20 Processing helix chain '0' and resid 24 through 46 removed outlier: 3.787A pdb=" N LYS 0 28 " --> pdb=" O SER 0 24 " (cutoff:3.500A) Processing helix chain '0' and resid 47 through 51 removed outlier: 3.512A pdb=" N PHE 0 50 " --> pdb=" O ASN 0 47 " (cutoff:3.500A) Processing helix chain '0' and resid 52 through 69 removed outlier: 3.753A pdb=" N VAL 0 67 " --> pdb=" O VAL 0 63 " (cutoff:3.500A) Processing helix chain '1' and resid 9 through 11 No H-bonds generated for 'chain '1' and resid 9 through 11' Processing helix chain '1' and resid 12 through 20 Processing helix chain '1' and resid 24 through 46 removed outlier: 3.787A pdb=" N LYS 1 28 " --> pdb=" O SER 1 24 " (cutoff:3.500A) Processing helix chain '1' and resid 47 through 51 removed outlier: 3.512A pdb=" N PHE 1 50 " --> pdb=" O ASN 1 47 " (cutoff:3.500A) Processing helix chain '1' and resid 52 through 69 removed outlier: 3.753A pdb=" N VAL 1 67 " --> pdb=" O VAL 1 63 " (cutoff:3.500A) Processing helix chain '2' and resid 9 through 11 No H-bonds generated for 'chain '2' and resid 9 through 11' Processing helix chain '2' and resid 12 through 20 Processing helix chain '2' and resid 24 through 46 removed outlier: 3.787A pdb=" N LYS 2 28 " --> pdb=" O SER 2 24 " (cutoff:3.500A) Processing helix chain '2' and resid 47 through 51 removed outlier: 3.512A pdb=" N PHE 2 50 " --> pdb=" O ASN 2 47 " (cutoff:3.500A) Processing helix chain '2' and resid 52 through 69 removed outlier: 3.753A pdb=" N VAL 2 67 " --> pdb=" O VAL 2 63 " (cutoff:3.500A) Processing helix chain '3' and resid 9 through 11 No H-bonds generated for 'chain '3' and resid 9 through 11' Processing helix chain '3' and resid 12 through 20 Processing helix chain '3' and resid 24 through 46 removed outlier: 3.787A pdb=" N LYS 3 28 " --> pdb=" O SER 3 24 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N MET 3 44 " --> pdb=" O VAL 3 40 " (cutoff:3.500A) Processing helix chain '3' and resid 47 through 51 removed outlier: 3.512A pdb=" N PHE 3 50 " --> pdb=" O ASN 3 47 " (cutoff:3.500A) Processing helix chain '3' and resid 52 through 69 removed outlier: 3.753A pdb=" N VAL 3 67 " --> pdb=" O VAL 3 63 " (cutoff:3.500A) Processing helix chain '4' and resid 9 through 11 No H-bonds generated for 'chain '4' and resid 9 through 11' Processing helix chain '4' and resid 12 through 20 Processing helix chain '4' and resid 24 through 46 removed outlier: 3.786A pdb=" N LYS 4 28 " --> pdb=" O SER 4 24 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N MET 4 44 " --> pdb=" O VAL 4 40 " (cutoff:3.500A) Processing helix chain '4' and resid 47 through 51 removed outlier: 3.512A pdb=" N PHE 4 50 " --> pdb=" O ASN 4 47 " (cutoff:3.500A) Processing helix chain '4' and resid 52 through 69 removed outlier: 3.753A pdb=" N VAL 4 67 " --> pdb=" O VAL 4 63 " (cutoff:3.500A) Processing helix chain '5' and resid 9 through 11 No H-bonds generated for 'chain '5' and resid 9 through 11' Processing helix chain '5' and resid 12 through 20 Processing helix chain '5' and resid 24 through 46 removed outlier: 3.787A pdb=" N LYS 5 28 " --> pdb=" O SER 5 24 " (cutoff:3.500A) Processing helix chain '5' and resid 47 through 51 removed outlier: 3.512A pdb=" N PHE 5 50 " --> pdb=" O ASN 5 47 " (cutoff:3.500A) Processing helix chain '5' and resid 52 through 69 removed outlier: 3.753A pdb=" N VAL 5 67 " --> pdb=" O VAL 5 63 " (cutoff:3.500A) Processing helix chain '6' and resid 9 through 11 No H-bonds generated for 'chain '6' and resid 9 through 11' Processing helix chain '6' and resid 12 through 20 Processing helix chain '6' and resid 24 through 46 removed outlier: 3.787A pdb=" N LYS 6 28 " --> pdb=" O SER 6 24 " (cutoff:3.500A) Processing helix chain '6' and resid 47 through 51 removed outlier: 3.512A pdb=" N PHE 6 50 " --> pdb=" O ASN 6 47 " (cutoff:3.500A) Processing helix chain '6' and resid 52 through 69 removed outlier: 3.753A pdb=" N VAL 6 67 " --> pdb=" O VAL 6 63 " (cutoff:3.500A) Processing helix chain '7' and resid 9 through 11 No H-bonds generated for 'chain '7' and resid 9 through 11' Processing helix chain '7' and resid 12 through 20 Processing helix chain '7' and resid 24 through 46 removed outlier: 3.787A pdb=" N LYS 7 28 " --> pdb=" O SER 7 24 " (cutoff:3.500A) Processing helix chain '7' and resid 47 through 51 removed outlier: 3.512A pdb=" N PHE 7 50 " --> pdb=" O ASN 7 47 " (cutoff:3.500A) Processing helix chain '7' and resid 52 through 69 removed outlier: 3.753A pdb=" N VAL 7 67 " --> pdb=" O VAL 7 63 " (cutoff:3.500A) Processing helix chain '8' and resid 9 through 11 No H-bonds generated for 'chain '8' and resid 9 through 11' Processing helix chain '8' and resid 12 through 20 Processing helix chain '8' and resid 24 through 46 removed outlier: 3.787A pdb=" N LYS 8 28 " --> pdb=" O SER 8 24 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N MET 8 44 " --> pdb=" O VAL 8 40 " (cutoff:3.500A) Processing helix chain '8' and resid 47 through 51 removed outlier: 3.512A pdb=" N PHE 8 50 " --> pdb=" O ASN 8 47 " (cutoff:3.500A) Processing helix chain '8' and resid 52 through 69 removed outlier: 3.753A pdb=" N VAL 8 67 " --> pdb=" O VAL 8 63 " (cutoff:3.500A) Processing helix chain '9' and resid 9 through 11 No H-bonds generated for 'chain '9' and resid 9 through 11' Processing helix chain '9' and resid 12 through 20 Processing helix chain '9' and resid 24 through 46 removed outlier: 3.788A pdb=" N LYS 9 28 " --> pdb=" O SER 9 24 " (cutoff:3.500A) Processing helix chain '9' and resid 47 through 51 removed outlier: 3.512A pdb=" N PHE 9 50 " --> pdb=" O ASN 9 47 " (cutoff:3.500A) Processing helix chain '9' and resid 52 through 69 removed outlier: 3.754A pdb=" N VAL 9 67 " --> pdb=" O VAL 9 63 " (cutoff:3.500A) Processing helix chain 'a' and resid 9 through 11 No H-bonds generated for 'chain 'a' and resid 9 through 11' Processing helix chain 'a' and resid 12 through 20 Processing helix chain 'a' and resid 24 through 46 removed outlier: 3.787A pdb=" N LYS a 28 " --> pdb=" O SER a 24 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N MET a 44 " --> pdb=" O VAL a 40 " (cutoff:3.500A) Processing helix chain 'a' and resid 47 through 51 removed outlier: 3.512A pdb=" N PHE a 50 " --> pdb=" O ASN a 47 " (cutoff:3.500A) Processing helix chain 'a' and resid 52 through 69 removed outlier: 3.753A pdb=" N VAL a 67 " --> pdb=" O VAL a 63 " (cutoff:3.500A) Processing helix chain 'b' and resid 9 through 11 No H-bonds generated for 'chain 'b' and resid 9 through 11' Processing helix chain 'b' and resid 12 through 20 Processing helix chain 'b' and resid 24 through 46 removed outlier: 3.787A pdb=" N LYS b 28 " --> pdb=" O SER b 24 " (cutoff:3.500A) Processing helix chain 'b' and resid 47 through 51 removed outlier: 3.512A pdb=" N PHE b 50 " --> pdb=" O ASN b 47 " (cutoff:3.500A) Processing helix chain 'b' and resid 52 through 69 removed outlier: 3.753A pdb=" N VAL b 67 " --> pdb=" O VAL b 63 " (cutoff:3.500A) Processing helix chain 'c' and resid 9 through 11 No H-bonds generated for 'chain 'c' and resid 9 through 11' Processing helix chain 'c' and resid 12 through 20 Processing helix chain 'c' and resid 24 through 46 removed outlier: 3.787A pdb=" N LYS c 28 " --> pdb=" O SER c 24 " (cutoff:3.500A) Processing helix chain 'c' and resid 47 through 51 removed outlier: 3.511A pdb=" N PHE c 50 " --> pdb=" O ASN c 47 " (cutoff:3.500A) Processing helix chain 'c' and resid 52 through 69 removed outlier: 3.753A pdb=" N VAL c 67 " --> pdb=" O VAL c 63 " (cutoff:3.500A) Processing helix chain 'd' and resid 9 through 11 No H-bonds generated for 'chain 'd' and resid 9 through 11' Processing helix chain 'd' and resid 12 through 20 Processing helix chain 'd' and resid 24 through 46 removed outlier: 3.787A pdb=" N LYS d 28 " --> pdb=" O SER d 24 " (cutoff:3.500A) Processing helix chain 'd' and resid 47 through 51 removed outlier: 3.511A pdb=" N PHE d 50 " --> pdb=" O ASN d 47 " (cutoff:3.500A) Processing helix chain 'd' and resid 52 through 69 removed outlier: 3.753A pdb=" N VAL d 67 " --> pdb=" O VAL d 63 " (cutoff:3.500A) Processing helix chain 'e' and resid 9 through 11 No H-bonds generated for 'chain 'e' and resid 9 through 11' Processing helix chain 'e' and resid 12 through 20 Processing helix chain 'e' and resid 24 through 46 removed outlier: 3.787A pdb=" N LYS e 28 " --> pdb=" O SER e 24 " (cutoff:3.500A) Processing helix chain 'e' and resid 47 through 51 removed outlier: 3.512A pdb=" N PHE e 50 " --> pdb=" O ASN e 47 " (cutoff:3.500A) Processing helix chain 'e' and resid 52 through 69 removed outlier: 3.753A pdb=" N VAL e 67 " --> pdb=" O VAL e 63 " (cutoff:3.500A) Processing helix chain 'f' and resid 9 through 11 No H-bonds generated for 'chain 'f' and resid 9 through 11' Processing helix chain 'f' and resid 12 through 20 Processing helix chain 'f' and resid 24 through 46 removed outlier: 3.787A pdb=" N LYS f 28 " --> pdb=" O SER f 24 " (cutoff:3.500A) Processing helix chain 'f' and resid 47 through 51 removed outlier: 3.512A pdb=" N PHE f 50 " --> pdb=" O ASN f 47 " (cutoff:3.500A) Processing helix chain 'f' and resid 52 through 69 removed outlier: 3.754A pdb=" N VAL f 67 " --> pdb=" O VAL f 63 " (cutoff:3.500A) Processing helix chain 'g' and resid 9 through 11 No H-bonds generated for 'chain 'g' and resid 9 through 11' Processing helix chain 'g' and resid 12 through 20 Processing helix chain 'g' and resid 24 through 46 removed outlier: 3.786A pdb=" N LYS g 28 " --> pdb=" O SER g 24 " (cutoff:3.500A) Processing helix chain 'g' and resid 47 through 51 removed outlier: 3.512A pdb=" N PHE g 50 " --> pdb=" O ASN g 47 " (cutoff:3.500A) Processing helix chain 'g' and resid 52 through 69 removed outlier: 3.753A pdb=" N VAL g 67 " --> pdb=" O VAL g 63 " (cutoff:3.500A) Processing helix chain 'h' and resid 9 through 11 No H-bonds generated for 'chain 'h' and resid 9 through 11' Processing helix chain 'h' and resid 12 through 20 Processing helix chain 'h' and resid 24 through 46 removed outlier: 3.786A pdb=" N LYS h 28 " --> pdb=" O SER h 24 " (cutoff:3.500A) Processing helix chain 'h' and resid 47 through 51 removed outlier: 3.512A pdb=" N PHE h 50 " --> pdb=" O ASN h 47 " (cutoff:3.500A) Processing helix chain 'h' and resid 52 through 69 removed outlier: 3.753A pdb=" N VAL h 67 " --> pdb=" O VAL h 63 " (cutoff:3.500A) Processing helix chain 'i' and resid 9 through 11 No H-bonds generated for 'chain 'i' and resid 9 through 11' Processing helix chain 'i' and resid 12 through 20 Processing helix chain 'i' and resid 24 through 46 removed outlier: 3.787A pdb=" N LYS i 28 " --> pdb=" O SER i 24 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N MET i 44 " --> pdb=" O VAL i 40 " (cutoff:3.500A) Processing helix chain 'i' and resid 47 through 51 removed outlier: 3.512A pdb=" N PHE i 50 " --> pdb=" O ASN i 47 " (cutoff:3.500A) Processing helix chain 'i' and resid 52 through 69 removed outlier: 3.753A pdb=" N VAL i 67 " --> pdb=" O VAL i 63 " (cutoff:3.500A) Processing helix chain 'j' and resid 9 through 11 No H-bonds generated for 'chain 'j' and resid 9 through 11' Processing helix chain 'j' and resid 12 through 20 Processing helix chain 'j' and resid 24 through 46 removed outlier: 3.786A pdb=" N LYS j 28 " --> pdb=" O SER j 24 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N MET j 44 " --> pdb=" O VAL j 40 " (cutoff:3.500A) Processing helix chain 'j' and resid 47 through 51 removed outlier: 3.512A pdb=" N PHE j 50 " --> pdb=" O ASN j 47 " (cutoff:3.500A) Processing helix chain 'j' and resid 52 through 69 removed outlier: 3.753A pdb=" N VAL j 67 " --> pdb=" O VAL j 63 " (cutoff:3.500A) Processing helix chain 'k' and resid 9 through 11 No H-bonds generated for 'chain 'k' and resid 9 through 11' Processing helix chain 'k' and resid 12 through 20 Processing helix chain 'k' and resid 24 through 46 removed outlier: 3.787A pdb=" N LYS k 28 " --> pdb=" O SER k 24 " (cutoff:3.500A) Processing helix chain 'k' and resid 47 through 51 removed outlier: 3.512A pdb=" N PHE k 50 " --> pdb=" O ASN k 47 " (cutoff:3.500A) Processing helix chain 'k' and resid 52 through 69 removed outlier: 3.753A pdb=" N VAL k 67 " --> pdb=" O VAL k 63 " (cutoff:3.500A) Processing helix chain 'l' and resid 9 through 11 No H-bonds generated for 'chain 'l' and resid 9 through 11' Processing helix chain 'l' and resid 12 through 20 Processing helix chain 'l' and resid 24 through 46 removed outlier: 3.787A pdb=" N LYS l 28 " --> pdb=" O SER l 24 " (cutoff:3.500A) Processing helix chain 'l' and resid 47 through 51 removed outlier: 3.512A pdb=" N PHE l 50 " --> pdb=" O ASN l 47 " (cutoff:3.500A) Processing helix chain 'l' and resid 52 through 69 removed outlier: 3.753A pdb=" N VAL l 67 " --> pdb=" O VAL l 63 " (cutoff:3.500A) Processing helix chain 'm' and resid 9 through 11 No H-bonds generated for 'chain 'm' and resid 9 through 11' Processing helix chain 'm' and resid 12 through 20 Processing helix chain 'm' and resid 24 through 46 removed outlier: 3.786A pdb=" N LYS m 28 " --> pdb=" O SER m 24 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N MET m 44 " --> pdb=" O VAL m 40 " (cutoff:3.500A) Processing helix chain 'm' and resid 47 through 51 removed outlier: 3.512A pdb=" N PHE m 50 " --> pdb=" O ASN m 47 " (cutoff:3.500A) Processing helix chain 'm' and resid 52 through 69 removed outlier: 3.753A pdb=" N VAL m 67 " --> pdb=" O VAL m 63 " (cutoff:3.500A) Processing helix chain 'n' and resid 9 through 11 No H-bonds generated for 'chain 'n' and resid 9 through 11' Processing helix chain 'n' and resid 12 through 20 Processing helix chain 'n' and resid 24 through 46 removed outlier: 3.786A pdb=" N LYS n 28 " --> pdb=" O SER n 24 " (cutoff:3.500A) Processing helix chain 'n' and resid 47 through 51 removed outlier: 3.512A pdb=" N PHE n 50 " --> pdb=" O ASN n 47 " (cutoff:3.500A) Processing helix chain 'n' and resid 52 through 69 removed outlier: 3.753A pdb=" N VAL n 67 " --> pdb=" O VAL n 63 " (cutoff:3.500A) 1836 hydrogen bonds defined for protein. 5358 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: 3.83 Time building geometry restraints manager: 2.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 3800 1.30 - 1.43: 5800 1.43 - 1.55: 15850 1.55 - 1.68: 100 1.68 - 1.80: 500 Bond restraints: 26050 Sorted by residual: bond pdb=" C12 X41 Y 101 " pdb=" C13 X41 Y 101 " ideal model delta sigma weight residual 1.333 1.522 -0.189 2.00e-02 2.50e+03 8.91e+01 bond pdb=" C12 X41 i 101 " pdb=" C13 X41 i 101 " ideal model delta sigma weight residual 1.333 1.522 -0.189 2.00e-02 2.50e+03 8.91e+01 bond pdb=" C12 X41 O 101 " pdb=" C13 X41 O 101 " ideal model delta sigma weight residual 1.333 1.522 -0.189 2.00e-02 2.50e+03 8.90e+01 bond pdb=" C12 X41 B 101 " pdb=" C13 X41 B 101 " ideal model delta sigma weight residual 1.333 1.522 -0.189 2.00e-02 2.50e+03 8.90e+01 bond pdb=" C12 X41 J 101 " pdb=" C13 X41 J 101 " ideal model delta sigma weight residual 1.333 1.522 -0.189 2.00e-02 2.50e+03 8.90e+01 ... (remaining 26045 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.44: 33804 3.44 - 6.87: 596 6.87 - 10.30: 200 10.30 - 13.74: 50 13.74 - 17.17: 100 Bond angle restraints: 34750 Sorted by residual: angle pdb=" C11 X41 j 101 " pdb=" C12 X41 j 101 " pdb=" C13 X41 j 101 " ideal model delta sigma weight residual 127.71 110.54 17.17 3.00e+00 1.11e-01 3.28e+01 angle pdb=" C11 X41 U 101 " pdb=" C12 X41 U 101 " pdb=" C13 X41 U 101 " ideal model delta sigma weight residual 127.71 110.55 17.16 3.00e+00 1.11e-01 3.27e+01 angle pdb=" C11 X41 O 101 " pdb=" C12 X41 O 101 " pdb=" C13 X41 O 101 " ideal model delta sigma weight residual 127.71 110.55 17.16 3.00e+00 1.11e-01 3.27e+01 angle pdb=" C11 X41 Y 101 " pdb=" C12 X41 Y 101 " pdb=" C13 X41 Y 101 " ideal model delta sigma weight residual 127.71 110.55 17.16 3.00e+00 1.11e-01 3.27e+01 angle pdb=" C11 X41 h 101 " pdb=" C12 X41 h 101 " pdb=" C13 X41 h 101 " ideal model delta sigma weight residual 127.71 110.56 17.15 3.00e+00 1.11e-01 3.27e+01 ... (remaining 34745 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.94: 13050 11.94 - 23.89: 1300 23.89 - 35.83: 450 35.83 - 47.77: 450 47.77 - 59.71: 100 Dihedral angle restraints: 15350 sinusoidal: 6200 harmonic: 9150 Sorted by residual: dihedral pdb=" CB MET h 41 " pdb=" CG MET h 41 " pdb=" SD MET h 41 " pdb=" CE MET h 41 " ideal model delta sinusoidal sigma weight residual 60.00 100.69 -40.69 3 1.50e+01 4.44e-03 7.26e+00 dihedral pdb=" CB MET k 41 " pdb=" CG MET k 41 " pdb=" SD MET k 41 " pdb=" CE MET k 41 " ideal model delta sinusoidal sigma weight residual 60.00 100.68 -40.68 3 1.50e+01 4.44e-03 7.26e+00 dihedral pdb=" CB MET 0 41 " pdb=" CG MET 0 41 " pdb=" SD MET 0 41 " pdb=" CE MET 0 41 " ideal model delta sinusoidal sigma weight residual 60.00 100.68 -40.68 3 1.50e+01 4.44e-03 7.26e+00 ... (remaining 15347 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1456 0.028 - 0.056: 1793 0.056 - 0.084: 850 0.084 - 0.112: 1 0.112 - 0.140: 150 Chirality restraints: 4250 Sorted by residual: chirality pdb=" C2 X41 5 101 " pdb=" C1 X41 5 101 " pdb=" C3 X41 5 101 " pdb=" O7 X41 5 101 " both_signs ideal model delta sigma weight residual False -2.35 -2.49 0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" C2 X41 a 101 " pdb=" C1 X41 a 101 " pdb=" C3 X41 a 101 " pdb=" O7 X41 a 101 " both_signs ideal model delta sigma weight residual False -2.35 -2.49 0.14 2.00e-01 2.50e+01 4.88e-01 chirality pdb=" C2 X41 l 101 " pdb=" C1 X41 l 101 " pdb=" C3 X41 l 101 " pdb=" O7 X41 l 101 " both_signs ideal model delta sigma weight residual False -2.35 -2.49 0.14 2.00e-01 2.50e+01 4.86e-01 ... (remaining 4247 not shown) Planarity restraints: 3950 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 X41 Z 101 " -0.301 2.00e-02 2.50e+03 3.17e-01 1.00e+03 pdb=" C12 X41 Z 101 " 0.266 2.00e-02 2.50e+03 pdb=" C13 X41 Z 101 " 0.363 2.00e-02 2.50e+03 pdb=" C14 X41 Z 101 " -0.329 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 X41 F 101 " -0.301 2.00e-02 2.50e+03 3.17e-01 1.00e+03 pdb=" C12 X41 F 101 " 0.266 2.00e-02 2.50e+03 pdb=" C13 X41 F 101 " 0.363 2.00e-02 2.50e+03 pdb=" C14 X41 F 101 " -0.329 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 X41 Q 101 " -0.300 2.00e-02 2.50e+03 3.17e-01 1.00e+03 pdb=" C12 X41 Q 101 " 0.264 2.00e-02 2.50e+03 pdb=" C13 X41 Q 101 " 0.365 2.00e-02 2.50e+03 pdb=" C14 X41 Q 101 " -0.329 2.00e-02 2.50e+03 ... (remaining 3947 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 9228 2.86 - 3.37: 22884 3.37 - 3.88: 36264 3.88 - 4.39: 39089 4.39 - 4.90: 73840 Nonbonded interactions: 181305 Sorted by model distance: nonbonded pdb=" O ALA 5 18 " pdb=" OD1 ASP 6 7 " model vdw 2.349 3.040 nonbonded pdb=" O ALA f 18 " pdb=" OD1 ASP g 7 " model vdw 2.350 3.040 nonbonded pdb=" O ALA 6 18 " pdb=" OD1 ASP 7 7 " model vdw 2.350 3.040 nonbonded pdb=" O ALA M 18 " pdb=" OD1 ASP N 7 " model vdw 2.350 3.040 nonbonded pdb=" O ALA U 18 " pdb=" OD1 ASP V 7 " model vdw 2.350 3.040 ... (remaining 181300 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: 0.11 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 '0' selection = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' selection = 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' } 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=0.30 max=1.00 mean=0.95 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 16.630 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 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 : 0.014 0.189 26050 Z= 0.680 Angle : 1.534 17.175 34750 Z= 0.597 Chirality : 0.047 0.140 4250 Planarity : 0.036 0.317 3950 Dihedral : 14.576 59.712 9450 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 13.73 % Favored : 86.27 % 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 are not related in a simple way. whole: -3.47 (0.12), residues: 3150 helix: -1.98 (0.08), residues: 2450 sheet: None (None), residues: 0 loop : -2.70 (0.16), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.003 TYR f 42 PHE 0.018 0.004 PHE D 54 TRP 0.006 0.002 TRP H 29 Details of bonding type rmsd/Z covalent geometry : bond 0.01407 / 0.68 (26050) covalent geometry : angle 1.53416 / 0.60 (34750) hydrogen bonds : bond 0.26598 / 17.46 ( 1836) hydrogen bonds : angle 8.03920 / 5.56 ( 5358) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 538 time to evaluate : 0.881 Fit side-chains REVERT: E 65 MET cc_start: 0.8611 (mmt) cc_final: 0.8120 (mmt) REVERT: O 65 MET cc_start: 0.9015 (mmt) cc_final: 0.8584 (mmt) REVERT: 8 65 MET cc_start: 0.9004 (mmt) cc_final: 0.8526 (mmt) REVERT: e 17 LYS cc_start: 0.6694 (tttt) cc_final: 0.6432 (tmtt) REVERT: i 65 MET cc_start: 0.9004 (mmt) cc_final: 0.8603 (mmt) outliers start: 0 outliers final: 0 residues processed: 538 average time/residue: 0.1566 time to fit residues: 132.6483 Evaluate side-chains 425 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 425 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 10.0000 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.139218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.124875 restraints weight = 35409.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.125399 restraints weight = 25997.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.126085 restraints weight = 21772.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.126525 restraints weight = 18235.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.126742 restraints weight = 16571.022| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3454 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3279 r_free = 0.3279 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.3279 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 26050 Z= 0.118 Angle : 0.465 3.920 34750 Z= 0.262 Chirality : 0.036 0.110 4250 Planarity : 0.002 0.009 3950 Dihedral : 13.157 57.893 4550 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.75 % Allowed : 10.63 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.14), residues: 3150 helix: 0.79 (0.10), residues: 2400 sheet: None (None), residues: 0 loop : -0.76 (0.18), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR I 42 PHE 0.016 0.001 PHE I 60 TRP 0.003 0.000 TRP 4 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.12 (26050) covalent geometry : angle 0.46523 / 0.26 (34750) hydrogen bonds : bond 0.05140 / 3.35 ( 1836) hydrogen bonds : angle 4.41461 / 3.04 ( 5358) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 454 time to evaluate : 0.952 Fit side-chains REVERT: Z 65 MET cc_start: 0.8539 (mmt) cc_final: 0.8227 (mmt) REVERT: 4 17 LYS cc_start: 0.7170 (tmtt) cc_final: 0.6755 (tttt) REVERT: 8 65 MET cc_start: 0.8672 (mmt) cc_final: 0.8200 (mmt) REVERT: d 42 TYR cc_start: 0.7234 (t80) cc_final: 0.6715 (t80) REVERT: k 43 MET cc_start: 0.9243 (tmm) cc_final: 0.9027 (tmm) REVERT: n 42 TYR cc_start: 0.7401 (t80) cc_final: 0.6854 (t80) outliers start: 19 outliers final: 14 residues processed: 462 average time/residue: 0.1551 time to fit residues: 114.1462 Evaluate side-chains 439 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 425 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain M residue 15 THR Chi-restraints excluded: chain V residue 15 THR Chi-restraints excluded: chain W residue 15 THR Chi-restraints excluded: chain Y residue 15 THR Chi-restraints excluded: chain 5 residue 15 THR Chi-restraints excluded: chain 6 residue 15 THR Chi-restraints excluded: chain 8 residue 15 THR Chi-restraints excluded: chain f residue 15 THR Chi-restraints excluded: chain g residue 15 THR Chi-restraints excluded: chain k residue 41 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 263 optimal weight: 3.9990 chunk 288 optimal weight: 10.0000 chunk 120 optimal weight: 70.0000 chunk 85 optimal weight: 7.9990 chunk 213 optimal weight: 0.9990 chunk 242 optimal weight: 8.9990 chunk 271 optimal weight: 0.1980 chunk 48 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 chunk 147 optimal weight: 4.9990 chunk 138 optimal weight: 9.9990 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 13 ASN M 13 ASN O 13 ASN V 13 ASN W 13 ASN Y 13 ASN 5 13 ASN 8 13 ASN g 13 ASN i 13 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.120776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.106165 restraints weight = 36835.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.108055 restraints weight = 21489.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.109132 restraints weight = 14608.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.110126 restraints weight = 11358.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.110581 restraints weight = 9438.206| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3204 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.3197 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 26050 Z= 0.141 Angle : 0.459 5.770 34750 Z= 0.255 Chirality : 0.037 0.119 4250 Planarity : 0.002 0.009 3950 Dihedral : 12.772 59.996 4550 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.03 % Favored : 99.97 % Rotamer: Outliers : 0.94 % Allowed : 13.84 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.14), residues: 3150 helix: 1.48 (0.10), residues: 2400 sheet: None (None), residues: 0 loop : -0.93 (0.18), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR g 42 PHE 0.011 0.002 PHE L 54 TRP 0.003 0.001 TRP F 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (26050) covalent geometry : angle 0.45915 / 0.26 (34750) hydrogen bonds : bond 0.06003 / 3.93 ( 1836) hydrogen bonds : angle 4.32555 / 2.98 ( 5358) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 471 time to evaluate : 0.661 Fit side-chains REVERT: K 17 LYS cc_start: 0.7217 (tttt) cc_final: 0.6972 (tttm) REVERT: 4 17 LYS cc_start: 0.7293 (tmtt) cc_final: 0.6847 (tttt) REVERT: 4 28 LYS cc_start: 0.7882 (mttt) cc_final: 0.7604 (mttp) REVERT: e 17 LYS cc_start: 0.7159 (tttt) cc_final: 0.6940 (tttm) REVERT: m 42 TYR cc_start: 0.8128 (t80) cc_final: 0.7918 (t80) REVERT: n 42 TYR cc_start: 0.7244 (t80) cc_final: 0.6681 (t80) outliers start: 24 outliers final: 18 residues processed: 481 average time/residue: 0.1531 time to fit residues: 116.6536 Evaluate side-chains 464 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 446 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain M residue 15 THR Chi-restraints excluded: chain O residue 15 THR Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain V residue 15 THR Chi-restraints excluded: chain W residue 15 THR Chi-restraints excluded: chain Y residue 15 THR Chi-restraints excluded: chain 5 residue 15 THR Chi-restraints excluded: chain 6 residue 15 THR Chi-restraints excluded: chain 8 residue 15 THR Chi-restraints excluded: chain e residue 15 THR Chi-restraints excluded: chain f residue 11 SER Chi-restraints excluded: chain f residue 15 THR Chi-restraints excluded: chain g residue 15 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 108 optimal weight: 9.9990 chunk 125 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 148 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 200 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 117 optimal weight: 3.9990 chunk 286 optimal weight: 9.9990 chunk 127 optimal weight: 7.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 13 ASN C 13 ASN E 13 ASN F 13 ASN G 13 ASN K 13 ASN L 13 ASN N 13 ASN U 13 ASN X 13 ASN Z 13 ASN 4 13 ASN 6 13 ASN 7 13 ASN 9 13 ASN e 13 ASN f 13 ASN h 13 ASN j 13 ASN l 13 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.122252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.108286 restraints weight = 36179.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.110147 restraints weight = 20644.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.111231 restraints weight = 13818.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.112154 restraints weight = 10609.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.112524 restraints weight = 8761.463| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3241 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3241 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 26050 Z= 0.115 Angle : 0.406 4.369 34750 Z= 0.231 Chirality : 0.036 0.113 4250 Planarity : 0.002 0.010 3950 Dihedral : 12.142 59.994 4550 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.14 % Allowed : 17.25 % Favored : 81.61 % 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 are not related in a simple way. whole: 2.05 (0.14), residues: 3150 helix: 2.08 (0.10), residues: 2400 sheet: None (None), residues: 0 loop : -1.06 (0.18), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR 6 42 PHE 0.022 0.002 PHE S 60 TRP 0.002 0.000 TRP i 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (26050) covalent geometry : angle 0.40644 / 0.23 (34750) hydrogen bonds : bond 0.04863 / 3.18 ( 1836) hydrogen bonds : angle 4.12626 / 2.85 ( 5358) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 453 time to evaluate : 0.753 Fit side-chains REVERT: K 17 LYS cc_start: 0.7184 (tttt) cc_final: 0.6963 (tttm) REVERT: 4 17 LYS cc_start: 0.7365 (tmtt) cc_final: 0.6956 (tttt) REVERT: e 22 LYS cc_start: 0.6741 (tptp) cc_final: 0.6434 (tptt) REVERT: m 42 TYR cc_start: 0.8055 (t80) cc_final: 0.7813 (t80) outliers start: 29 outliers final: 21 residues processed: 464 average time/residue: 0.1481 time to fit residues: 109.2902 Evaluate side-chains 449 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 428 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain M residue 14 THR Chi-restraints excluded: chain M residue 15 THR Chi-restraints excluded: chain O residue 15 THR Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain V residue 15 THR Chi-restraints excluded: chain W residue 15 THR Chi-restraints excluded: chain Y residue 15 THR Chi-restraints excluded: chain Z residue 41 MET Chi-restraints excluded: chain 5 residue 15 THR Chi-restraints excluded: chain 6 residue 15 THR Chi-restraints excluded: chain 8 residue 15 THR Chi-restraints excluded: chain f residue 11 SER Chi-restraints excluded: chain f residue 15 THR Chi-restraints excluded: chain g residue 15 THR Chi-restraints excluded: chain i residue 23 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 39 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 286 optimal weight: 8.9990 chunk 61 optimal weight: 20.0000 chunk 158 optimal weight: 0.9990 chunk 166 optimal weight: 0.4980 chunk 165 optimal weight: 0.9980 chunk 77 optimal weight: 7.9990 chunk 255 optimal weight: 4.9990 chunk 244 optimal weight: 10.0000 chunk 217 optimal weight: 9.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 ASN H 13 ASN J 13 ASN P 13 ASN Q 13 ASN R 13 ASN 0 13 ASN 3 13 ASN a 13 ASN k 13 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.121528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.107761 restraints weight = 36251.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.109579 restraints weight = 20589.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.110817 restraints weight = 13796.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.111488 restraints weight = 10410.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.112089 restraints weight = 8735.268| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3243 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3243 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 26050 Z= 0.107 Angle : 0.396 5.846 34750 Z= 0.223 Chirality : 0.036 0.124 4250 Planarity : 0.002 0.011 3950 Dihedral : 11.845 59.839 4550 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.03 % Favored : 99.97 % Rotamer: Outliers : 1.18 % Allowed : 18.27 % Favored : 80.55 % 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 are not related in a simple way. whole: 2.43 (0.14), residues: 3150 helix: 2.40 (0.10), residues: 2400 sheet: None (None), residues: 0 loop : -1.15 (0.18), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR I 42 PHE 0.016 0.002 PHE J 60 TRP 0.002 0.000 TRP F 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (26050) covalent geometry : angle 0.39582 / 0.22 (34750) hydrogen bonds : bond 0.04605 / 3.02 ( 1836) hydrogen bonds : angle 4.02797 / 2.78 ( 5358) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 433 time to evaluate : 0.837 Fit side-chains REVERT: K 17 LYS cc_start: 0.7371 (tttt) cc_final: 0.7115 (tttm) REVERT: Y 43 MET cc_start: 0.9056 (tmm) cc_final: 0.8830 (tmm) REVERT: 4 17 LYS cc_start: 0.7353 (tmtt) cc_final: 0.6980 (tttt) REVERT: e 22 LYS cc_start: 0.6740 (tptp) cc_final: 0.6449 (tptt) REVERT: m 42 TYR cc_start: 0.7996 (t80) cc_final: 0.7724 (t80) outliers start: 30 outliers final: 24 residues processed: 450 average time/residue: 0.1491 time to fit residues: 106.5418 Evaluate side-chains 447 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 423 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 65 MET Chi-restraints excluded: chain M residue 14 THR Chi-restraints excluded: chain M residue 15 THR Chi-restraints excluded: chain M residue 57 ILE Chi-restraints excluded: chain O residue 15 THR Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain V residue 15 THR Chi-restraints excluded: chain W residue 14 THR Chi-restraints excluded: chain W residue 15 THR Chi-restraints excluded: chain Y residue 15 THR Chi-restraints excluded: chain Z residue 41 MET Chi-restraints excluded: chain 5 residue 15 THR Chi-restraints excluded: chain 6 residue 15 THR Chi-restraints excluded: chain 8 residue 15 THR Chi-restraints excluded: chain c residue 44 MET Chi-restraints excluded: chain f residue 11 SER Chi-restraints excluded: chain f residue 15 THR Chi-restraints excluded: chain g residue 15 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 62 optimal weight: 2.9990 chunk 174 optimal weight: 0.5980 chunk 190 optimal weight: 10.0000 chunk 102 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 chunk 184 optimal weight: 9.9990 chunk 42 optimal weight: 7.9990 chunk 178 optimal weight: 6.9990 chunk 299 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 165 optimal weight: 1.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... T 13 ASN 1 13 ASN b 13 ASN d 13 ASN n 13 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.122378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.108711 restraints weight = 36185.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.110605 restraints weight = 20475.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.111828 restraints weight = 13494.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.112472 restraints weight = 10163.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.113068 restraints weight = 8535.729| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3261 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3261 r_free = 0.3261 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3261 r_free = 0.3261 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3261 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 26050 Z= 0.102 Angle : 0.390 5.116 34750 Z= 0.219 Chirality : 0.035 0.121 4250 Planarity : 0.002 0.012 3950 Dihedral : 11.584 59.972 4550 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Rotamer: Outliers : 1.25 % Allowed : 18.67 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.63 (0.14), residues: 3150 helix: 2.60 (0.10), residues: 2400 sheet: None (None), residues: 0 loop : -1.24 (0.18), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR 6 42 PHE 0.025 0.001 PHE n 60 TRP 0.002 0.000 TRP n 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 (26050) covalent geometry : angle 0.38957 / 0.22 (34750) hydrogen bonds : bond 0.04317 / 2.83 ( 1836) hydrogen bonds : angle 3.95808 / 2.74 ( 5358) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 442 time to evaluate : 0.874 Fit side-chains REVERT: 3 36 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7410 (mp) REVERT: 4 17 LYS cc_start: 0.7381 (tmtt) cc_final: 0.7000 (tttt) REVERT: e 22 LYS cc_start: 0.6710 (tptp) cc_final: 0.6446 (tptt) REVERT: m 42 TYR cc_start: 0.7955 (t80) cc_final: 0.7687 (t80) outliers start: 32 outliers final: 27 residues processed: 459 average time/residue: 0.1529 time to fit residues: 112.4344 Evaluate side-chains 454 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 426 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 65 MET Chi-restraints excluded: chain M residue 14 THR Chi-restraints excluded: chain M residue 15 THR Chi-restraints excluded: chain M residue 57 ILE Chi-restraints excluded: chain O residue 15 THR Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain U residue 57 ILE Chi-restraints excluded: chain V residue 15 THR Chi-restraints excluded: chain W residue 14 THR Chi-restraints excluded: chain W residue 15 THR Chi-restraints excluded: chain Y residue 15 THR Chi-restraints excluded: chain Z residue 41 MET Chi-restraints excluded: chain 3 residue 36 LEU Chi-restraints excluded: chain 5 residue 15 THR Chi-restraints excluded: chain 6 residue 15 THR Chi-restraints excluded: chain 8 residue 15 THR Chi-restraints excluded: chain c residue 44 MET Chi-restraints excluded: chain f residue 11 SER Chi-restraints excluded: chain f residue 15 THR Chi-restraints excluded: chain g residue 15 THR Chi-restraints excluded: chain g residue 57 ILE Chi-restraints excluded: chain i residue 23 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 247 optimal weight: 8.9990 chunk 237 optimal weight: 2.9990 chunk 265 optimal weight: 5.9990 chunk 168 optimal weight: 0.5980 chunk 52 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 285 optimal weight: 2.9990 chunk 269 optimal weight: 3.9990 chunk 133 optimal weight: 8.9990 chunk 148 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.119988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.106419 restraints weight = 36401.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.108263 restraints weight = 20624.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.109479 restraints weight = 13659.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.110126 restraints weight = 10303.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.110678 restraints weight = 8700.838| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3217 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3217 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 26050 Z= 0.141 Angle : 0.449 7.434 34750 Z= 0.249 Chirality : 0.037 0.126 4250 Planarity : 0.002 0.016 3950 Dihedral : 12.396 59.908 4550 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 1.29 % Allowed : 19.02 % Favored : 79.69 % 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 are not related in a simple way. whole: 2.47 (0.14), residues: 3150 helix: 2.51 (0.10), residues: 2400 sheet: None (None), residues: 0 loop : -1.43 (0.17), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR 6 42 PHE 0.018 0.002 PHE n 60 TRP 0.002 0.000 TRP F 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (26050) covalent geometry : angle 0.44854 / 0.25 (34750) hydrogen bonds : bond 0.05654 / 3.70 ( 1836) hydrogen bonds : angle 4.02293 / 2.78 ( 5358) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 432 time to evaluate : 0.836 Fit side-chains REVERT: Y 43 MET cc_start: 0.9040 (tmm) cc_final: 0.8836 (tmm) REVERT: 3 36 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7483 (mp) REVERT: 4 17 LYS cc_start: 0.7476 (tmtt) cc_final: 0.7075 (tttt) REVERT: 4 28 LYS cc_start: 0.7984 (mttt) cc_final: 0.7712 (mttp) REVERT: m 42 TYR cc_start: 0.8016 (t80) cc_final: 0.7733 (t80) outliers start: 33 outliers final: 27 residues processed: 447 average time/residue: 0.1543 time to fit residues: 110.2091 Evaluate side-chains 453 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 425 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 65 MET Chi-restraints excluded: chain M residue 14 THR Chi-restraints excluded: chain M residue 15 THR Chi-restraints excluded: chain M residue 57 ILE Chi-restraints excluded: chain O residue 15 THR Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain V residue 15 THR Chi-restraints excluded: chain W residue 14 THR Chi-restraints excluded: chain W residue 15 THR Chi-restraints excluded: chain Y residue 15 THR Chi-restraints excluded: chain Z residue 41 MET Chi-restraints excluded: chain 3 residue 36 LEU Chi-restraints excluded: chain 5 residue 15 THR Chi-restraints excluded: chain 6 residue 15 THR Chi-restraints excluded: chain 8 residue 15 THR Chi-restraints excluded: chain c residue 44 MET Chi-restraints excluded: chain f residue 11 SER Chi-restraints excluded: chain f residue 15 THR Chi-restraints excluded: chain g residue 14 THR Chi-restraints excluded: chain g residue 15 THR Chi-restraints excluded: chain g residue 57 ILE Chi-restraints excluded: chain h residue 14 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 48 optimal weight: 8.9990 chunk 171 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 168 optimal weight: 5.9990 chunk 79 optimal weight: 0.0040 chunk 265 optimal weight: 8.9990 chunk 62 optimal weight: 0.9990 chunk 31 optimal weight: 9.9990 chunk 282 optimal weight: 4.9990 chunk 178 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 overall best weight: 2.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.122036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.108486 restraints weight = 36258.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.110328 restraints weight = 20482.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.111617 restraints weight = 13477.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.112354 restraints weight = 10100.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.112707 restraints weight = 8408.098| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3237 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3237 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 26050 Z= 0.116 Angle : 0.418 6.500 34750 Z= 0.233 Chirality : 0.036 0.112 4250 Planarity : 0.002 0.014 3950 Dihedral : 12.067 59.988 4550 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 1.37 % Allowed : 19.02 % Favored : 79.61 % 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 are not related in a simple way. whole: 2.67 (0.14), residues: 3150 helix: 2.70 (0.10), residues: 2400 sheet: None (None), residues: 0 loop : -1.54 (0.18), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR I 42 PHE 0.031 0.002 PHE T 60 TRP 0.001 0.000 TRP n 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (26050) covalent geometry : angle 0.41768 / 0.23 (34750) hydrogen bonds : bond 0.04777 / 3.13 ( 1836) hydrogen bonds : angle 3.93439 / 2.72 ( 5358) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 431 time to evaluate : 0.885 Fit side-chains REVERT: Y 43 MET cc_start: 0.9037 (tmm) cc_final: 0.8806 (tmm) REVERT: 3 36 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.7408 (mp) REVERT: 4 28 LYS cc_start: 0.7915 (mttt) cc_final: 0.7636 (mttp) REVERT: 5 9 MET cc_start: 0.8103 (mtt) cc_final: 0.7880 (mtt) REVERT: l 36 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8249 (mm) REVERT: m 42 TYR cc_start: 0.7959 (t80) cc_final: 0.7686 (t80) outliers start: 35 outliers final: 28 residues processed: 447 average time/residue: 0.1519 time to fit residues: 108.6898 Evaluate side-chains 452 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 422 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 65 MET Chi-restraints excluded: chain M residue 14 THR Chi-restraints excluded: chain M residue 15 THR Chi-restraints excluded: chain M residue 57 ILE Chi-restraints excluded: chain O residue 15 THR Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain V residue 15 THR Chi-restraints excluded: chain W residue 14 THR Chi-restraints excluded: chain W residue 15 THR Chi-restraints excluded: chain Y residue 15 THR Chi-restraints excluded: chain Z residue 41 MET Chi-restraints excluded: chain 3 residue 36 LEU Chi-restraints excluded: chain 5 residue 15 THR Chi-restraints excluded: chain 6 residue 15 THR Chi-restraints excluded: chain 8 residue 15 THR Chi-restraints excluded: chain c residue 44 MET Chi-restraints excluded: chain f residue 11 SER Chi-restraints excluded: chain f residue 15 THR Chi-restraints excluded: chain g residue 15 THR Chi-restraints excluded: chain g residue 44 MET Chi-restraints excluded: chain g residue 57 ILE Chi-restraints excluded: chain h residue 14 THR Chi-restraints excluded: chain i residue 23 ASP Chi-restraints excluded: chain l residue 36 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 274 optimal weight: 7.9990 chunk 262 optimal weight: 5.9990 chunk 199 optimal weight: 0.0980 chunk 276 optimal weight: 7.9990 chunk 178 optimal weight: 8.9990 chunk 219 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 31 optimal weight: 8.9990 chunk 229 optimal weight: 8.9990 chunk 68 optimal weight: 0.9990 chunk 234 optimal weight: 10.0000 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 13 ASN c 13 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.122199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.108787 restraints weight = 36317.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.110671 restraints weight = 20353.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.111751 restraints weight = 13387.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.112646 restraints weight = 10152.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.113030 restraints weight = 8356.579| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3252 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3252 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 26050 Z= 0.107 Angle : 0.411 6.754 34750 Z= 0.229 Chirality : 0.035 0.110 4250 Planarity : 0.002 0.013 3950 Dihedral : 11.707 59.934 4550 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 1.14 % Allowed : 19.29 % Favored : 79.57 % 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 are not related in a simple way. whole: 2.86 (0.14), residues: 3150 helix: 2.87 (0.10), residues: 2400 sheet: None (None), residues: 0 loop : -1.59 (0.18), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR 6 42 PHE 0.028 0.002 PHE T 60 TRP 0.001 0.000 TRP k 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (26050) covalent geometry : angle 0.41147 / 0.23 (34750) hydrogen bonds : bond 0.04385 / 2.88 ( 1836) hydrogen bonds : angle 3.89887 / 2.69 ( 5358) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 435 time to evaluate : 0.985 Fit side-chains REVERT: Y 43 MET cc_start: 0.9036 (tmm) cc_final: 0.8813 (tmm) REVERT: 3 36 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7438 (mp) REVERT: 4 28 LYS cc_start: 0.7898 (mttt) cc_final: 0.7597 (mttp) REVERT: 5 9 MET cc_start: 0.8088 (mtt) cc_final: 0.7870 (mtt) REVERT: e 22 LYS cc_start: 0.6718 (tptp) cc_final: 0.6423 (tptt) REVERT: l 36 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8215 (mm) REVERT: m 42 TYR cc_start: 0.7929 (t80) cc_final: 0.7681 (t80) outliers start: 29 outliers final: 27 residues processed: 447 average time/residue: 0.1523 time to fit residues: 108.5582 Evaluate side-chains 451 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 422 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 65 MET Chi-restraints excluded: chain M residue 14 THR Chi-restraints excluded: chain M residue 15 THR Chi-restraints excluded: chain M residue 57 ILE Chi-restraints excluded: chain O residue 15 THR Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain V residue 15 THR Chi-restraints excluded: chain W residue 14 THR Chi-restraints excluded: chain W residue 15 THR Chi-restraints excluded: chain Y residue 15 THR Chi-restraints excluded: chain Z residue 41 MET Chi-restraints excluded: chain 3 residue 36 LEU Chi-restraints excluded: chain 5 residue 15 THR Chi-restraints excluded: chain 6 residue 15 THR Chi-restraints excluded: chain 8 residue 15 THR Chi-restraints excluded: chain f residue 11 SER Chi-restraints excluded: chain f residue 15 THR Chi-restraints excluded: chain g residue 15 THR Chi-restraints excluded: chain g residue 44 MET Chi-restraints excluded: chain g residue 57 ILE Chi-restraints excluded: chain i residue 23 ASP Chi-restraints excluded: chain j residue 57 ILE Chi-restraints excluded: chain l residue 36 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 236 optimal weight: 3.9990 chunk 223 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 259 optimal weight: 5.9990 chunk 264 optimal weight: 9.9990 chunk 180 optimal weight: 60.0000 chunk 214 optimal weight: 0.9980 chunk 227 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 253 optimal weight: 6.9990 chunk 240 optimal weight: 60.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.118677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.105389 restraints weight = 36348.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.107108 restraints weight = 20502.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.108204 restraints weight = 13533.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.109049 restraints weight = 10232.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.109426 restraints weight = 8466.703| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3206 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3206 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 26050 Z= 0.154 Angle : 0.474 6.801 34750 Z= 0.261 Chirality : 0.037 0.119 4250 Planarity : 0.002 0.017 3950 Dihedral : 12.660 59.833 4550 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 1.10 % Allowed : 19.69 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.51 (0.14), residues: 3150 helix: 2.62 (0.10), residues: 2400 sheet: None (None), residues: 0 loop : -1.74 (0.18), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYR I 42 PHE 0.025 0.002 PHE T 60 TRP 0.003 0.000 TRP e 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.15 (26050) covalent geometry : angle 0.47382 / 0.26 (34750) hydrogen bonds : bond 0.05966 / 3.91 ( 1836) hydrogen bonds : angle 3.99432 / 2.76 ( 5358) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 425 time to evaluate : 0.816 Fit side-chains REVERT: U 28 LYS cc_start: 0.7893 (mttt) cc_final: 0.7595 (mttp) REVERT: 0 43 MET cc_start: 0.9210 (tmm) cc_final: 0.8812 (tmm) REVERT: 4 28 LYS cc_start: 0.8035 (mttt) cc_final: 0.7709 (mttp) REVERT: 5 9 MET cc_start: 0.8154 (mtt) cc_final: 0.7926 (mtt) REVERT: l 36 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8292 (mm) REVERT: m 42 TYR cc_start: 0.8037 (t80) cc_final: 0.7785 (t80) outliers start: 28 outliers final: 26 residues processed: 438 average time/residue: 0.1596 time to fit residues: 110.9832 Evaluate side-chains 450 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 423 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain M residue 14 THR Chi-restraints excluded: chain M residue 15 THR Chi-restraints excluded: chain M residue 57 ILE Chi-restraints excluded: chain O residue 15 THR Chi-restraints excluded: chain O residue 57 ILE Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain V residue 15 THR Chi-restraints excluded: chain W residue 14 THR Chi-restraints excluded: chain W residue 15 THR Chi-restraints excluded: chain Y residue 15 THR Chi-restraints excluded: chain Z residue 41 MET Chi-restraints excluded: chain 5 residue 15 THR Chi-restraints excluded: chain 6 residue 15 THR Chi-restraints excluded: chain 8 residue 15 THR Chi-restraints excluded: chain f residue 11 SER Chi-restraints excluded: chain f residue 15 THR Chi-restraints excluded: chain g residue 15 THR Chi-restraints excluded: chain g residue 57 ILE Chi-restraints excluded: chain h residue 14 THR Chi-restraints excluded: chain i residue 23 ASP Chi-restraints excluded: chain l residue 36 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 170 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 chunk 67 optimal weight: 10.0000 chunk 70 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 chunk 180 optimal weight: 60.0000 chunk 51 optimal weight: 5.9990 chunk 240 optimal weight: 60.0000 chunk 172 optimal weight: 0.0980 chunk 153 optimal weight: 2.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.121432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.108191 restraints weight = 35832.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.109958 restraints weight = 20239.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.111160 restraints weight = 13338.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.111770 restraints weight = 10011.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.112237 restraints weight = 8427.436| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3241 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3241 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 26050 Z= 0.114 Angle : 0.432 6.741 34750 Z= 0.239 Chirality : 0.035 0.112 4250 Planarity : 0.002 0.014 3950 Dihedral : 12.092 59.939 4550 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.10 % Allowed : 19.73 % Favored : 79.18 % 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 are not related in a simple way. whole: 2.80 (0.14), residues: 3150 helix: 2.87 (0.10), residues: 2400 sheet: None (None), residues: 0 loop : -1.80 (0.18), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR I 42 PHE 0.026 0.002 PHE T 60 TRP 0.001 0.000 TRP e 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (26050) covalent geometry : angle 0.43217 / 0.24 (34750) hydrogen bonds : bond 0.04618 / 3.03 ( 1836) hydrogen bonds : angle 3.89120 / 2.69 ( 5358) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3608.97 seconds wall clock time: 63 minutes 6.12 seconds (3786.12 seconds total)