Starting phenix.real_space_refine on Tue Aug 26 10:54:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wkw_37609/08_2025/8wkw_37609.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wkw_37609/08_2025/8wkw_37609.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wkw_37609/08_2025/8wkw_37609.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wkw_37609/08_2025/8wkw_37609.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wkw_37609/08_2025/8wkw_37609.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wkw_37609/08_2025/8wkw_37609.map" } resolution = 3.21 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= 0.004 sd= 0.165 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 19994 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 156 5.16 5 C 13182 2.51 5 N 3536 2.21 5 O 3796 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20670 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 795 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 5, 'TRANS': 91} 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 Time building chain proxies: 1.59, per 1000 atoms: 0.08 Number of scatterers: 20670 At special positions: 0 Unit cell: (102, 102, 176.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 156 16.00 O 3796 8.00 N 3536 7.00 C 13182 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: 1.07 Conformation dependent library (CDL) restraints added in 818.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4888 Finding SS restraints... Secondary structure from input PDB file: 182 helices and 0 sheets defined 79.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 3 through 15 removed outlier: 3.658A pdb=" N TYR A 9 " --> pdb=" O GLU A 5 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS A 10 " --> pdb=" O ASP A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 28 removed outlier: 3.570A pdb=" N ILE A 27 " --> pdb=" O ASP A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 31 No H-bonds generated for 'chain 'A' and resid 29 through 31' Processing helix chain 'A' and resid 35 through 49 removed outlier: 3.605A pdb=" N LEU A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ARG A 43 " --> pdb=" O GLN A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 63 removed outlier: 3.625A pdb=" N LEU A 55 " --> pdb=" O ASN A 51 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TRP A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N HIS A 57 " --> pdb=" O ASP A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 79 removed outlier: 4.105A pdb=" N TYR A 71 " --> pdb=" O GLY A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 94 Processing helix chain 'B' and resid 3 through 15 removed outlier: 3.658A pdb=" N TYR B 9 " --> pdb=" O GLU B 5 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS B 10 " --> pdb=" O ASP B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 28 removed outlier: 3.571A pdb=" N ILE B 27 " --> pdb=" O ASP B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 31 No H-bonds generated for 'chain 'B' and resid 29 through 31' Processing helix chain 'B' and resid 35 through 49 removed outlier: 3.606A pdb=" N LEU B 42 " --> pdb=" O ASP B 38 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ARG B 43 " --> pdb=" O GLN B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 63 removed outlier: 3.624A pdb=" N LEU B 55 " --> pdb=" O ASN B 51 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TRP B 56 " --> pdb=" O ARG B 52 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N HIS B 57 " --> pdb=" O ASP B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 79 removed outlier: 4.105A pdb=" N TYR B 71 " --> pdb=" O GLY B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 94 Processing helix chain 'C' and resid 3 through 15 removed outlier: 3.659A pdb=" N TYR C 9 " --> pdb=" O GLU C 5 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS C 10 " --> pdb=" O ASP C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 28 removed outlier: 3.571A pdb=" N ILE C 27 " --> pdb=" O ASP C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing helix chain 'C' and resid 35 through 49 removed outlier: 3.605A pdb=" N LEU C 42 " --> pdb=" O ASP C 38 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ARG C 43 " --> pdb=" O GLN C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 63 removed outlier: 3.624A pdb=" N LEU C 55 " --> pdb=" O ASN C 51 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TRP C 56 " --> pdb=" O ARG C 52 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N HIS C 57 " --> pdb=" O ASP C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 79 removed outlier: 4.104A pdb=" N TYR C 71 " --> pdb=" O GLY C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 94 Processing helix chain 'D' and resid 3 through 15 removed outlier: 3.659A pdb=" N TYR D 9 " --> pdb=" O GLU D 5 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS D 10 " --> pdb=" O ASP D 6 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 28 removed outlier: 3.570A pdb=" N ILE D 27 " --> pdb=" O ASP D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 31 No H-bonds generated for 'chain 'D' and resid 29 through 31' Processing helix chain 'D' and resid 35 through 49 removed outlier: 3.605A pdb=" N LEU D 42 " --> pdb=" O ASP D 38 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ARG D 43 " --> pdb=" O GLN D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 63 removed outlier: 3.625A pdb=" N LEU D 55 " --> pdb=" O ASN D 51 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TRP D 56 " --> pdb=" O ARG D 52 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N HIS D 57 " --> pdb=" O ASP D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 79 removed outlier: 4.104A pdb=" N TYR D 71 " --> pdb=" O GLY D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 94 Processing helix chain 'E' and resid 3 through 15 removed outlier: 3.658A pdb=" N TYR E 9 " --> pdb=" O GLU E 5 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS E 10 " --> pdb=" O ASP E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 28 removed outlier: 3.570A pdb=" N ILE E 27 " --> pdb=" O ASP E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 35 through 49 removed outlier: 3.605A pdb=" N LEU E 42 " --> pdb=" O ASP E 38 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG E 43 " --> pdb=" O GLN E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 63 removed outlier: 3.625A pdb=" N LEU E 55 " --> pdb=" O ASN E 51 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N TRP E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N HIS E 57 " --> pdb=" O ASP E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 79 removed outlier: 4.104A pdb=" N TYR E 71 " --> pdb=" O GLY E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 94 Processing helix chain 'F' and resid 3 through 15 removed outlier: 3.658A pdb=" N TYR F 9 " --> pdb=" O GLU F 5 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS F 10 " --> pdb=" O ASP F 6 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 28 removed outlier: 3.570A pdb=" N ILE F 27 " --> pdb=" O ASP F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 31 No H-bonds generated for 'chain 'F' and resid 29 through 31' Processing helix chain 'F' and resid 35 through 49 removed outlier: 3.606A pdb=" N LEU F 42 " --> pdb=" O ASP F 38 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG F 43 " --> pdb=" O GLN F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 63 removed outlier: 3.624A pdb=" N LEU F 55 " --> pdb=" O ASN F 51 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TRP F 56 " --> pdb=" O ARG F 52 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N HIS F 57 " --> pdb=" O ASP F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 79 removed outlier: 4.105A pdb=" N TYR F 71 " --> pdb=" O GLY F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 94 Processing helix chain 'G' and resid 3 through 15 removed outlier: 3.658A pdb=" N TYR G 9 " --> pdb=" O GLU G 5 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS G 10 " --> pdb=" O ASP G 6 " (cutoff:3.500A) Processing helix chain 'G' and resid 23 through 28 removed outlier: 3.571A pdb=" N ILE G 27 " --> pdb=" O ASP G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 31 No H-bonds generated for 'chain 'G' and resid 29 through 31' Processing helix chain 'G' and resid 35 through 49 removed outlier: 3.606A pdb=" N LEU G 42 " --> pdb=" O ASP G 38 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG G 43 " --> pdb=" O GLN G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 63 removed outlier: 3.624A pdb=" N LEU G 55 " --> pdb=" O ASN G 51 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TRP G 56 " --> pdb=" O ARG G 52 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N HIS G 57 " --> pdb=" O ASP G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 79 removed outlier: 4.105A pdb=" N TYR G 71 " --> pdb=" O GLY G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 94 Processing helix chain 'H' and resid 3 through 15 removed outlier: 3.659A pdb=" N TYR H 9 " --> pdb=" O GLU H 5 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS H 10 " --> pdb=" O ASP H 6 " (cutoff:3.500A) Processing helix chain 'H' and resid 23 through 28 removed outlier: 3.571A pdb=" N ILE H 27 " --> pdb=" O ASP H 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 35 through 49 removed outlier: 3.606A pdb=" N LEU H 42 " --> pdb=" O ASP H 38 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG H 43 " --> pdb=" O GLN H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 63 removed outlier: 3.624A pdb=" N LEU H 55 " --> pdb=" O ASN H 51 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TRP H 56 " --> pdb=" O ARG H 52 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N HIS H 57 " --> pdb=" O ASP H 53 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 79 removed outlier: 4.104A pdb=" N TYR H 71 " --> pdb=" O GLY H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 94 Processing helix chain 'I' and resid 3 through 15 removed outlier: 3.659A pdb=" N TYR I 9 " --> pdb=" O GLU I 5 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS I 10 " --> pdb=" O ASP I 6 " (cutoff:3.500A) Processing helix chain 'I' and resid 23 through 28 removed outlier: 3.571A pdb=" N ILE I 27 " --> pdb=" O ASP I 23 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 31 No H-bonds generated for 'chain 'I' and resid 29 through 31' Processing helix chain 'I' and resid 35 through 49 removed outlier: 3.606A pdb=" N LEU I 42 " --> pdb=" O ASP I 38 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG I 43 " --> pdb=" O GLN I 39 " (cutoff:3.500A) Processing helix chain 'I' and resid 51 through 63 removed outlier: 3.624A pdb=" N LEU I 55 " --> pdb=" O ASN I 51 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TRP I 56 " --> pdb=" O ARG I 52 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N HIS I 57 " --> pdb=" O ASP I 53 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 79 removed outlier: 4.104A pdb=" N TYR I 71 " --> pdb=" O GLY I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 94 Processing helix chain 'J' and resid 3 through 15 removed outlier: 3.659A pdb=" N TYR J 9 " --> pdb=" O GLU J 5 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS J 10 " --> pdb=" O ASP J 6 " (cutoff:3.500A) Processing helix chain 'J' and resid 23 through 28 removed outlier: 3.570A pdb=" N ILE J 27 " --> pdb=" O ASP J 23 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 31 No H-bonds generated for 'chain 'J' and resid 29 through 31' Processing helix chain 'J' and resid 35 through 49 removed outlier: 3.606A pdb=" N LEU J 42 " --> pdb=" O ASP J 38 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ARG J 43 " --> pdb=" O GLN J 39 " (cutoff:3.500A) Processing helix chain 'J' and resid 51 through 63 removed outlier: 3.624A pdb=" N LEU J 55 " --> pdb=" O ASN J 51 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TRP J 56 " --> pdb=" O ARG J 52 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N HIS J 57 " --> pdb=" O ASP J 53 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 79 removed outlier: 4.104A pdb=" N TYR J 71 " --> pdb=" O GLY J 67 " (cutoff:3.500A) Processing helix chain 'J' and resid 81 through 94 Processing helix chain 'K' and resid 3 through 15 removed outlier: 3.659A pdb=" N TYR K 9 " --> pdb=" O GLU K 5 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS K 10 " --> pdb=" O ASP K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 23 through 28 removed outlier: 3.571A pdb=" N ILE K 27 " --> pdb=" O ASP K 23 " (cutoff:3.500A) Processing helix chain 'K' and resid 29 through 31 No H-bonds generated for 'chain 'K' and resid 29 through 31' Processing helix chain 'K' and resid 35 through 49 removed outlier: 3.605A pdb=" N LEU K 42 " --> pdb=" O ASP K 38 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ARG K 43 " --> pdb=" O GLN K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 63 removed outlier: 3.624A pdb=" N LEU K 55 " --> pdb=" O ASN K 51 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N TRP K 56 " --> pdb=" O ARG K 52 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N HIS K 57 " --> pdb=" O ASP K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 79 removed outlier: 4.105A pdb=" N TYR K 71 " --> pdb=" O GLY K 67 " (cutoff:3.500A) Processing helix chain 'K' and resid 81 through 94 Processing helix chain 'L' and resid 3 through 15 removed outlier: 3.658A pdb=" N TYR L 9 " --> pdb=" O GLU L 5 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS L 10 " --> pdb=" O ASP L 6 " (cutoff:3.500A) Processing helix chain 'L' and resid 23 through 28 removed outlier: 3.570A pdb=" N ILE L 27 " --> pdb=" O ASP L 23 " (cutoff:3.500A) Processing helix chain 'L' and resid 29 through 31 No H-bonds generated for 'chain 'L' and resid 29 through 31' Processing helix chain 'L' and resid 35 through 49 removed outlier: 3.605A pdb=" N LEU L 42 " --> pdb=" O ASP L 38 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ARG L 43 " --> pdb=" O GLN L 39 " (cutoff:3.500A) Processing helix chain 'L' and resid 51 through 63 removed outlier: 3.624A pdb=" N LEU L 55 " --> pdb=" O ASN L 51 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N TRP L 56 " --> pdb=" O ARG L 52 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N HIS L 57 " --> pdb=" O ASP L 53 " (cutoff:3.500A) Processing helix chain 'L' and resid 67 through 79 removed outlier: 4.104A pdb=" N TYR L 71 " --> pdb=" O GLY L 67 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 94 Processing helix chain 'M' and resid 3 through 15 removed outlier: 3.658A pdb=" N TYR M 9 " --> pdb=" O GLU M 5 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS M 10 " --> pdb=" O ASP M 6 " (cutoff:3.500A) Processing helix chain 'M' and resid 23 through 28 removed outlier: 3.570A pdb=" N ILE M 27 " --> pdb=" O ASP M 23 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 31 No H-bonds generated for 'chain 'M' and resid 29 through 31' Processing helix chain 'M' and resid 35 through 49 removed outlier: 3.605A pdb=" N LEU M 42 " --> pdb=" O ASP M 38 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ARG M 43 " --> pdb=" O GLN M 39 " (cutoff:3.500A) Processing helix chain 'M' and resid 51 through 63 removed outlier: 3.624A pdb=" N LEU M 55 " --> pdb=" O ASN M 51 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N TRP M 56 " --> pdb=" O ARG M 52 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N HIS M 57 " --> pdb=" O ASP M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 67 through 79 removed outlier: 4.104A pdb=" N TYR M 71 " --> pdb=" O GLY M 67 " (cutoff:3.500A) Processing helix chain 'M' and resid 81 through 94 Processing helix chain 'N' and resid 3 through 15 removed outlier: 3.658A pdb=" N TYR N 9 " --> pdb=" O GLU N 5 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS N 10 " --> pdb=" O ASP N 6 " (cutoff:3.500A) Processing helix chain 'N' and resid 23 through 28 removed outlier: 3.571A pdb=" N ILE N 27 " --> pdb=" O ASP N 23 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 35 through 49 removed outlier: 3.605A pdb=" N LEU N 42 " --> pdb=" O ASP N 38 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG N 43 " --> pdb=" O GLN N 39 " (cutoff:3.500A) Processing helix chain 'N' and resid 51 through 63 removed outlier: 3.624A pdb=" N LEU N 55 " --> pdb=" O ASN N 51 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N TRP N 56 " --> pdb=" O ARG N 52 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N HIS N 57 " --> pdb=" O ASP N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 67 through 79 removed outlier: 4.104A pdb=" N TYR N 71 " --> pdb=" O GLY N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 81 through 94 Processing helix chain 'O' and resid 3 through 15 removed outlier: 3.658A pdb=" N TYR O 9 " --> pdb=" O GLU O 5 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS O 10 " --> pdb=" O ASP O 6 " (cutoff:3.500A) Processing helix chain 'O' and resid 23 through 28 removed outlier: 3.570A pdb=" N ILE O 27 " --> pdb=" O ASP O 23 " (cutoff:3.500A) Processing helix chain 'O' and resid 29 through 31 No H-bonds generated for 'chain 'O' and resid 29 through 31' Processing helix chain 'O' and resid 35 through 49 removed outlier: 3.606A pdb=" N LEU O 42 " --> pdb=" O ASP O 38 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ARG O 43 " --> pdb=" O GLN O 39 " (cutoff:3.500A) Processing helix chain 'O' and resid 51 through 63 removed outlier: 3.624A pdb=" N LEU O 55 " --> pdb=" O ASN O 51 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N TRP O 56 " --> pdb=" O ARG O 52 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N HIS O 57 " --> pdb=" O ASP O 53 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 79 removed outlier: 4.104A pdb=" N TYR O 71 " --> pdb=" O GLY O 67 " (cutoff:3.500A) Processing helix chain 'O' and resid 81 through 94 Processing helix chain 'P' and resid 3 through 15 removed outlier: 3.658A pdb=" N TYR P 9 " --> pdb=" O GLU P 5 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS P 10 " --> pdb=" O ASP P 6 " (cutoff:3.500A) Processing helix chain 'P' and resid 23 through 28 removed outlier: 3.570A pdb=" N ILE P 27 " --> pdb=" O ASP P 23 " (cutoff:3.500A) Processing helix chain 'P' and resid 29 through 31 No H-bonds generated for 'chain 'P' and resid 29 through 31' Processing helix chain 'P' and resid 35 through 49 removed outlier: 3.606A pdb=" N LEU P 42 " --> pdb=" O ASP P 38 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ARG P 43 " --> pdb=" O GLN P 39 " (cutoff:3.500A) Processing helix chain 'P' and resid 51 through 63 removed outlier: 3.625A pdb=" N LEU P 55 " --> pdb=" O ASN P 51 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TRP P 56 " --> pdb=" O ARG P 52 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N HIS P 57 " --> pdb=" O ASP P 53 " (cutoff:3.500A) Processing helix chain 'P' and resid 67 through 79 removed outlier: 4.104A pdb=" N TYR P 71 " --> pdb=" O GLY P 67 " (cutoff:3.500A) Processing helix chain 'P' and resid 81 through 94 Processing helix chain 'Q' and resid 3 through 15 removed outlier: 3.658A pdb=" N TYR Q 9 " --> pdb=" O GLU Q 5 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS Q 10 " --> pdb=" O ASP Q 6 " (cutoff:3.500A) Processing helix chain 'Q' and resid 23 through 28 removed outlier: 3.570A pdb=" N ILE Q 27 " --> pdb=" O ASP Q 23 " (cutoff:3.500A) Processing helix chain 'Q' and resid 29 through 31 No H-bonds generated for 'chain 'Q' and resid 29 through 31' Processing helix chain 'Q' and resid 35 through 49 removed outlier: 3.605A pdb=" N LEU Q 42 " --> pdb=" O ASP Q 38 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ARG Q 43 " --> pdb=" O GLN Q 39 " (cutoff:3.500A) Processing helix chain 'Q' and resid 51 through 63 removed outlier: 3.625A pdb=" N LEU Q 55 " --> pdb=" O ASN Q 51 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TRP Q 56 " --> pdb=" O ARG Q 52 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N HIS Q 57 " --> pdb=" O ASP Q 53 " (cutoff:3.500A) Processing helix chain 'Q' and resid 67 through 79 removed outlier: 4.104A pdb=" N TYR Q 71 " --> pdb=" O GLY Q 67 " (cutoff:3.500A) Processing helix chain 'Q' and resid 81 through 94 Processing helix chain 'R' and resid 3 through 15 removed outlier: 3.659A pdb=" N TYR R 9 " --> pdb=" O GLU R 5 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS R 10 " --> pdb=" O ASP R 6 " (cutoff:3.500A) Processing helix chain 'R' and resid 23 through 28 removed outlier: 3.570A pdb=" N ILE R 27 " --> pdb=" O ASP R 23 " (cutoff:3.500A) Processing helix chain 'R' and resid 29 through 31 No H-bonds generated for 'chain 'R' and resid 29 through 31' Processing helix chain 'R' and resid 35 through 49 removed outlier: 3.606A pdb=" N LEU R 42 " --> pdb=" O ASP R 38 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG R 43 " --> pdb=" O GLN R 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 63 removed outlier: 3.624A pdb=" N LEU R 55 " --> pdb=" O ASN R 51 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TRP R 56 " --> pdb=" O ARG R 52 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N HIS R 57 " --> pdb=" O ASP R 53 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 79 removed outlier: 4.105A pdb=" N TYR R 71 " --> pdb=" O GLY R 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 94 Processing helix chain 'S' and resid 3 through 15 removed outlier: 3.659A pdb=" N TYR S 9 " --> pdb=" O GLU S 5 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS S 10 " --> pdb=" O ASP S 6 " (cutoff:3.500A) Processing helix chain 'S' and resid 23 through 28 removed outlier: 3.570A pdb=" N ILE S 27 " --> pdb=" O ASP S 23 " (cutoff:3.500A) Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 35 through 49 removed outlier: 3.606A pdb=" N LEU S 42 " --> pdb=" O ASP S 38 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ARG S 43 " --> pdb=" O GLN S 39 " (cutoff:3.500A) Processing helix chain 'S' and resid 51 through 63 removed outlier: 3.623A pdb=" N LEU S 55 " --> pdb=" O ASN S 51 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TRP S 56 " --> pdb=" O ARG S 52 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N HIS S 57 " --> pdb=" O ASP S 53 " (cutoff:3.500A) Processing helix chain 'S' and resid 67 through 79 removed outlier: 4.105A pdb=" N TYR S 71 " --> pdb=" O GLY S 67 " (cutoff:3.500A) Processing helix chain 'S' and resid 81 through 94 Processing helix chain 'T' and resid 3 through 15 removed outlier: 3.658A pdb=" N TYR T 9 " --> pdb=" O GLU T 5 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS T 10 " --> pdb=" O ASP T 6 " (cutoff:3.500A) Processing helix chain 'T' and resid 23 through 28 removed outlier: 3.570A pdb=" N ILE T 27 " --> pdb=" O ASP T 23 " (cutoff:3.500A) Processing helix chain 'T' and resid 29 through 31 No H-bonds generated for 'chain 'T' and resid 29 through 31' Processing helix chain 'T' and resid 35 through 49 removed outlier: 3.606A pdb=" N LEU T 42 " --> pdb=" O ASP T 38 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG T 43 " --> pdb=" O GLN T 39 " (cutoff:3.500A) Processing helix chain 'T' and resid 51 through 63 removed outlier: 3.624A pdb=" N LEU T 55 " --> pdb=" O ASN T 51 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TRP T 56 " --> pdb=" O ARG T 52 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N HIS T 57 " --> pdb=" O ASP T 53 " (cutoff:3.500A) Processing helix chain 'T' and resid 67 through 79 removed outlier: 4.104A pdb=" N TYR T 71 " --> pdb=" O GLY T 67 " (cutoff:3.500A) Processing helix chain 'T' and resid 81 through 94 Processing helix chain 'U' and resid 3 through 15 removed outlier: 3.658A pdb=" N TYR U 9 " --> pdb=" O GLU U 5 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS U 10 " --> pdb=" O ASP U 6 " (cutoff:3.500A) Processing helix chain 'U' and resid 23 through 28 removed outlier: 3.570A pdb=" N ILE U 27 " --> pdb=" O ASP U 23 " (cutoff:3.500A) Processing helix chain 'U' and resid 29 through 31 No H-bonds generated for 'chain 'U' and resid 29 through 31' Processing helix chain 'U' and resid 35 through 49 removed outlier: 3.606A pdb=" N LEU U 42 " --> pdb=" O ASP U 38 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ARG U 43 " --> pdb=" O GLN U 39 " (cutoff:3.500A) Processing helix chain 'U' and resid 51 through 63 removed outlier: 3.624A pdb=" N LEU U 55 " --> pdb=" O ASN U 51 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TRP U 56 " --> pdb=" O ARG U 52 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N HIS U 57 " --> pdb=" O ASP U 53 " (cutoff:3.500A) Processing helix chain 'U' and resid 67 through 79 removed outlier: 4.104A pdb=" N TYR U 71 " --> pdb=" O GLY U 67 " (cutoff:3.500A) Processing helix chain 'U' and resid 81 through 94 Processing helix chain 'V' and resid 3 through 15 removed outlier: 3.658A pdb=" N TYR V 9 " --> pdb=" O GLU V 5 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS V 10 " --> pdb=" O ASP V 6 " (cutoff:3.500A) Processing helix chain 'V' and resid 23 through 28 removed outlier: 3.571A pdb=" N ILE V 27 " --> pdb=" O ASP V 23 " (cutoff:3.500A) Processing helix chain 'V' and resid 29 through 31 No H-bonds generated for 'chain 'V' and resid 29 through 31' Processing helix chain 'V' and resid 35 through 49 removed outlier: 3.605A pdb=" N LEU V 42 " --> pdb=" O ASP V 38 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ARG V 43 " --> pdb=" O GLN V 39 " (cutoff:3.500A) Processing helix chain 'V' and resid 51 through 63 removed outlier: 3.624A pdb=" N LEU V 55 " --> pdb=" O ASN V 51 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TRP V 56 " --> pdb=" O ARG V 52 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N HIS V 57 " --> pdb=" O ASP V 53 " (cutoff:3.500A) Processing helix chain 'V' and resid 67 through 79 removed outlier: 4.104A pdb=" N TYR V 71 " --> pdb=" O GLY V 67 " (cutoff:3.500A) Processing helix chain 'V' and resid 81 through 94 Processing helix chain 'W' and resid 3 through 15 removed outlier: 3.658A pdb=" N TYR W 9 " --> pdb=" O GLU W 5 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS W 10 " --> pdb=" O ASP W 6 " (cutoff:3.500A) Processing helix chain 'W' and resid 23 through 28 removed outlier: 3.571A pdb=" N ILE W 27 " --> pdb=" O ASP W 23 " (cutoff:3.500A) Processing helix chain 'W' and resid 29 through 31 No H-bonds generated for 'chain 'W' and resid 29 through 31' Processing helix chain 'W' and resid 35 through 49 removed outlier: 3.605A pdb=" N LEU W 42 " --> pdb=" O ASP W 38 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG W 43 " --> pdb=" O GLN W 39 " (cutoff:3.500A) Processing helix chain 'W' and resid 51 through 63 removed outlier: 3.625A pdb=" N LEU W 55 " --> pdb=" O ASN W 51 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TRP W 56 " --> pdb=" O ARG W 52 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N HIS W 57 " --> pdb=" O ASP W 53 " (cutoff:3.500A) Processing helix chain 'W' and resid 67 through 79 removed outlier: 4.104A pdb=" N TYR W 71 " --> pdb=" O GLY W 67 " (cutoff:3.500A) Processing helix chain 'W' and resid 81 through 94 Processing helix chain 'X' and resid 3 through 15 removed outlier: 3.658A pdb=" N TYR X 9 " --> pdb=" O GLU X 5 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS X 10 " --> pdb=" O ASP X 6 " (cutoff:3.500A) Processing helix chain 'X' and resid 23 through 28 removed outlier: 3.571A pdb=" N ILE X 27 " --> pdb=" O ASP X 23 " (cutoff:3.500A) Processing helix chain 'X' and resid 29 through 31 No H-bonds generated for 'chain 'X' and resid 29 through 31' Processing helix chain 'X' and resid 35 through 49 removed outlier: 3.606A pdb=" N LEU X 42 " --> pdb=" O ASP X 38 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG X 43 " --> pdb=" O GLN X 39 " (cutoff:3.500A) Processing helix chain 'X' and resid 51 through 63 removed outlier: 3.624A pdb=" N LEU X 55 " --> pdb=" O ASN X 51 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N TRP X 56 " --> pdb=" O ARG X 52 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N HIS X 57 " --> pdb=" O ASP X 53 " (cutoff:3.500A) Processing helix chain 'X' and resid 67 through 79 removed outlier: 4.104A pdb=" N TYR X 71 " --> pdb=" O GLY X 67 " (cutoff:3.500A) Processing helix chain 'X' and resid 81 through 94 Processing helix chain 'Y' and resid 3 through 15 removed outlier: 3.659A pdb=" N TYR Y 9 " --> pdb=" O GLU Y 5 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS Y 10 " --> pdb=" O ASP Y 6 " (cutoff:3.500A) Processing helix chain 'Y' and resid 23 through 28 removed outlier: 3.571A pdb=" N ILE Y 27 " --> pdb=" O ASP Y 23 " (cutoff:3.500A) Processing helix chain 'Y' and resid 29 through 31 No H-bonds generated for 'chain 'Y' and resid 29 through 31' Processing helix chain 'Y' and resid 35 through 49 removed outlier: 3.605A pdb=" N LEU Y 42 " --> pdb=" O ASP Y 38 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ARG Y 43 " --> pdb=" O GLN Y 39 " (cutoff:3.500A) Processing helix chain 'Y' and resid 51 through 63 removed outlier: 3.623A pdb=" N LEU Y 55 " --> pdb=" O ASN Y 51 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TRP Y 56 " --> pdb=" O ARG Y 52 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N HIS Y 57 " --> pdb=" O ASP Y 53 " (cutoff:3.500A) Processing helix chain 'Y' and resid 67 through 79 removed outlier: 4.105A pdb=" N TYR Y 71 " --> pdb=" O GLY Y 67 " (cutoff:3.500A) Processing helix chain 'Y' and resid 81 through 94 Processing helix chain 'Z' and resid 3 through 15 removed outlier: 3.659A pdb=" N TYR Z 9 " --> pdb=" O GLU Z 5 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS Z 10 " --> pdb=" O ASP Z 6 " (cutoff:3.500A) Processing helix chain 'Z' and resid 23 through 28 removed outlier: 3.571A pdb=" N ILE Z 27 " --> pdb=" O ASP Z 23 " (cutoff:3.500A) Processing helix chain 'Z' and resid 29 through 31 No H-bonds generated for 'chain 'Z' and resid 29 through 31' Processing helix chain 'Z' and resid 35 through 49 removed outlier: 3.605A pdb=" N LEU Z 42 " --> pdb=" O ASP Z 38 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG Z 43 " --> pdb=" O GLN Z 39 " (cutoff:3.500A) Processing helix chain 'Z' and resid 51 through 63 removed outlier: 3.624A pdb=" N LEU Z 55 " --> pdb=" O ASN Z 51 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TRP Z 56 " --> pdb=" O ARG Z 52 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N HIS Z 57 " --> pdb=" O ASP Z 53 " (cutoff:3.500A) Processing helix chain 'Z' and resid 67 through 79 removed outlier: 4.105A pdb=" N TYR Z 71 " --> pdb=" O GLY Z 67 " (cutoff:3.500A) Processing helix chain 'Z' and resid 81 through 94 1066 hydrogen bonds defined for protein. 3198 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: 2.72 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6786 1.34 - 1.46: 5006 1.46 - 1.58: 9216 1.58 - 1.69: 0 1.69 - 1.81: 182 Bond restraints: 21190 Sorted by residual: bond pdb=" C ARG M 14 " pdb=" N ASN M 15 " ideal model delta sigma weight residual 1.331 1.338 -0.007 1.29e-02 6.01e+03 3.08e-01 bond pdb=" C ARG G 14 " pdb=" N ASN G 15 " ideal model delta sigma weight residual 1.331 1.337 -0.007 1.29e-02 6.01e+03 2.74e-01 bond pdb=" CA PHE O 3 " pdb=" CB PHE O 3 " ideal model delta sigma weight residual 1.532 1.541 -0.009 1.74e-02 3.30e+03 2.63e-01 bond pdb=" C ARG T 14 " pdb=" N ASN T 15 " ideal model delta sigma weight residual 1.331 1.337 -0.007 1.29e-02 6.01e+03 2.59e-01 bond pdb=" CA PHE M 3 " pdb=" CB PHE M 3 " ideal model delta sigma weight residual 1.532 1.541 -0.009 1.74e-02 3.30e+03 2.56e-01 ... (remaining 21185 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.90: 28037 0.90 - 1.80: 693 1.80 - 2.71: 104 2.71 - 3.61: 0 3.61 - 4.51: 26 Bond angle restraints: 28860 Sorted by residual: angle pdb=" C LEU T 28 " pdb=" N PRO T 29 " pdb=" CD PRO T 29 " ideal model delta sigma weight residual 125.00 129.51 -4.51 4.10e+00 5.95e-02 1.21e+00 angle pdb=" C LEU F 28 " pdb=" N PRO F 29 " pdb=" CD PRO F 29 " ideal model delta sigma weight residual 125.00 129.50 -4.50 4.10e+00 5.95e-02 1.20e+00 angle pdb=" C LEU M 28 " pdb=" N PRO M 29 " pdb=" CD PRO M 29 " ideal model delta sigma weight residual 125.00 129.50 -4.50 4.10e+00 5.95e-02 1.20e+00 angle pdb=" C LEU C 28 " pdb=" N PRO C 29 " pdb=" CD PRO C 29 " ideal model delta sigma weight residual 125.00 129.49 -4.49 4.10e+00 5.95e-02 1.20e+00 angle pdb=" C LEU Q 28 " pdb=" N PRO Q 29 " pdb=" CD PRO Q 29 " ideal model delta sigma weight residual 125.00 129.49 -4.49 4.10e+00 5.95e-02 1.20e+00 ... (remaining 28855 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.94: 11320 15.94 - 31.87: 952 31.87 - 47.81: 208 47.81 - 63.74: 104 63.74 - 79.68: 26 Dihedral angle restraints: 12610 sinusoidal: 5070 harmonic: 7540 Sorted by residual: dihedral pdb=" CB GLU Y 5 " pdb=" CG GLU Y 5 " pdb=" CD GLU Y 5 " pdb=" OE1 GLU Y 5 " ideal model delta sinusoidal sigma weight residual 0.00 79.68 -79.68 1 3.00e+01 1.11e-03 8.76e+00 dihedral pdb=" CB GLU E 5 " pdb=" CG GLU E 5 " pdb=" CD GLU E 5 " pdb=" OE1 GLU E 5 " ideal model delta sinusoidal sigma weight residual 0.00 79.68 -79.68 1 3.00e+01 1.11e-03 8.76e+00 dihedral pdb=" CB GLU Z 5 " pdb=" CG GLU Z 5 " pdb=" CD GLU Z 5 " pdb=" OE1 GLU Z 5 " ideal model delta sinusoidal sigma weight residual 0.00 79.68 -79.68 1 3.00e+01 1.11e-03 8.75e+00 ... (remaining 12607 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.021: 1465 0.021 - 0.042: 942 0.042 - 0.062: 546 0.062 - 0.083: 89 0.083 - 0.104: 104 Chirality restraints: 3146 Sorted by residual: chirality pdb=" CA PRO H 32 " pdb=" N PRO H 32 " pdb=" C PRO H 32 " pdb=" CB PRO H 32 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.10 2.00e-01 2.50e+01 2.71e-01 chirality pdb=" CA PRO S 32 " pdb=" N PRO S 32 " pdb=" C PRO S 32 " pdb=" CB PRO S 32 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.65e-01 chirality pdb=" CA PRO J 32 " pdb=" N PRO J 32 " pdb=" C PRO J 32 " pdb=" CB PRO J 32 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.64e-01 ... (remaining 3143 not shown) Planarity restraints: 3744 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU M 28 " 0.013 5.00e-02 4.00e+02 1.89e-02 5.73e-01 pdb=" N PRO M 29 " -0.033 5.00e-02 4.00e+02 pdb=" CA PRO M 29 " 0.009 5.00e-02 4.00e+02 pdb=" CD PRO M 29 " 0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU Y 28 " -0.013 5.00e-02 4.00e+02 1.89e-02 5.70e-01 pdb=" N PRO Y 29 " 0.033 5.00e-02 4.00e+02 pdb=" CA PRO Y 29 " -0.009 5.00e-02 4.00e+02 pdb=" CD PRO Y 29 " -0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU J 28 " -0.013 5.00e-02 4.00e+02 1.88e-02 5.68e-01 pdb=" N PRO J 29 " 0.033 5.00e-02 4.00e+02 pdb=" CA PRO J 29 " -0.009 5.00e-02 4.00e+02 pdb=" CD PRO J 29 " -0.011 5.00e-02 4.00e+02 ... (remaining 3741 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.96: 8919 2.96 - 3.45: 20690 3.45 - 3.93: 31142 3.93 - 4.42: 34888 4.42 - 4.90: 60734 Nonbonded interactions: 156373 Sorted by model distance: nonbonded pdb=" NH2 ARG F 64 " pdb=" OE2 GLU J 26 " model vdw 2.477 3.120 nonbonded pdb=" OE2 GLU O 26 " pdb=" NH2 ARG Z 64 " model vdw 2.488 3.120 nonbonded pdb=" NH2 ARG A 64 " pdb=" OE2 GLU F 26 " model vdw 2.503 3.120 nonbonded pdb=" NH2 ARG O 64 " pdb=" OE2 GLU W 26 " model vdw 2.508 3.120 nonbonded pdb=" NH2 ARG M 64 " pdb=" OE2 GLU X 26 " model vdw 2.520 3.120 ... (remaining 156368 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: 0.07 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 12.930 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 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 : 0.002 0.015 21190 Z= 0.095 Angle : 0.370 4.512 28860 Z= 0.204 Chirality : 0.035 0.104 3146 Planarity : 0.003 0.019 3744 Dihedral : 14.286 79.680 7722 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 0.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.16), residues: 2470 helix: -0.24 (0.11), residues: 1898 sheet: None (None), residues: 0 loop : 0.96 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Y 41 TYR 0.005 0.001 TYR D 30 PHE 0.003 0.001 PHE Q 72 TRP 0.003 0.001 TRP R 68 HIS 0.001 0.000 HIS R 57 Details of bonding type rmsd covalent geometry : bond 0.00217 (21190) covalent geometry : angle 0.37011 (28860) hydrogen bonds : bond 0.28324 ( 1066) hydrogen bonds : angle 5.46489 ( 3198) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 572 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7893 (m-30) cc_final: 0.7648 (m-30) REVERT: C 41 ARG cc_start: 0.8082 (mtp-110) cc_final: 0.7876 (mtp85) REVERT: C 48 LEU cc_start: 0.8906 (tp) cc_final: 0.8599 (tp) REVERT: D 1 MET cc_start: 0.6906 (mmt) cc_final: 0.6521 (mmt) REVERT: D 38 ASP cc_start: 0.8065 (m-30) cc_final: 0.7858 (m-30) REVERT: D 48 LEU cc_start: 0.8981 (tp) cc_final: 0.8645 (tp) REVERT: E 1 MET cc_start: 0.6017 (mmt) cc_final: 0.5607 (mmt) REVERT: E 53 ASP cc_start: 0.8102 (m-30) cc_final: 0.7679 (m-30) REVERT: I 1 MET cc_start: 0.5848 (mmt) cc_final: 0.5188 (mmm) REVERT: I 87 GLU cc_start: 0.8079 (tt0) cc_final: 0.7832 (tt0) REVERT: J 40 ASP cc_start: 0.8001 (t0) cc_final: 0.7677 (t0) REVERT: J 60 ASN cc_start: 0.9073 (t0) cc_final: 0.8823 (t0) REVERT: J 63 GLN cc_start: 0.9053 (pp30) cc_final: 0.8776 (pp30) REVERT: K 1 MET cc_start: 0.5914 (mmt) cc_final: 0.5434 (mmt) REVERT: K 53 ASP cc_start: 0.7990 (m-30) cc_final: 0.7687 (m-30) REVERT: L 3 PHE cc_start: 0.8439 (m-10) cc_final: 0.8106 (m-80) REVERT: L 7 LYS cc_start: 0.8783 (mtmm) cc_final: 0.8535 (mtmt) REVERT: L 10 LYS cc_start: 0.8502 (mmtt) cc_final: 0.8252 (mptt) REVERT: L 53 ASP cc_start: 0.8243 (m-30) cc_final: 0.7968 (m-30) REVERT: M 3 PHE cc_start: 0.8265 (m-10) cc_final: 0.8016 (m-80) REVERT: M 93 GLN cc_start: 0.7917 (mp10) cc_final: 0.7630 (mp10) REVERT: N 14 ARG cc_start: 0.8290 (mtm-85) cc_final: 0.7866 (mtt-85) REVERT: N 41 ARG cc_start: 0.8223 (mtp-110) cc_final: 0.7901 (mtp-110) REVERT: O 1 MET cc_start: 0.5590 (mmt) cc_final: 0.5331 (mmt) REVERT: O 11 TYR cc_start: 0.8781 (t80) cc_final: 0.8373 (t80) REVERT: O 53 ASP cc_start: 0.7779 (m-30) cc_final: 0.7541 (m-30) REVERT: P 1 MET cc_start: 0.4923 (mmt) cc_final: 0.4695 (mmt) REVERT: Q 10 LYS cc_start: 0.8217 (mmtt) cc_final: 0.7893 (mmtt) REVERT: Q 14 ARG cc_start: 0.8140 (mtm-85) cc_final: 0.7617 (mtt-85) REVERT: Q 39 GLN cc_start: 0.8607 (tt0) cc_final: 0.8299 (tp40) REVERT: Q 60 ASN cc_start: 0.8954 (t0) cc_final: 0.8737 (t0) REVERT: Q 71 TYR cc_start: 0.8759 (m-80) cc_final: 0.8309 (m-80) REVERT: R 38 ASP cc_start: 0.8399 (m-30) cc_final: 0.7917 (m-30) REVERT: S 1 MET cc_start: 0.6321 (mmt) cc_final: 0.6004 (mmt) REVERT: S 3 PHE cc_start: 0.8398 (m-10) cc_final: 0.7980 (m-10) REVERT: S 80 GLU cc_start: 0.7849 (mp0) cc_final: 0.7392 (mp0) REVERT: S 93 GLN cc_start: 0.8063 (mp10) cc_final: 0.7811 (mp10) REVERT: U 3 PHE cc_start: 0.8337 (m-10) cc_final: 0.7999 (m-10) REVERT: U 5 GLU cc_start: 0.8615 (tt0) cc_final: 0.8298 (tt0) REVERT: U 38 ASP cc_start: 0.8065 (m-30) cc_final: 0.7702 (m-30) REVERT: U 40 ASP cc_start: 0.8056 (t0) cc_final: 0.7755 (t0) REVERT: U 41 ARG cc_start: 0.8060 (mtp-110) cc_final: 0.7709 (mtp85) REVERT: U 93 GLN cc_start: 0.7947 (mp10) cc_final: 0.7619 (mp10) REVERT: V 53 ASP cc_start: 0.8267 (m-30) cc_final: 0.7881 (m-30) REVERT: W 14 ARG cc_start: 0.8133 (mtm-85) cc_final: 0.7785 (mtt-85) REVERT: W 84 LEU cc_start: 0.8652 (tp) cc_final: 0.8355 (tp) REVERT: W 93 GLN cc_start: 0.8092 (mp10) cc_final: 0.7716 (mp10) REVERT: X 10 LYS cc_start: 0.8448 (mmtt) cc_final: 0.8231 (mmtt) REVERT: Y 1 MET cc_start: 0.6058 (mmt) cc_final: 0.5559 (mmt) REVERT: Z 5 GLU cc_start: 0.8487 (tt0) cc_final: 0.8198 (tt0) REVERT: Z 8 THR cc_start: 0.8771 (m) cc_final: 0.8384 (m) REVERT: Z 41 ARG cc_start: 0.8047 (mtp-110) cc_final: 0.7650 (mtp85) REVERT: Z 52 ARG cc_start: 0.8108 (ttm170) cc_final: 0.7873 (ttm170) REVERT: Z 53 ASP cc_start: 0.7916 (m-30) cc_final: 0.7564 (m-30) REVERT: Z 80 GLU cc_start: 0.7471 (mp0) cc_final: 0.7206 (mp0) outliers start: 0 outliers final: 0 residues processed: 572 average time/residue: 0.1594 time to fit residues: 132.0451 Evaluate side-chains 441 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 441 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.2980 chunk 227 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 200 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 93 GLN G 39 GLN X 39 GLN Y 93 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.094061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.082915 restraints weight = 32480.795| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 1.69 r_work: 0.2746 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 21190 Z= 0.148 Angle : 0.452 4.752 28860 Z= 0.237 Chirality : 0.038 0.112 3146 Planarity : 0.003 0.024 3744 Dihedral : 3.202 12.000 2860 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.41 % Allowed : 6.90 % Favored : 91.69 % 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 aren not related in a simple way. whole: 0.87 (0.17), residues: 2470 helix: 0.72 (0.12), residues: 1872 sheet: None (None), residues: 0 loop : 0.52 (0.27), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 41 TYR 0.008 0.001 TYR H 30 PHE 0.009 0.001 PHE I 72 TRP 0.008 0.001 TRP Q 68 HIS 0.003 0.001 HIS P 57 Details of bonding type rmsd covalent geometry : bond 0.00356 (21190) covalent geometry : angle 0.45226 (28860) hydrogen bonds : bond 0.04790 ( 1066) hydrogen bonds : angle 3.27376 ( 3198) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 403 time to evaluate : 0.767 Fit side-chains REVERT: A 53 ASP cc_start: 0.8443 (m-30) cc_final: 0.8180 (m-30) REVERT: B 80 GLU cc_start: 0.8553 (mp0) cc_final: 0.8307 (mp0) REVERT: D 38 ASP cc_start: 0.8615 (m-30) cc_final: 0.8394 (m-30) REVERT: D 48 LEU cc_start: 0.8859 (tp) cc_final: 0.8586 (tp) REVERT: D 80 GLU cc_start: 0.8570 (mp0) cc_final: 0.8008 (mp0) REVERT: E 53 ASP cc_start: 0.8503 (m-30) cc_final: 0.8198 (m-30) REVERT: F 40 ASP cc_start: 0.8187 (t0) cc_final: 0.7936 (t0) REVERT: F 53 ASP cc_start: 0.8542 (m-30) cc_final: 0.8258 (m-30) REVERT: G 14 ARG cc_start: 0.8657 (mtm-85) cc_final: 0.8409 (mtm-85) REVERT: J 53 ASP cc_start: 0.8803 (m-30) cc_final: 0.8507 (m-30) REVERT: K 53 ASP cc_start: 0.8475 (m-30) cc_final: 0.8124 (m-30) REVERT: L 10 LYS cc_start: 0.8452 (mmtt) cc_final: 0.8182 (mptt) REVERT: L 38 ASP cc_start: 0.8773 (m-30) cc_final: 0.8542 (m-30) REVERT: L 53 ASP cc_start: 0.8739 (m-30) cc_final: 0.8494 (m-30) REVERT: N 14 ARG cc_start: 0.8589 (mtm-85) cc_final: 0.7753 (mmt180) REVERT: N 41 ARG cc_start: 0.8473 (mtp-110) cc_final: 0.8037 (mtp-110) REVERT: O 7 LYS cc_start: 0.8701 (mtpp) cc_final: 0.8469 (mtmt) REVERT: O 53 ASP cc_start: 0.8555 (m-30) cc_final: 0.8222 (m-30) REVERT: Q 10 LYS cc_start: 0.8212 (mmtt) cc_final: 0.7855 (mmtt) REVERT: Q 60 ASN cc_start: 0.9080 (t0) cc_final: 0.8853 (t0) REVERT: R 38 ASP cc_start: 0.9044 (m-30) cc_final: 0.8671 (m-30) REVERT: R 53 ASP cc_start: 0.8712 (m-30) cc_final: 0.8499 (m-30) REVERT: R 80 GLU cc_start: 0.8618 (mp0) cc_final: 0.8206 (mp0) REVERT: S 1 MET cc_start: 0.6303 (mmt) cc_final: 0.5683 (mmt) REVERT: T 39 GLN cc_start: 0.9111 (tt0) cc_final: 0.8888 (tt0) REVERT: T 41 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.8424 (mtm110) REVERT: U 11 TYR cc_start: 0.8993 (t80) cc_final: 0.8677 (t80) REVERT: U 38 ASP cc_start: 0.8689 (m-30) cc_final: 0.8302 (m-30) REVERT: U 40 ASP cc_start: 0.8275 (t0) cc_final: 0.7851 (t0) REVERT: U 53 ASP cc_start: 0.8724 (m-30) cc_final: 0.8324 (m-30) REVERT: V 53 ASP cc_start: 0.8651 (m-30) cc_final: 0.8371 (m-30) REVERT: W 48 LEU cc_start: 0.8822 (tp) cc_final: 0.8557 (tp) REVERT: W 80 GLU cc_start: 0.8934 (mp0) cc_final: 0.8709 (mp0) REVERT: W 91 VAL cc_start: 0.8942 (t) cc_final: 0.8674 (t) REVERT: X 10 LYS cc_start: 0.8483 (mmtt) cc_final: 0.8126 (mptt) REVERT: X 53 ASP cc_start: 0.8660 (m-30) cc_final: 0.8459 (m-30) REVERT: Y 1 MET cc_start: 0.6141 (mmt) cc_final: 0.5309 (mmt) REVERT: Y 53 ASP cc_start: 0.8594 (OUTLIER) cc_final: 0.8094 (m-30) REVERT: Y 80 GLU cc_start: 0.8462 (mp0) cc_final: 0.8164 (mp0) REVERT: Z 41 ARG cc_start: 0.8381 (mtp-110) cc_final: 0.8131 (mtp85) REVERT: Z 53 ASP cc_start: 0.8300 (m-30) cc_final: 0.7915 (m-30) REVERT: Z 80 GLU cc_start: 0.8353 (mp0) cc_final: 0.8066 (mm-30) outliers start: 32 outliers final: 25 residues processed: 422 average time/residue: 0.1498 time to fit residues: 93.8466 Evaluate side-chains 400 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 373 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 94 SER Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain I residue 94 SER Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain L residue 18 ASN Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain N residue 47 THR Chi-restraints excluded: chain O residue 17 SER Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain S residue 25 VAL Chi-restraints excluded: chain S residue 94 SER Chi-restraints excluded: chain T residue 41 ARG Chi-restraints excluded: chain U residue 94 SER Chi-restraints excluded: chain X residue 39 GLN Chi-restraints excluded: chain Y residue 17 SER Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain Y residue 91 VAL Chi-restraints excluded: chain Z residue 17 SER Chi-restraints excluded: chain Z residue 94 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 121 optimal weight: 3.9990 chunk 185 optimal weight: 5.9990 chunk 43 optimal weight: 0.2980 chunk 3 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 192 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 chunk 105 optimal weight: 0.5980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN J 93 GLN K 93 GLN N 93 GLN W 93 GLN Y 93 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.092926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.082001 restraints weight = 32519.144| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 1.70 r_work: 0.2739 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 21190 Z= 0.124 Angle : 0.405 4.718 28860 Z= 0.212 Chirality : 0.036 0.110 3146 Planarity : 0.003 0.021 3744 Dihedral : 3.197 12.165 2860 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.68 % Allowed : 8.27 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.18), residues: 2470 helix: 0.71 (0.12), residues: 2054 sheet: None (None), residues: 0 loop : 2.67 (0.34), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 41 TYR 0.010 0.001 TYR H 30 PHE 0.009 0.001 PHE Z 3 TRP 0.006 0.001 TRP L 56 HIS 0.003 0.001 HIS P 57 Details of bonding type rmsd covalent geometry : bond 0.00304 (21190) covalent geometry : angle 0.40541 (28860) hydrogen bonds : bond 0.03858 ( 1066) hydrogen bonds : angle 2.99695 ( 3198) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 381 time to evaluate : 0.516 Fit side-chains REVERT: A 53 ASP cc_start: 0.8533 (m-30) cc_final: 0.8271 (m-30) REVERT: B 80 GLU cc_start: 0.8519 (mp0) cc_final: 0.8285 (mp0) REVERT: D 38 ASP cc_start: 0.8518 (m-30) cc_final: 0.8296 (m-30) REVERT: D 40 ASP cc_start: 0.8316 (t0) cc_final: 0.7971 (t0) REVERT: D 48 LEU cc_start: 0.8871 (tp) cc_final: 0.8589 (tp) REVERT: D 80 GLU cc_start: 0.8602 (mp0) cc_final: 0.8152 (mp0) REVERT: E 21 ASN cc_start: 0.8705 (m-40) cc_final: 0.8233 (m-40) REVERT: E 53 ASP cc_start: 0.8458 (m-30) cc_final: 0.8182 (m-30) REVERT: F 40 ASP cc_start: 0.8152 (t0) cc_final: 0.7874 (t0) REVERT: F 41 ARG cc_start: 0.8510 (mtp-110) cc_final: 0.8299 (mtp85) REVERT: F 53 ASP cc_start: 0.8562 (m-30) cc_final: 0.8147 (m-30) REVERT: H 18 ASN cc_start: 0.8965 (p0) cc_final: 0.8557 (p0) REVERT: H 93 GLN cc_start: 0.9176 (OUTLIER) cc_final: 0.8734 (tm-30) REVERT: J 53 ASP cc_start: 0.8799 (m-30) cc_final: 0.8512 (m-30) REVERT: K 53 ASP cc_start: 0.8511 (m-30) cc_final: 0.8165 (m-30) REVERT: L 10 LYS cc_start: 0.8588 (mmtt) cc_final: 0.8288 (mptt) REVERT: L 38 ASP cc_start: 0.9026 (m-30) cc_final: 0.8717 (m-30) REVERT: L 41 ARG cc_start: 0.8652 (mtm110) cc_final: 0.7870 (ttp80) REVERT: N 14 ARG cc_start: 0.8606 (mtm-85) cc_final: 0.7777 (mmt180) REVERT: N 41 ARG cc_start: 0.8473 (mtp-110) cc_final: 0.8148 (mtp-110) REVERT: O 7 LYS cc_start: 0.8764 (mtpp) cc_final: 0.8538 (mtmt) REVERT: O 53 ASP cc_start: 0.8370 (m-30) cc_final: 0.8023 (m-30) REVERT: Q 10 LYS cc_start: 0.8426 (mmtt) cc_final: 0.8083 (mmtt) REVERT: Q 60 ASN cc_start: 0.9001 (t0) cc_final: 0.8743 (t0) REVERT: R 38 ASP cc_start: 0.8985 (m-30) cc_final: 0.8550 (m-30) REVERT: R 53 ASP cc_start: 0.8763 (m-30) cc_final: 0.8487 (m-30) REVERT: S 1 MET cc_start: 0.6321 (mmt) cc_final: 0.5520 (mmt) REVERT: T 7 LYS cc_start: 0.8701 (mtpp) cc_final: 0.8491 (mtpt) REVERT: U 7 LYS cc_start: 0.8831 (mtpp) cc_final: 0.8516 (mtpt) REVERT: U 38 ASP cc_start: 0.8638 (m-30) cc_final: 0.8314 (m-30) REVERT: U 53 ASP cc_start: 0.8682 (m-30) cc_final: 0.8188 (m-30) REVERT: V 53 ASP cc_start: 0.8667 (m-30) cc_final: 0.8424 (m-30) REVERT: W 48 LEU cc_start: 0.8812 (tp) cc_final: 0.8563 (tp) REVERT: W 53 ASP cc_start: 0.8780 (m-30) cc_final: 0.8434 (m-30) REVERT: W 60 ASN cc_start: 0.9066 (t0) cc_final: 0.8673 (t0) REVERT: W 80 GLU cc_start: 0.8918 (mp0) cc_final: 0.8636 (mp0) REVERT: W 91 VAL cc_start: 0.8939 (t) cc_final: 0.8703 (t) REVERT: X 10 LYS cc_start: 0.8528 (mmtt) cc_final: 0.8190 (mptt) REVERT: Y 38 ASP cc_start: 0.8696 (m-30) cc_final: 0.8266 (m-30) REVERT: Y 53 ASP cc_start: 0.8640 (m-30) cc_final: 0.8175 (m-30) REVERT: Y 80 GLU cc_start: 0.8444 (mp0) cc_final: 0.8219 (mp0) REVERT: Z 53 ASP cc_start: 0.8310 (m-30) cc_final: 0.7947 (m-30) REVERT: Z 80 GLU cc_start: 0.8326 (mp0) cc_final: 0.8061 (mm-30) outliers start: 38 outliers final: 33 residues processed: 401 average time/residue: 0.1558 time to fit residues: 93.1086 Evaluate side-chains 399 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 365 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 94 SER Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 94 SER Chi-restraints excluded: chain G residue 39 GLN Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 93 GLN Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain I residue 94 SER Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain L residue 18 ASN Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 47 THR Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain O residue 17 SER Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain P residue 90 SER Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 25 VAL Chi-restraints excluded: chain S residue 94 SER Chi-restraints excluded: chain U residue 94 SER Chi-restraints excluded: chain X residue 17 SER Chi-restraints excluded: chain Y residue 17 SER Chi-restraints excluded: chain Z residue 17 SER Chi-restraints excluded: chain Z residue 94 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 72 optimal weight: 7.9990 chunk 143 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 221 optimal weight: 6.9990 chunk 214 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 chunk 135 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 93 GLN J 93 GLN X 39 GLN Y 93 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.089839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.079240 restraints weight = 32857.587| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 1.64 r_work: 0.2673 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2545 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 21190 Z= 0.226 Angle : 0.493 5.053 28860 Z= 0.258 Chirality : 0.041 0.126 3146 Planarity : 0.004 0.042 3744 Dihedral : 3.605 14.689 2860 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.25 % Allowed : 9.02 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.17), residues: 2470 helix: 0.83 (0.12), residues: 1898 sheet: None (None), residues: 0 loop : 0.58 (0.28), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG Q 43 TYR 0.019 0.001 TYR H 30 PHE 0.010 0.002 PHE W 3 TRP 0.009 0.002 TRP E 68 HIS 0.006 0.002 HIS P 57 Details of bonding type rmsd covalent geometry : bond 0.00563 (21190) covalent geometry : angle 0.49263 (28860) hydrogen bonds : bond 0.05109 ( 1066) hydrogen bonds : angle 3.17585 ( 3198) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 378 time to evaluate : 0.813 Fit side-chains REVERT: A 38 ASP cc_start: 0.8724 (m-30) cc_final: 0.8505 (m-30) REVERT: A 53 ASP cc_start: 0.8593 (m-30) cc_final: 0.8379 (m-30) REVERT: C 40 ASP cc_start: 0.8253 (t0) cc_final: 0.8047 (t0) REVERT: D 38 ASP cc_start: 0.8511 (m-30) cc_final: 0.8269 (m-30) REVERT: D 40 ASP cc_start: 0.8375 (t0) cc_final: 0.7929 (t0) REVERT: D 48 LEU cc_start: 0.8920 (tp) cc_final: 0.8654 (tp) REVERT: D 80 GLU cc_start: 0.8512 (mp0) cc_final: 0.7989 (mp0) REVERT: E 21 ASN cc_start: 0.8686 (m-40) cc_final: 0.8233 (m110) REVERT: E 53 ASP cc_start: 0.8512 (m-30) cc_final: 0.8246 (m-30) REVERT: F 40 ASP cc_start: 0.8154 (t0) cc_final: 0.7864 (t0) REVERT: G 10 LYS cc_start: 0.8609 (mmtt) cc_final: 0.8292 (mmtt) REVERT: G 93 GLN cc_start: 0.9147 (OUTLIER) cc_final: 0.8806 (tm-30) REVERT: H 93 GLN cc_start: 0.9220 (OUTLIER) cc_final: 0.8840 (tm-30) REVERT: I 1 MET cc_start: 0.5935 (mmt) cc_final: 0.5698 (mtt) REVERT: I 40 ASP cc_start: 0.8298 (t0) cc_final: 0.8064 (t0) REVERT: K 53 ASP cc_start: 0.8577 (m-30) cc_final: 0.8212 (m-30) REVERT: L 38 ASP cc_start: 0.9008 (m-30) cc_final: 0.8599 (m-30) REVERT: L 41 ARG cc_start: 0.8692 (mtm110) cc_final: 0.7902 (ttp80) REVERT: N 14 ARG cc_start: 0.8620 (mtm-85) cc_final: 0.7803 (mmt180) REVERT: N 41 ARG cc_start: 0.8532 (mtp-110) cc_final: 0.8282 (mtp-110) REVERT: O 53 ASP cc_start: 0.8345 (m-30) cc_final: 0.7993 (m-30) REVERT: P 40 ASP cc_start: 0.8127 (t0) cc_final: 0.7905 (t0) REVERT: Q 10 LYS cc_start: 0.8460 (mmtt) cc_final: 0.8107 (mmtt) REVERT: Q 93 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.7534 (mp10) REVERT: R 38 ASP cc_start: 0.9025 (m-30) cc_final: 0.8427 (m-30) REVERT: R 53 ASP cc_start: 0.8904 (m-30) cc_final: 0.8672 (m-30) REVERT: S 41 ARG cc_start: 0.8474 (mtp-110) cc_final: 0.8190 (mtp-110) REVERT: U 7 LYS cc_start: 0.8869 (mtpp) cc_final: 0.8518 (mtpt) REVERT: U 38 ASP cc_start: 0.8762 (m-30) cc_final: 0.8418 (m-30) REVERT: U 40 ASP cc_start: 0.8237 (t0) cc_final: 0.7808 (t0) REVERT: V 7 LYS cc_start: 0.9149 (mtpp) cc_final: 0.8859 (mttt) REVERT: V 53 ASP cc_start: 0.8693 (m-30) cc_final: 0.8449 (m-30) REVERT: W 48 LEU cc_start: 0.8835 (tp) cc_final: 0.8536 (tp) REVERT: W 53 ASP cc_start: 0.8857 (m-30) cc_final: 0.8512 (m-30) REVERT: W 80 GLU cc_start: 0.8782 (mp0) cc_final: 0.8446 (mp0) REVERT: W 93 GLN cc_start: 0.8476 (tp40) cc_final: 0.8057 (tp-100) REVERT: X 10 LYS cc_start: 0.8531 (mmtt) cc_final: 0.8192 (mptt) REVERT: Y 38 ASP cc_start: 0.8731 (m-30) cc_final: 0.8266 (m-30) REVERT: Y 80 GLU cc_start: 0.8379 (mp0) cc_final: 0.8127 (mp0) REVERT: Y 93 GLN cc_start: 0.8497 (tp40) cc_final: 0.8268 (tp-100) REVERT: Z 5 GLU cc_start: 0.8533 (tt0) cc_final: 0.8327 (tt0) REVERT: Z 53 ASP cc_start: 0.8485 (m-30) cc_final: 0.8120 (m-30) REVERT: Z 80 GLU cc_start: 0.8268 (mp0) cc_final: 0.8059 (mm-30) REVERT: Z 93 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.8210 (mp10) outliers start: 51 outliers final: 44 residues processed: 411 average time/residue: 0.1459 time to fit residues: 89.4319 Evaluate side-chains 417 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 369 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 94 SER Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 94 SER Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 39 GLN Chi-restraints excluded: chain G residue 93 GLN Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 93 GLN Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain I residue 94 SER Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain K residue 39 GLN Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain L residue 18 ASN Chi-restraints excluded: chain M residue 5 GLU Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 47 THR Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain O residue 17 SER Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain P residue 90 SER Chi-restraints excluded: chain Q residue 39 GLN Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 93 GLN Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 25 VAL Chi-restraints excluded: chain S residue 94 SER Chi-restraints excluded: chain T residue 90 SER Chi-restraints excluded: chain U residue 94 SER Chi-restraints excluded: chain V residue 25 VAL Chi-restraints excluded: chain X residue 17 SER Chi-restraints excluded: chain X residue 39 GLN Chi-restraints excluded: chain X residue 94 SER Chi-restraints excluded: chain Y residue 17 SER Chi-restraints excluded: chain Z residue 17 SER Chi-restraints excluded: chain Z residue 93 GLN Chi-restraints excluded: chain Z residue 94 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 58 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 135 optimal weight: 8.9990 chunk 171 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 121 optimal weight: 8.9990 chunk 209 optimal weight: 0.3980 chunk 113 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 93 GLN M 39 GLN X 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.093847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.082449 restraints weight = 32270.449| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 1.84 r_work: 0.2728 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2596 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 21190 Z= 0.094 Angle : 0.378 4.670 28860 Z= 0.198 Chirality : 0.035 0.116 3146 Planarity : 0.002 0.026 3744 Dihedral : 3.171 12.157 2860 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.72 % Allowed : 10.21 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.17), residues: 2470 helix: 1.03 (0.12), residues: 1898 sheet: None (None), residues: 0 loop : 0.86 (0.28), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 41 TYR 0.007 0.001 TYR H 30 PHE 0.008 0.001 PHE Z 3 TRP 0.007 0.001 TRP Q 56 HIS 0.001 0.000 HIS P 57 Details of bonding type rmsd covalent geometry : bond 0.00225 (21190) covalent geometry : angle 0.37814 (28860) hydrogen bonds : bond 0.03030 ( 1066) hydrogen bonds : angle 2.76134 ( 3198) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 365 time to evaluate : 0.656 Fit side-chains REVERT: A 53 ASP cc_start: 0.8595 (m-30) cc_final: 0.8340 (m-30) REVERT: B 40 ASP cc_start: 0.8372 (t0) cc_final: 0.8151 (t0) REVERT: C 40 ASP cc_start: 0.8132 (t0) cc_final: 0.7880 (t0) REVERT: D 38 ASP cc_start: 0.8551 (m-30) cc_final: 0.8311 (m-30) REVERT: D 48 LEU cc_start: 0.8781 (tp) cc_final: 0.8511 (tp) REVERT: D 80 GLU cc_start: 0.8584 (mp0) cc_final: 0.8056 (mp0) REVERT: E 21 ASN cc_start: 0.8701 (m-40) cc_final: 0.8233 (m110) REVERT: E 53 ASP cc_start: 0.8401 (m-30) cc_final: 0.8158 (m-30) REVERT: F 41 ARG cc_start: 0.8591 (mtp-110) cc_final: 0.8193 (mtp85) REVERT: F 53 ASP cc_start: 0.8598 (m-30) cc_final: 0.8262 (m-30) REVERT: G 10 LYS cc_start: 0.8544 (mmtt) cc_final: 0.8193 (mmtt) REVERT: G 39 GLN cc_start: 0.9070 (OUTLIER) cc_final: 0.8822 (mt0) REVERT: H 93 GLN cc_start: 0.9218 (OUTLIER) cc_final: 0.8889 (tm-30) REVERT: K 53 ASP cc_start: 0.8579 (m-30) cc_final: 0.8208 (m-30) REVERT: L 38 ASP cc_start: 0.9064 (m-30) cc_final: 0.8705 (m-30) REVERT: L 41 ARG cc_start: 0.8744 (mtm110) cc_final: 0.7935 (ttp80) REVERT: M 39 GLN cc_start: 0.9150 (OUTLIER) cc_final: 0.8711 (tp40) REVERT: N 14 ARG cc_start: 0.8586 (mtm-85) cc_final: 0.7775 (mmt180) REVERT: N 41 ARG cc_start: 0.8565 (mtp-110) cc_final: 0.8260 (mtp-110) REVERT: O 53 ASP cc_start: 0.8325 (m-30) cc_final: 0.8021 (m-30) REVERT: P 40 ASP cc_start: 0.8090 (t0) cc_final: 0.7852 (t0) REVERT: R 38 ASP cc_start: 0.9029 (m-30) cc_final: 0.8319 (m-30) REVERT: U 7 LYS cc_start: 0.8825 (mtpp) cc_final: 0.8575 (mtpt) REVERT: U 38 ASP cc_start: 0.8771 (m-30) cc_final: 0.8437 (m-30) REVERT: V 53 ASP cc_start: 0.8680 (m-30) cc_final: 0.8475 (m-30) REVERT: W 48 LEU cc_start: 0.8790 (tp) cc_final: 0.8519 (tp) REVERT: W 53 ASP cc_start: 0.8773 (m-30) cc_final: 0.8552 (m-30) REVERT: W 80 GLU cc_start: 0.8789 (mp0) cc_final: 0.8487 (mp0) REVERT: W 91 VAL cc_start: 0.8903 (t) cc_final: 0.8663 (t) REVERT: W 93 GLN cc_start: 0.8456 (tp40) cc_final: 0.8079 (tp-100) REVERT: X 10 LYS cc_start: 0.8678 (mmtt) cc_final: 0.8414 (mptt) REVERT: Y 38 ASP cc_start: 0.8765 (m-30) cc_final: 0.8277 (m-30) REVERT: Y 53 ASP cc_start: 0.8793 (m-30) cc_final: 0.8359 (m-30) REVERT: Z 53 ASP cc_start: 0.8397 (m-30) cc_final: 0.8061 (m-30) REVERT: Z 80 GLU cc_start: 0.8266 (mp0) cc_final: 0.7578 (mp0) outliers start: 39 outliers final: 31 residues processed: 389 average time/residue: 0.1512 time to fit residues: 87.4969 Evaluate side-chains 385 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 351 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 94 SER Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 94 SER Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 39 GLN Chi-restraints excluded: chain G residue 93 GLN Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain H residue 93 GLN Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain I residue 94 SER Chi-restraints excluded: chain J residue 39 GLN Chi-restraints excluded: chain L residue 18 ASN Chi-restraints excluded: chain L residue 26 GLU Chi-restraints excluded: chain M residue 39 GLN Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain P residue 90 SER Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 25 VAL Chi-restraints excluded: chain S residue 94 SER Chi-restraints excluded: chain T residue 90 SER Chi-restraints excluded: chain U residue 94 SER Chi-restraints excluded: chain X residue 17 SER Chi-restraints excluded: chain X residue 39 GLN Chi-restraints excluded: chain Y residue 17 SER Chi-restraints excluded: chain Z residue 17 SER Chi-restraints excluded: chain Z residue 25 VAL Chi-restraints excluded: chain Z residue 94 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 198 optimal weight: 8.9990 chunk 38 optimal weight: 4.9990 chunk 227 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 chunk 185 optimal weight: 3.9990 chunk 209 optimal weight: 0.6980 chunk 147 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 99 optimal weight: 8.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 93 GLN K 93 GLN M 39 GLN Q 93 GLN X 39 GLN Y 93 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.092262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.081519 restraints weight = 32341.379| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 1.69 r_work: 0.2715 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2587 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 21190 Z= 0.120 Angle : 0.398 4.765 28860 Z= 0.208 Chirality : 0.036 0.109 3146 Planarity : 0.003 0.027 3744 Dihedral : 3.188 12.687 2860 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.17 % Allowed : 9.95 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.17), residues: 2470 helix: 1.08 (0.12), residues: 1898 sheet: None (None), residues: 0 loop : 0.91 (0.28), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 41 TYR 0.010 0.001 TYR H 30 PHE 0.007 0.001 PHE Z 3 TRP 0.006 0.001 TRP M 56 HIS 0.003 0.001 HIS P 57 Details of bonding type rmsd covalent geometry : bond 0.00299 (21190) covalent geometry : angle 0.39833 (28860) hydrogen bonds : bond 0.03463 ( 1066) hydrogen bonds : angle 2.79758 ( 3198) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 362 time to evaluate : 0.651 Fit side-chains REVERT: C 40 ASP cc_start: 0.8124 (t0) cc_final: 0.7837 (t0) REVERT: D 38 ASP cc_start: 0.8625 (m-30) cc_final: 0.8402 (m-30) REVERT: D 48 LEU cc_start: 0.8800 (tp) cc_final: 0.8536 (tp) REVERT: D 80 GLU cc_start: 0.8544 (mp0) cc_final: 0.8007 (mp0) REVERT: E 21 ASN cc_start: 0.8691 (m-40) cc_final: 0.8136 (m110) REVERT: E 53 ASP cc_start: 0.8518 (m-30) cc_final: 0.8277 (m-30) REVERT: F 41 ARG cc_start: 0.8561 (mtp-110) cc_final: 0.8179 (mtp85) REVERT: F 53 ASP cc_start: 0.8384 (m-30) cc_final: 0.8069 (m-30) REVERT: G 10 LYS cc_start: 0.8573 (mmtt) cc_final: 0.8221 (mmtt) REVERT: G 39 GLN cc_start: 0.9074 (OUTLIER) cc_final: 0.8838 (mt0) REVERT: I 1 MET cc_start: 0.6017 (mmt) cc_final: 0.4999 (mmt) REVERT: K 53 ASP cc_start: 0.8587 (m-30) cc_final: 0.8229 (m-30) REVERT: L 38 ASP cc_start: 0.9028 (m-30) cc_final: 0.8671 (m-30) REVERT: L 41 ARG cc_start: 0.8747 (mtm110) cc_final: 0.7936 (ttp80) REVERT: N 14 ARG cc_start: 0.8602 (mtm-85) cc_final: 0.7814 (mmt180) REVERT: N 39 GLN cc_start: 0.9243 (OUTLIER) cc_final: 0.8858 (tp40) REVERT: N 41 ARG cc_start: 0.8540 (mtp-110) cc_final: 0.8260 (mtp-110) REVERT: O 53 ASP cc_start: 0.8288 (m-30) cc_final: 0.8026 (m-30) REVERT: P 40 ASP cc_start: 0.8056 (t0) cc_final: 0.7815 (t0) REVERT: Q 93 GLN cc_start: 0.8380 (tp40) cc_final: 0.8138 (tp-100) REVERT: R 38 ASP cc_start: 0.9021 (m-30) cc_final: 0.8311 (m-30) REVERT: S 41 ARG cc_start: 0.8535 (mtp-110) cc_final: 0.8255 (mtp-110) REVERT: U 7 LYS cc_start: 0.8832 (mtpp) cc_final: 0.8558 (mtpt) REVERT: U 38 ASP cc_start: 0.8728 (m-30) cc_final: 0.8378 (m-30) REVERT: U 40 ASP cc_start: 0.8361 (t0) cc_final: 0.7873 (t0) REVERT: V 53 ASP cc_start: 0.8687 (m-30) cc_final: 0.8475 (m-30) REVERT: W 48 LEU cc_start: 0.8826 (tp) cc_final: 0.8533 (tp) REVERT: W 53 ASP cc_start: 0.8690 (m-30) cc_final: 0.8471 (m-30) REVERT: W 80 GLU cc_start: 0.8752 (mp0) cc_final: 0.8408 (mp0) REVERT: W 91 VAL cc_start: 0.8921 (t) cc_final: 0.8675 (t) REVERT: W 93 GLN cc_start: 0.8427 (tp40) cc_final: 0.8103 (tp-100) REVERT: X 10 LYS cc_start: 0.8653 (mmtt) cc_final: 0.8405 (mptt) REVERT: Y 38 ASP cc_start: 0.8750 (m-30) cc_final: 0.8257 (m-30) REVERT: Y 53 ASP cc_start: 0.8789 (m-30) cc_final: 0.8346 (m-30) REVERT: Z 53 ASP cc_start: 0.8461 (m-30) cc_final: 0.8119 (m-30) outliers start: 49 outliers final: 39 residues processed: 396 average time/residue: 0.1501 time to fit residues: 88.0401 Evaluate side-chains 402 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 361 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 94 SER Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 94 SER Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 39 GLN Chi-restraints excluded: chain G residue 93 GLN Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain H residue 93 GLN Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain I residue 94 SER Chi-restraints excluded: chain J residue 39 GLN Chi-restraints excluded: chain K residue 39 GLN Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain L residue 18 ASN Chi-restraints excluded: chain L residue 26 GLU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain O residue 17 SER Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain P residue 54 THR Chi-restraints excluded: chain P residue 90 SER Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 25 VAL Chi-restraints excluded: chain S residue 94 SER Chi-restraints excluded: chain T residue 90 SER Chi-restraints excluded: chain U residue 94 SER Chi-restraints excluded: chain W residue 39 GLN Chi-restraints excluded: chain X residue 17 SER Chi-restraints excluded: chain Y residue 17 SER Chi-restraints excluded: chain Z residue 17 SER Chi-restraints excluded: chain Z residue 25 VAL Chi-restraints excluded: chain Z residue 26 GLU Chi-restraints excluded: chain Z residue 94 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 16 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 163 optimal weight: 4.9990 chunk 210 optimal weight: 3.9990 chunk 93 optimal weight: 0.0370 chunk 135 optimal weight: 8.9990 chunk 214 optimal weight: 0.8980 chunk 184 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 165 optimal weight: 0.6980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 93 GLN N 93 GLN Y 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.094795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.083751 restraints weight = 32149.076| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 1.73 r_work: 0.2763 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 21190 Z= 0.080 Angle : 0.364 4.599 28860 Z= 0.190 Chirality : 0.034 0.104 3146 Planarity : 0.002 0.029 3744 Dihedral : 2.952 11.301 2860 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.90 % Allowed : 10.12 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.85 (0.18), residues: 2470 helix: 1.03 (0.12), residues: 2054 sheet: None (None), residues: 0 loop : 2.96 (0.34), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 41 TYR 0.005 0.001 TYR H 30 PHE 0.007 0.001 PHE Z 3 TRP 0.006 0.001 TRP Q 56 HIS 0.001 0.000 HIS P 57 Details of bonding type rmsd covalent geometry : bond 0.00190 (21190) covalent geometry : angle 0.36391 (28860) hydrogen bonds : bond 0.02611 ( 1066) hydrogen bonds : angle 2.62563 ( 3198) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 364 time to evaluate : 0.739 Fit side-chains REVERT: B 80 GLU cc_start: 0.8546 (mp0) cc_final: 0.8322 (mp0) REVERT: C 40 ASP cc_start: 0.8054 (t0) cc_final: 0.7754 (t0) REVERT: D 38 ASP cc_start: 0.8615 (m-30) cc_final: 0.8397 (m-30) REVERT: D 48 LEU cc_start: 0.8736 (tp) cc_final: 0.8478 (tp) REVERT: D 80 GLU cc_start: 0.8596 (mp0) cc_final: 0.8074 (mp0) REVERT: E 21 ASN cc_start: 0.8692 (m-40) cc_final: 0.8125 (m110) REVERT: F 53 ASP cc_start: 0.8575 (m-30) cc_final: 0.8196 (m-30) REVERT: G 10 LYS cc_start: 0.8549 (mmtt) cc_final: 0.8177 (mmtt) REVERT: H 93 GLN cc_start: 0.9168 (OUTLIER) cc_final: 0.8878 (tm-30) REVERT: I 1 MET cc_start: 0.5941 (mmt) cc_final: 0.4830 (mmt) REVERT: I 53 ASP cc_start: 0.8459 (m-30) cc_final: 0.8247 (m-30) REVERT: K 53 ASP cc_start: 0.8554 (m-30) cc_final: 0.8202 (m-30) REVERT: L 38 ASP cc_start: 0.9026 (m-30) cc_final: 0.8692 (m-30) REVERT: L 41 ARG cc_start: 0.8723 (mtm110) cc_final: 0.7944 (ttp80) REVERT: N 14 ARG cc_start: 0.8590 (mtm-85) cc_final: 0.7789 (mmt180) REVERT: N 41 ARG cc_start: 0.8541 (mtp-110) cc_final: 0.8067 (mtp-110) REVERT: O 53 ASP cc_start: 0.8263 (m-30) cc_final: 0.8006 (m-30) REVERT: P 40 ASP cc_start: 0.7976 (t0) cc_final: 0.7755 (t0) REVERT: Q 93 GLN cc_start: 0.8470 (tp40) cc_final: 0.8255 (tp-100) REVERT: R 38 ASP cc_start: 0.8924 (m-30) cc_final: 0.8176 (m-30) REVERT: T 7 LYS cc_start: 0.8786 (mttt) cc_final: 0.8581 (mtpt) REVERT: U 7 LYS cc_start: 0.8787 (mtpp) cc_final: 0.8545 (mtpt) REVERT: U 38 ASP cc_start: 0.8731 (m-30) cc_final: 0.8407 (m-30) REVERT: V 7 LYS cc_start: 0.9084 (mtpp) cc_final: 0.8856 (mttt) REVERT: W 48 LEU cc_start: 0.8773 (tp) cc_final: 0.8489 (tp) REVERT: W 80 GLU cc_start: 0.8749 (mp0) cc_final: 0.8458 (mp0) REVERT: W 91 VAL cc_start: 0.8905 (t) cc_final: 0.8653 (t) REVERT: W 93 GLN cc_start: 0.8442 (tp40) cc_final: 0.8137 (tp-100) REVERT: Y 38 ASP cc_start: 0.8687 (m-30) cc_final: 0.8231 (m-30) REVERT: Y 53 ASP cc_start: 0.8739 (m-30) cc_final: 0.8333 (m-30) REVERT: Z 53 ASP cc_start: 0.8372 (m-30) cc_final: 0.8051 (m-30) outliers start: 43 outliers final: 33 residues processed: 395 average time/residue: 0.1497 time to fit residues: 87.7911 Evaluate side-chains 388 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 354 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 94 SER Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 94 SER Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain H residue 93 GLN Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain I residue 39 GLN Chi-restraints excluded: chain I residue 94 SER Chi-restraints excluded: chain J residue 39 GLN Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain L residue 5 GLU Chi-restraints excluded: chain L residue 18 ASN Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain M residue 26 GLU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain O residue 17 SER Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain P residue 54 THR Chi-restraints excluded: chain P residue 90 SER Chi-restraints excluded: chain Q residue 54 THR Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 25 VAL Chi-restraints excluded: chain S residue 94 SER Chi-restraints excluded: chain T residue 90 SER Chi-restraints excluded: chain U residue 94 SER Chi-restraints excluded: chain W residue 26 GLU Chi-restraints excluded: chain Y residue 17 SER Chi-restraints excluded: chain Z residue 17 SER Chi-restraints excluded: chain Z residue 25 VAL Chi-restraints excluded: chain Z residue 94 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 55 optimal weight: 4.9990 chunk 27 optimal weight: 8.9990 chunk 152 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 53 optimal weight: 8.9990 chunk 52 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 135 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 105 optimal weight: 0.5980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 93 GLN Y 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.091535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.080762 restraints weight = 32548.572| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 1.71 r_work: 0.2725 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 21190 Z= 0.129 Angle : 0.411 5.299 28860 Z= 0.215 Chirality : 0.037 0.123 3146 Planarity : 0.003 0.029 3744 Dihedral : 3.171 13.185 2860 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.17 % Allowed : 9.95 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.17), residues: 2470 helix: 1.19 (0.12), residues: 1898 sheet: None (None), residues: 0 loop : 1.09 (0.29), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 41 TYR 0.011 0.001 TYR H 30 PHE 0.006 0.001 PHE Z 3 TRP 0.006 0.001 TRP Q 56 HIS 0.003 0.001 HIS P 57 Details of bonding type rmsd covalent geometry : bond 0.00322 (21190) covalent geometry : angle 0.41132 (28860) hydrogen bonds : bond 0.03596 ( 1066) hydrogen bonds : angle 2.75496 ( 3198) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 359 time to evaluate : 0.843 Fit side-chains REVERT: C 40 ASP cc_start: 0.8110 (t0) cc_final: 0.7802 (t0) REVERT: D 38 ASP cc_start: 0.8596 (m-30) cc_final: 0.8390 (m-30) REVERT: D 48 LEU cc_start: 0.8805 (tp) cc_final: 0.8545 (tp) REVERT: D 80 GLU cc_start: 0.8556 (mp0) cc_final: 0.8021 (mp0) REVERT: E 21 ASN cc_start: 0.8703 (m-40) cc_final: 0.8178 (m-40) REVERT: F 53 ASP cc_start: 0.8431 (m-30) cc_final: 0.8089 (m-30) REVERT: G 10 LYS cc_start: 0.8590 (mmtt) cc_final: 0.8238 (mmtt) REVERT: I 1 MET cc_start: 0.6188 (mmt) cc_final: 0.5946 (mtt) REVERT: I 41 ARG cc_start: 0.8163 (mtp-110) cc_final: 0.7895 (mtp-110) REVERT: K 53 ASP cc_start: 0.8612 (m-30) cc_final: 0.8246 (m-30) REVERT: L 38 ASP cc_start: 0.9042 (m-30) cc_final: 0.8669 (m-30) REVERT: L 41 ARG cc_start: 0.8614 (mtm110) cc_final: 0.7983 (ttp80) REVERT: N 14 ARG cc_start: 0.8602 (mtm-85) cc_final: 0.7802 (mmt180) REVERT: N 39 GLN cc_start: 0.9258 (OUTLIER) cc_final: 0.8876 (tp40) REVERT: N 41 ARG cc_start: 0.8566 (mtp-110) cc_final: 0.8276 (mtp-110) REVERT: O 53 ASP cc_start: 0.8393 (m-30) cc_final: 0.8158 (m-30) REVERT: P 40 ASP cc_start: 0.8073 (t0) cc_final: 0.7818 (t0) REVERT: R 38 ASP cc_start: 0.8931 (m-30) cc_final: 0.8212 (m-30) REVERT: U 7 LYS cc_start: 0.8856 (mtpp) cc_final: 0.8577 (mtpt) REVERT: U 38 ASP cc_start: 0.8723 (m-30) cc_final: 0.8408 (m-30) REVERT: V 7 LYS cc_start: 0.9141 (mtpp) cc_final: 0.8907 (mttt) REVERT: W 48 LEU cc_start: 0.8819 (tp) cc_final: 0.8513 (tp) REVERT: W 80 GLU cc_start: 0.8713 (mp0) cc_final: 0.8346 (mp0) REVERT: W 93 GLN cc_start: 0.8493 (tp40) cc_final: 0.8187 (tp-100) REVERT: Y 38 ASP cc_start: 0.8755 (m-30) cc_final: 0.8276 (m-30) REVERT: Y 80 GLU cc_start: 0.8408 (mp0) cc_final: 0.8145 (mp0) REVERT: Z 7 LYS cc_start: 0.8929 (mtpp) cc_final: 0.8622 (mttp) REVERT: Z 53 ASP cc_start: 0.8473 (m-30) cc_final: 0.8120 (m-30) outliers start: 49 outliers final: 45 residues processed: 392 average time/residue: 0.1729 time to fit residues: 100.5453 Evaluate side-chains 402 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 356 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 94 SER Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 94 SER Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain H residue 93 GLN Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain I residue 39 GLN Chi-restraints excluded: chain I residue 94 SER Chi-restraints excluded: chain J residue 39 GLN Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain K residue 39 GLN Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain L residue 5 GLU Chi-restraints excluded: chain L residue 18 ASN Chi-restraints excluded: chain L residue 26 GLU Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain M residue 26 GLU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain O residue 17 SER Chi-restraints excluded: chain O residue 39 GLN Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain P residue 54 THR Chi-restraints excluded: chain P residue 90 SER Chi-restraints excluded: chain Q residue 39 GLN Chi-restraints excluded: chain Q residue 54 THR Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 25 VAL Chi-restraints excluded: chain S residue 94 SER Chi-restraints excluded: chain T residue 90 SER Chi-restraints excluded: chain U residue 94 SER Chi-restraints excluded: chain W residue 26 GLU Chi-restraints excluded: chain X residue 94 SER Chi-restraints excluded: chain Y residue 17 SER Chi-restraints excluded: chain Z residue 17 SER Chi-restraints excluded: chain Z residue 25 VAL Chi-restraints excluded: chain Z residue 26 GLU Chi-restraints excluded: chain Z residue 94 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 93 optimal weight: 0.9980 chunk 133 optimal weight: 0.9990 chunk 54 optimal weight: 7.9990 chunk 135 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 112 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 185 optimal weight: 0.8980 chunk 72 optimal weight: 7.9990 chunk 38 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 93 GLN Q 93 GLN R 93 GLN Y 93 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.094156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.082841 restraints weight = 32156.477| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 1.82 r_work: 0.2740 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 21190 Z= 0.091 Angle : 0.381 5.051 28860 Z= 0.199 Chirality : 0.035 0.106 3146 Planarity : 0.002 0.034 3744 Dihedral : 2.994 12.018 2860 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.25 % Allowed : 10.04 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.94 (0.18), residues: 2470 helix: 1.09 (0.12), residues: 2054 sheet: None (None), residues: 0 loop : 3.03 (0.34), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 41 TYR 0.007 0.001 TYR H 30 PHE 0.006 0.001 PHE Z 3 TRP 0.006 0.001 TRP Q 56 HIS 0.002 0.000 HIS P 57 Details of bonding type rmsd covalent geometry : bond 0.00221 (21190) covalent geometry : angle 0.38051 (28860) hydrogen bonds : bond 0.02836 ( 1066) hydrogen bonds : angle 2.61707 ( 3198) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 354 time to evaluate : 0.864 Fit side-chains REVERT: B 80 GLU cc_start: 0.8538 (mp0) cc_final: 0.8302 (mp0) REVERT: C 40 ASP cc_start: 0.8075 (t0) cc_final: 0.7730 (t0) REVERT: D 38 ASP cc_start: 0.8603 (m-30) cc_final: 0.8403 (m-30) REVERT: D 48 LEU cc_start: 0.8749 (tp) cc_final: 0.8507 (tp) REVERT: D 80 GLU cc_start: 0.8633 (mp0) cc_final: 0.8097 (mp0) REVERT: F 53 ASP cc_start: 0.8605 (m-30) cc_final: 0.8238 (m-30) REVERT: G 10 LYS cc_start: 0.8575 (mmtt) cc_final: 0.8227 (mmtt) REVERT: H 93 GLN cc_start: 0.9195 (OUTLIER) cc_final: 0.8917 (tm-30) REVERT: I 1 MET cc_start: 0.5875 (mmt) cc_final: 0.4878 (mmt) REVERT: I 41 ARG cc_start: 0.8105 (mtp-110) cc_final: 0.7835 (mtp-110) REVERT: I 53 ASP cc_start: 0.8486 (m-30) cc_final: 0.8265 (m-30) REVERT: K 53 ASP cc_start: 0.8588 (m-30) cc_final: 0.8222 (m-30) REVERT: L 38 ASP cc_start: 0.9004 (m-30) cc_final: 0.8636 (m-30) REVERT: L 41 ARG cc_start: 0.8632 (mtm110) cc_final: 0.7974 (ttp80) REVERT: N 14 ARG cc_start: 0.8595 (mtm-85) cc_final: 0.7792 (mmt180) REVERT: N 41 ARG cc_start: 0.8561 (mtp-110) cc_final: 0.8098 (mtp-110) REVERT: O 53 ASP cc_start: 0.8387 (m-30) cc_final: 0.8104 (m-30) REVERT: P 40 ASP cc_start: 0.8041 (t0) cc_final: 0.7791 (t0) REVERT: R 38 ASP cc_start: 0.8936 (m-30) cc_final: 0.8196 (m-30) REVERT: U 7 LYS cc_start: 0.8815 (mtpp) cc_final: 0.8557 (mtpt) REVERT: U 38 ASP cc_start: 0.8741 (m-30) cc_final: 0.8435 (m-30) REVERT: W 48 LEU cc_start: 0.8778 (tp) cc_final: 0.8487 (tp) REVERT: W 51 ASN cc_start: 0.8809 (t0) cc_final: 0.8013 (t0) REVERT: W 80 GLU cc_start: 0.8707 (mp0) cc_final: 0.8393 (mp0) REVERT: W 91 VAL cc_start: 0.8899 (t) cc_final: 0.8639 (t) REVERT: W 93 GLN cc_start: 0.8481 (tp40) cc_final: 0.8183 (tp-100) REVERT: Y 38 ASP cc_start: 0.8763 (m-30) cc_final: 0.8268 (m-30) REVERT: Z 7 LYS cc_start: 0.8906 (mtpp) cc_final: 0.8618 (mttp) REVERT: Z 53 ASP cc_start: 0.8461 (m-30) cc_final: 0.8113 (m-30) outliers start: 51 outliers final: 44 residues processed: 393 average time/residue: 0.1733 time to fit residues: 100.9450 Evaluate side-chains 397 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 352 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 94 SER Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 94 SER Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain H residue 93 GLN Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain I residue 39 GLN Chi-restraints excluded: chain I residue 90 SER Chi-restraints excluded: chain I residue 94 SER Chi-restraints excluded: chain J residue 39 GLN Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain L residue 5 GLU Chi-restraints excluded: chain L residue 18 ASN Chi-restraints excluded: chain L residue 26 GLU Chi-restraints excluded: chain L residue 39 GLN Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain M residue 26 GLU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain O residue 17 SER Chi-restraints excluded: chain O residue 39 GLN Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain P residue 54 THR Chi-restraints excluded: chain P residue 90 SER Chi-restraints excluded: chain Q residue 54 THR Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 25 VAL Chi-restraints excluded: chain S residue 94 SER Chi-restraints excluded: chain T residue 39 GLN Chi-restraints excluded: chain T residue 90 SER Chi-restraints excluded: chain U residue 94 SER Chi-restraints excluded: chain W residue 26 GLU Chi-restraints excluded: chain W residue 39 GLN Chi-restraints excluded: chain Y residue 17 SER Chi-restraints excluded: chain Z residue 17 SER Chi-restraints excluded: chain Z residue 25 VAL Chi-restraints excluded: chain Z residue 26 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 230 optimal weight: 5.9990 chunk 218 optimal weight: 0.9980 chunk 190 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 232 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 221 optimal weight: 0.0470 chunk 161 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 93 GLN Q 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.095384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.083999 restraints weight = 32072.603| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 1.83 r_work: 0.2754 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 21190 Z= 0.084 Angle : 0.379 6.058 28860 Z= 0.198 Chirality : 0.034 0.118 3146 Planarity : 0.002 0.037 3744 Dihedral : 2.887 11.646 2860 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.86 % Allowed : 10.34 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.04 (0.18), residues: 2470 helix: 1.15 (0.12), residues: 2054 sheet: None (None), residues: 0 loop : 3.09 (0.35), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 41 TYR 0.006 0.001 TYR H 30 PHE 0.006 0.001 PHE Z 3 TRP 0.006 0.001 TRP T 56 HIS 0.001 0.000 HIS P 57 Details of bonding type rmsd covalent geometry : bond 0.00202 (21190) covalent geometry : angle 0.37859 (28860) hydrogen bonds : bond 0.02585 ( 1066) hydrogen bonds : angle 2.56821 ( 3198) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 359 time to evaluate : 0.784 Fit side-chains REVERT: B 80 GLU cc_start: 0.8573 (mp0) cc_final: 0.8372 (mp0) REVERT: C 40 ASP cc_start: 0.8054 (t0) cc_final: 0.7717 (t0) REVERT: D 48 LEU cc_start: 0.8727 (tp) cc_final: 0.8485 (tp) REVERT: D 80 GLU cc_start: 0.8634 (mp0) cc_final: 0.8096 (mp0) REVERT: E 53 ASP cc_start: 0.8488 (m-30) cc_final: 0.8234 (m-30) REVERT: F 53 ASP cc_start: 0.8581 (m-30) cc_final: 0.8224 (m-30) REVERT: G 10 LYS cc_start: 0.8563 (mmtt) cc_final: 0.8203 (mmtt) REVERT: H 93 GLN cc_start: 0.9184 (OUTLIER) cc_final: 0.8918 (tm-30) REVERT: I 1 MET cc_start: 0.5844 (mmt) cc_final: 0.4679 (mmt) REVERT: I 41 ARG cc_start: 0.8087 (mtp-110) cc_final: 0.7747 (mtp-110) REVERT: I 53 ASP cc_start: 0.8442 (m-30) cc_final: 0.8232 (m-30) REVERT: K 53 ASP cc_start: 0.8552 (m-30) cc_final: 0.8210 (m-30) REVERT: L 38 ASP cc_start: 0.8953 (m-30) cc_final: 0.8578 (m-30) REVERT: L 41 ARG cc_start: 0.8606 (mtm110) cc_final: 0.7964 (ttp80) REVERT: N 14 ARG cc_start: 0.8587 (mtm-85) cc_final: 0.7789 (mmt180) REVERT: N 41 ARG cc_start: 0.8545 (mtp-110) cc_final: 0.8071 (mtp-110) REVERT: O 53 ASP cc_start: 0.8443 (m-30) cc_final: 0.8240 (m-30) REVERT: P 40 ASP cc_start: 0.7959 (t0) cc_final: 0.7731 (t0) REVERT: R 38 ASP cc_start: 0.8914 (m-30) cc_final: 0.8162 (m-30) REVERT: U 7 LYS cc_start: 0.8786 (mtpp) cc_final: 0.8542 (mtpt) REVERT: U 38 ASP cc_start: 0.8744 (m-30) cc_final: 0.8354 (m-30) REVERT: U 40 ASP cc_start: 0.8351 (t0) cc_final: 0.7870 (t0) REVERT: V 93 GLN cc_start: 0.8641 (mm-40) cc_final: 0.8295 (tm-30) REVERT: W 48 LEU cc_start: 0.8762 (tp) cc_final: 0.8466 (tp) REVERT: W 51 ASN cc_start: 0.8754 (t0) cc_final: 0.8001 (t0) REVERT: W 80 GLU cc_start: 0.8693 (mp0) cc_final: 0.8381 (mp0) REVERT: W 91 VAL cc_start: 0.8896 (t) cc_final: 0.8657 (t) REVERT: W 93 GLN cc_start: 0.8466 (tp40) cc_final: 0.8178 (tp-100) REVERT: Y 38 ASP cc_start: 0.8755 (m-30) cc_final: 0.8365 (m-30) REVERT: Y 53 ASP cc_start: 0.8698 (m-30) cc_final: 0.8283 (m-30) REVERT: Y 80 GLU cc_start: 0.8393 (mp0) cc_final: 0.8134 (mp0) REVERT: Z 7 LYS cc_start: 0.8860 (mtpp) cc_final: 0.8558 (mttp) REVERT: Z 53 ASP cc_start: 0.8447 (m-30) cc_final: 0.8139 (m-30) outliers start: 42 outliers final: 39 residues processed: 389 average time/residue: 0.1752 time to fit residues: 100.9310 Evaluate side-chains 398 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 358 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 94 SER Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain H residue 93 GLN Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain I residue 39 GLN Chi-restraints excluded: chain I residue 94 SER Chi-restraints excluded: chain J residue 39 GLN Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain K residue 39 GLN Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain L residue 5 GLU Chi-restraints excluded: chain L residue 18 ASN Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain O residue 17 SER Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain P residue 54 THR Chi-restraints excluded: chain P residue 90 SER Chi-restraints excluded: chain Q residue 54 THR Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 25 VAL Chi-restraints excluded: chain S residue 94 SER Chi-restraints excluded: chain T residue 39 GLN Chi-restraints excluded: chain T residue 90 SER Chi-restraints excluded: chain U residue 94 SER Chi-restraints excluded: chain W residue 26 GLU Chi-restraints excluded: chain X residue 17 SER Chi-restraints excluded: chain Y residue 17 SER Chi-restraints excluded: chain Z residue 17 SER Chi-restraints excluded: chain Z residue 25 VAL Chi-restraints excluded: chain Z residue 26 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.7539 > 50: distance: 47 - 52: 15.299 distance: 52 - 53: 16.289 distance: 53 - 54: 10.881 distance: 53 - 56: 37.622 distance: 54 - 55: 7.755 distance: 54 - 58: 18.676 distance: 56 - 57: 31.927 distance: 58 - 59: 22.183 distance: 59 - 60: 39.899 distance: 59 - 62: 57.553 distance: 60 - 61: 6.511 distance: 60 - 66: 32.102 distance: 62 - 63: 37.391 distance: 63 - 64: 34.591 distance: 63 - 65: 49.293 distance: 66 - 67: 18.048 distance: 67 - 68: 39.179 distance: 67 - 70: 17.618 distance: 68 - 69: 11.854 distance: 68 - 73: 15.319 distance: 70 - 71: 48.521 distance: 70 - 72: 17.684 distance: 73 - 74: 12.481 distance: 74 - 75: 23.636 distance: 74 - 77: 33.954 distance: 75 - 76: 23.566 distance: 75 - 81: 27.025 distance: 77 - 78: 23.573 distance: 78 - 79: 48.789 distance: 78 - 80: 11.891 distance: 81 - 82: 21.403 distance: 82 - 83: 34.364 distance: 82 - 85: 6.121 distance: 83 - 84: 18.816 distance: 83 - 88: 13.479 distance: 84 - 112: 41.421 distance: 85 - 86: 41.966 distance: 85 - 87: 39.237 distance: 88 - 89: 35.630 distance: 89 - 90: 16.882 distance: 89 - 92: 35.584 distance: 90 - 91: 44.134 distance: 90 - 95: 9.768 distance: 92 - 93: 17.937 distance: 92 - 94: 26.648 distance: 95 - 96: 11.036 distance: 96 - 97: 35.261 distance: 96 - 99: 30.094 distance: 97 - 98: 8.961 distance: 97 - 104: 29.943 distance: 99 - 100: 20.811 distance: 100 - 101: 25.436 distance: 101 - 102: 37.007 distance: 101 - 103: 24.569 distance: 104 - 105: 16.577 distance: 105 - 106: 18.402 distance: 105 - 108: 28.466 distance: 106 - 107: 29.354 distance: 106 - 112: 21.729 distance: 108 - 109: 43.227 distance: 108 - 110: 11.920 distance: 109 - 111: 26.944 distance: 112 - 113: 45.455 distance: 113 - 114: 42.448 distance: 113 - 116: 57.877 distance: 114 - 120: 15.941 distance: 116 - 117: 9.665 distance: 117 - 118: 20.726 distance: 117 - 119: 27.965 distance: 120 - 121: 19.113 distance: 120 - 126: 18.641 distance: 121 - 124: 47.330 distance: 122 - 123: 39.593 distance: 122 - 127: 34.259 distance: 124 - 125: 31.434 distance: 125 - 126: 26.636