Starting phenix.real_space_refine on Sat Aug 23 07:30:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6n1i_8903/08_2025/6n1i_8903.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n1i_8903/08_2025/6n1i_8903.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6n1i_8903/08_2025/6n1i_8903.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n1i_8903/08_2025/6n1i_8903.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6n1i_8903/08_2025/6n1i_8903.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n1i_8903/08_2025/6n1i_8903.map" } resolution = 3.58 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 112 5.16 5 C 7088 2.51 5 N 1920 2.21 5 O 2016 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s 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: 11136 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 696 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N, O, P Time building chain proxies: 0.82, per 1000 atoms: 0.07 Number of scatterers: 11136 At special positions: 0 Unit cell: (84.48, 84.48, 112.2, 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 112 16.00 O 2016 8.00 N 1920 7.00 C 7088 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 289.6 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2624 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 0 sheets defined 86.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 1 through 7 removed outlier: 3.592A pdb=" N LYS A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 7 through 12 Processing helix chain 'A' and resid 16 through 30 removed outlier: 4.153A pdb=" N GLN A 22 " --> pdb=" O THR A 18 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP A 25 " --> pdb=" O LYS A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 43 removed outlier: 3.898A pdb=" N ILE A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS A 43 " --> pdb=" O ASN A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 59 removed outlier: 3.511A pdb=" N ILE A 55 " --> pdb=" O ALA A 51 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET A 57 " --> pdb=" O GLY A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.832A pdb=" N ASN A 67 " --> pdb=" O SER A 63 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU A 68 " --> pdb=" O GLU A 64 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE A 69 " --> pdb=" O SER A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 85 removed outlier: 3.662A pdb=" N PHE A 81 " --> pdb=" O ASN A 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 7 Processing helix chain 'B' and resid 7 through 12 Processing helix chain 'B' and resid 16 through 30 removed outlier: 4.153A pdb=" N GLN B 22 " --> pdb=" O THR B 18 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP B 25 " --> pdb=" O LYS B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 43 removed outlier: 3.897A pdb=" N ILE B 41 " --> pdb=" O GLU B 37 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS B 43 " --> pdb=" O ASN B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 59 removed outlier: 3.510A pdb=" N ILE B 55 " --> pdb=" O ALA B 51 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET B 57 " --> pdb=" O GLY B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 76 removed outlier: 3.833A pdb=" N ASN B 67 " --> pdb=" O SER B 63 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU B 68 " --> pdb=" O GLU B 64 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N PHE B 69 " --> pdb=" O SER B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 85 removed outlier: 3.662A pdb=" N PHE B 81 " --> pdb=" O ASN B 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 7 Processing helix chain 'C' and resid 7 through 12 Processing helix chain 'C' and resid 16 through 30 removed outlier: 4.153A pdb=" N GLN C 22 " --> pdb=" O THR C 18 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP C 25 " --> pdb=" O LYS C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 43 removed outlier: 3.897A pdb=" N ILE C 41 " --> pdb=" O GLU C 37 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS C 43 " --> pdb=" O ASN C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 59 removed outlier: 3.510A pdb=" N ILE C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET C 57 " --> pdb=" O GLY C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 76 removed outlier: 3.833A pdb=" N ASN C 67 " --> pdb=" O SER C 63 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU C 68 " --> pdb=" O GLU C 64 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE C 69 " --> pdb=" O SER C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 85 removed outlier: 3.662A pdb=" N PHE C 81 " --> pdb=" O ASN C 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 7 Processing helix chain 'D' and resid 7 through 12 Processing helix chain 'D' and resid 16 through 30 removed outlier: 4.153A pdb=" N GLN D 22 " --> pdb=" O THR D 18 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP D 25 " --> pdb=" O LYS D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 43 removed outlier: 3.897A pdb=" N ILE D 41 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS D 43 " --> pdb=" O ASN D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 59 removed outlier: 3.510A pdb=" N ILE D 55 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET D 57 " --> pdb=" O GLY D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 76 removed outlier: 3.833A pdb=" N ASN D 67 " --> pdb=" O SER D 63 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU D 68 " --> pdb=" O GLU D 64 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE D 69 " --> pdb=" O SER D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 85 removed outlier: 3.662A pdb=" N PHE D 81 " --> pdb=" O ASN D 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 7 Processing helix chain 'E' and resid 7 through 12 Processing helix chain 'E' and resid 16 through 30 removed outlier: 4.153A pdb=" N GLN E 22 " --> pdb=" O THR E 18 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP E 25 " --> pdb=" O LYS E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 43 removed outlier: 3.898A pdb=" N ILE E 41 " --> pdb=" O GLU E 37 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS E 43 " --> pdb=" O ASN E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 59 removed outlier: 3.510A pdb=" N ILE E 55 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET E 57 " --> pdb=" O GLY E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.833A pdb=" N ASN E 67 " --> pdb=" O SER E 63 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU E 68 " --> pdb=" O GLU E 64 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N PHE E 69 " --> pdb=" O SER E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 85 removed outlier: 3.661A pdb=" N PHE E 81 " --> pdb=" O ASN E 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 7 Processing helix chain 'F' and resid 7 through 12 Processing helix chain 'F' and resid 16 through 30 removed outlier: 4.154A pdb=" N GLN F 22 " --> pdb=" O THR F 18 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP F 25 " --> pdb=" O LYS F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 43 removed outlier: 3.897A pdb=" N ILE F 41 " --> pdb=" O GLU F 37 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS F 43 " --> pdb=" O ASN F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 59 removed outlier: 3.510A pdb=" N ILE F 55 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET F 57 " --> pdb=" O GLY F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 76 removed outlier: 3.833A pdb=" N ASN F 67 " --> pdb=" O SER F 63 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU F 68 " --> pdb=" O GLU F 64 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE F 69 " --> pdb=" O SER F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 85 removed outlier: 3.662A pdb=" N PHE F 81 " --> pdb=" O ASN F 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 7 Processing helix chain 'G' and resid 7 through 12 Processing helix chain 'G' and resid 16 through 30 removed outlier: 4.154A pdb=" N GLN G 22 " --> pdb=" O THR G 18 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP G 25 " --> pdb=" O LYS G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 43 removed outlier: 3.897A pdb=" N ILE G 41 " --> pdb=" O GLU G 37 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS G 43 " --> pdb=" O ASN G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 59 removed outlier: 3.510A pdb=" N ILE G 55 " --> pdb=" O ALA G 51 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET G 57 " --> pdb=" O GLY G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 76 removed outlier: 3.832A pdb=" N ASN G 67 " --> pdb=" O SER G 63 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU G 68 " --> pdb=" O GLU G 64 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N PHE G 69 " --> pdb=" O SER G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 85 removed outlier: 3.662A pdb=" N PHE G 81 " --> pdb=" O ASN G 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 7 Processing helix chain 'H' and resid 7 through 12 Processing helix chain 'H' and resid 16 through 30 removed outlier: 4.153A pdb=" N GLN H 22 " --> pdb=" O THR H 18 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP H 25 " --> pdb=" O LYS H 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 43 removed outlier: 3.897A pdb=" N ILE H 41 " --> pdb=" O GLU H 37 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS H 43 " --> pdb=" O ASN H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 59 removed outlier: 3.510A pdb=" N ILE H 55 " --> pdb=" O ALA H 51 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET H 57 " --> pdb=" O GLY H 53 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 76 removed outlier: 3.833A pdb=" N ASN H 67 " --> pdb=" O SER H 63 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU H 68 " --> pdb=" O GLU H 64 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE H 69 " --> pdb=" O SER H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 85 removed outlier: 3.663A pdb=" N PHE H 81 " --> pdb=" O ASN H 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 7 Processing helix chain 'I' and resid 7 through 12 Processing helix chain 'I' and resid 16 through 30 removed outlier: 4.153A pdb=" N GLN I 22 " --> pdb=" O THR I 18 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP I 25 " --> pdb=" O LYS I 21 " (cutoff:3.500A) Processing helix chain 'I' and resid 35 through 43 removed outlier: 3.897A pdb=" N ILE I 41 " --> pdb=" O GLU I 37 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS I 43 " --> pdb=" O ASN I 39 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 59 removed outlier: 3.511A pdb=" N ILE I 55 " --> pdb=" O ALA I 51 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET I 57 " --> pdb=" O GLY I 53 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 76 removed outlier: 3.833A pdb=" N ASN I 67 " --> pdb=" O SER I 63 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU I 68 " --> pdb=" O GLU I 64 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE I 69 " --> pdb=" O SER I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 77 through 85 removed outlier: 3.662A pdb=" N PHE I 81 " --> pdb=" O ASN I 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 7 Processing helix chain 'J' and resid 7 through 12 Processing helix chain 'J' and resid 16 through 30 removed outlier: 4.153A pdb=" N GLN J 22 " --> pdb=" O THR J 18 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP J 25 " --> pdb=" O LYS J 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 35 through 43 removed outlier: 3.897A pdb=" N ILE J 41 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS J 43 " --> pdb=" O ASN J 39 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 59 removed outlier: 3.510A pdb=" N ILE J 55 " --> pdb=" O ALA J 51 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET J 57 " --> pdb=" O GLY J 53 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 76 removed outlier: 3.833A pdb=" N ASN J 67 " --> pdb=" O SER J 63 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU J 68 " --> pdb=" O GLU J 64 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE J 69 " --> pdb=" O SER J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 85 removed outlier: 3.662A pdb=" N PHE J 81 " --> pdb=" O ASN J 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 7 Processing helix chain 'K' and resid 7 through 12 Processing helix chain 'K' and resid 16 through 30 removed outlier: 4.153A pdb=" N GLN K 22 " --> pdb=" O THR K 18 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP K 25 " --> pdb=" O LYS K 21 " (cutoff:3.500A) Processing helix chain 'K' and resid 35 through 43 removed outlier: 3.897A pdb=" N ILE K 41 " --> pdb=" O GLU K 37 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS K 43 " --> pdb=" O ASN K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 59 removed outlier: 3.510A pdb=" N ILE K 55 " --> pdb=" O ALA K 51 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET K 57 " --> pdb=" O GLY K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 76 removed outlier: 3.834A pdb=" N ASN K 67 " --> pdb=" O SER K 63 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU K 68 " --> pdb=" O GLU K 64 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE K 69 " --> pdb=" O SER K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 85 removed outlier: 3.662A pdb=" N PHE K 81 " --> pdb=" O ASN K 77 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 7 Processing helix chain 'L' and resid 7 through 12 Processing helix chain 'L' and resid 16 through 30 removed outlier: 4.154A pdb=" N GLN L 22 " --> pdb=" O THR L 18 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP L 25 " --> pdb=" O LYS L 21 " (cutoff:3.500A) Processing helix chain 'L' and resid 35 through 43 removed outlier: 3.898A pdb=" N ILE L 41 " --> pdb=" O GLU L 37 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS L 43 " --> pdb=" O ASN L 39 " (cutoff:3.500A) Processing helix chain 'L' and resid 46 through 59 removed outlier: 3.510A pdb=" N ILE L 55 " --> pdb=" O ALA L 51 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET L 57 " --> pdb=" O GLY L 53 " (cutoff:3.500A) Processing helix chain 'L' and resid 63 through 76 removed outlier: 3.833A pdb=" N ASN L 67 " --> pdb=" O SER L 63 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU L 68 " --> pdb=" O GLU L 64 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N PHE L 69 " --> pdb=" O SER L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 85 removed outlier: 3.661A pdb=" N PHE L 81 " --> pdb=" O ASN L 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 7 Processing helix chain 'M' and resid 7 through 12 Processing helix chain 'M' and resid 16 through 30 removed outlier: 4.152A pdb=" N GLN M 22 " --> pdb=" O THR M 18 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP M 25 " --> pdb=" O LYS M 21 " (cutoff:3.500A) Processing helix chain 'M' and resid 35 through 43 removed outlier: 3.898A pdb=" N ILE M 41 " --> pdb=" O GLU M 37 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS M 43 " --> pdb=" O ASN M 39 " (cutoff:3.500A) Processing helix chain 'M' and resid 46 through 59 removed outlier: 3.510A pdb=" N ILE M 55 " --> pdb=" O ALA M 51 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET M 57 " --> pdb=" O GLY M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 76 removed outlier: 3.834A pdb=" N ASN M 67 " --> pdb=" O SER M 63 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU M 68 " --> pdb=" O GLU M 64 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N PHE M 69 " --> pdb=" O SER M 65 " (cutoff:3.500A) Processing helix chain 'M' and resid 77 through 85 removed outlier: 3.661A pdb=" N PHE M 81 " --> pdb=" O ASN M 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 7 Processing helix chain 'N' and resid 7 through 12 Processing helix chain 'N' and resid 16 through 30 removed outlier: 4.153A pdb=" N GLN N 22 " --> pdb=" O THR N 18 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP N 25 " --> pdb=" O LYS N 21 " (cutoff:3.500A) Processing helix chain 'N' and resid 35 through 43 removed outlier: 3.897A pdb=" N ILE N 41 " --> pdb=" O GLU N 37 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS N 43 " --> pdb=" O ASN N 39 " (cutoff:3.500A) Processing helix chain 'N' and resid 46 through 59 removed outlier: 3.510A pdb=" N ILE N 55 " --> pdb=" O ALA N 51 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET N 57 " --> pdb=" O GLY N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 63 through 76 removed outlier: 3.833A pdb=" N ASN N 67 " --> pdb=" O SER N 63 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU N 68 " --> pdb=" O GLU N 64 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE N 69 " --> pdb=" O SER N 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 77 through 85 removed outlier: 3.662A pdb=" N PHE N 81 " --> pdb=" O ASN N 77 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 7 Processing helix chain 'O' and resid 7 through 12 Processing helix chain 'O' and resid 16 through 30 removed outlier: 4.154A pdb=" N GLN O 22 " --> pdb=" O THR O 18 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP O 25 " --> pdb=" O LYS O 21 " (cutoff:3.500A) Processing helix chain 'O' and resid 35 through 43 removed outlier: 3.896A pdb=" N ILE O 41 " --> pdb=" O GLU O 37 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS O 43 " --> pdb=" O ASN O 39 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 59 removed outlier: 3.510A pdb=" N ILE O 55 " --> pdb=" O ALA O 51 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET O 57 " --> pdb=" O GLY O 53 " (cutoff:3.500A) Processing helix chain 'O' and resid 63 through 76 removed outlier: 3.832A pdb=" N ASN O 67 " --> pdb=" O SER O 63 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU O 68 " --> pdb=" O GLU O 64 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE O 69 " --> pdb=" O SER O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 77 through 85 removed outlier: 3.663A pdb=" N PHE O 81 " --> pdb=" O ASN O 77 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 7 Processing helix chain 'P' and resid 7 through 12 Processing helix chain 'P' and resid 16 through 30 removed outlier: 4.153A pdb=" N GLN P 22 " --> pdb=" O THR P 18 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP P 25 " --> pdb=" O LYS P 21 " (cutoff:3.500A) Processing helix chain 'P' and resid 35 through 43 removed outlier: 3.896A pdb=" N ILE P 41 " --> pdb=" O GLU P 37 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS P 43 " --> pdb=" O ASN P 39 " (cutoff:3.500A) Processing helix chain 'P' and resid 46 through 59 removed outlier: 3.511A pdb=" N ILE P 55 " --> pdb=" O ALA P 51 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET P 57 " --> pdb=" O GLY P 53 " (cutoff:3.500A) Processing helix chain 'P' and resid 63 through 76 removed outlier: 3.833A pdb=" N ASN P 67 " --> pdb=" O SER P 63 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU P 68 " --> pdb=" O GLU P 64 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE P 69 " --> pdb=" O SER P 65 " (cutoff:3.500A) Processing helix chain 'P' and resid 77 through 85 removed outlier: 3.663A pdb=" N PHE P 81 " --> pdb=" O ASN P 77 " (cutoff:3.500A) 560 hydrogen bonds defined for protein. 1680 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: 1.63 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3544 1.34 - 1.45: 1292 1.45 - 1.57: 6284 1.57 - 1.69: 0 1.69 - 1.81: 176 Bond restraints: 11296 Sorted by residual: bond pdb=" C TYR P 78 " pdb=" N PRO P 79 " ideal model delta sigma weight residual 1.335 1.358 -0.024 1.19e-02 7.06e+03 4.01e+00 bond pdb=" C TYR G 78 " pdb=" N PRO G 79 " ideal model delta sigma weight residual 1.335 1.358 -0.023 1.19e-02 7.06e+03 3.85e+00 bond pdb=" C TYR H 78 " pdb=" N PRO H 79 " ideal model delta sigma weight residual 1.335 1.358 -0.023 1.19e-02 7.06e+03 3.85e+00 bond pdb=" C TYR A 78 " pdb=" N PRO A 79 " ideal model delta sigma weight residual 1.335 1.358 -0.023 1.19e-02 7.06e+03 3.79e+00 bond pdb=" C TYR F 78 " pdb=" N PRO F 79 " ideal model delta sigma weight residual 1.335 1.358 -0.023 1.19e-02 7.06e+03 3.76e+00 ... (remaining 11291 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 13335 1.58 - 3.16: 1526 3.16 - 4.74: 194 4.74 - 6.32: 97 6.32 - 7.90: 16 Bond angle restraints: 15168 Sorted by residual: angle pdb=" C TRP P 30 " pdb=" N ASN P 31 " pdb=" CA ASN P 31 " ideal model delta sigma weight residual 122.40 127.15 -4.75 1.45e+00 4.76e-01 1.07e+01 angle pdb=" C TRP H 30 " pdb=" N ASN H 31 " pdb=" CA ASN H 31 " ideal model delta sigma weight residual 122.40 127.13 -4.73 1.45e+00 4.76e-01 1.06e+01 angle pdb=" C TRP I 30 " pdb=" N ASN I 31 " pdb=" CA ASN I 31 " ideal model delta sigma weight residual 122.40 127.11 -4.71 1.45e+00 4.76e-01 1.05e+01 angle pdb=" C TRP J 30 " pdb=" N ASN J 31 " pdb=" CA ASN J 31 " ideal model delta sigma weight residual 122.40 127.09 -4.69 1.45e+00 4.76e-01 1.05e+01 angle pdb=" C TRP A 30 " pdb=" N ASN A 31 " pdb=" CA ASN A 31 " ideal model delta sigma weight residual 122.40 127.08 -4.68 1.45e+00 4.76e-01 1.04e+01 ... (remaining 15163 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.94: 5900 9.94 - 19.87: 834 19.87 - 29.81: 133 29.81 - 39.75: 61 39.75 - 49.68: 16 Dihedral angle restraints: 6944 sinusoidal: 2960 harmonic: 3984 Sorted by residual: dihedral pdb=" CA LEU J 68 " pdb=" C LEU J 68 " pdb=" N PHE J 69 " pdb=" CA PHE J 69 " ideal model delta harmonic sigma weight residual 180.00 162.95 17.05 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA LEU B 68 " pdb=" C LEU B 68 " pdb=" N PHE B 69 " pdb=" CA PHE B 69 " ideal model delta harmonic sigma weight residual 180.00 162.99 17.01 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA LEU A 68 " pdb=" C LEU A 68 " pdb=" N PHE A 69 " pdb=" CA PHE A 69 " ideal model delta harmonic sigma weight residual 180.00 163.03 16.97 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 6941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1103 0.048 - 0.097: 497 0.097 - 0.145: 64 0.145 - 0.193: 32 0.193 - 0.242: 16 Chirality restraints: 1712 Sorted by residual: chirality pdb=" CB ILE M 20 " pdb=" CA ILE M 20 " pdb=" CG1 ILE M 20 " pdb=" CG2 ILE M 20 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CB ILE A 20 " pdb=" CA ILE A 20 " pdb=" CG1 ILE A 20 " pdb=" CG2 ILE A 20 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CB ILE E 20 " pdb=" CA ILE E 20 " pdb=" CG1 ILE E 20 " pdb=" CG2 ILE E 20 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 1709 not shown) Planarity restraints: 1920 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 78 " -0.032 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PRO B 79 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 79 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 79 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR O 78 " 0.032 5.00e-02 4.00e+02 4.76e-02 3.63e+00 pdb=" N PRO O 79 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO O 79 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO O 79 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR H 78 " -0.032 5.00e-02 4.00e+02 4.76e-02 3.63e+00 pdb=" N PRO H 79 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO H 79 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO H 79 " -0.027 5.00e-02 4.00e+02 ... (remaining 1917 not shown) Histogram of nonbonded interaction distances: 1.15 - 1.90: 154 1.90 - 2.65: 326 2.65 - 3.40: 15715 3.40 - 4.15: 26803 4.15 - 4.90: 49850 Nonbonded interactions: 92848 Sorted by model distance: nonbonded pdb=" CD GLN N 48 " pdb=" CG GLU O 36 " model vdw 1.147 3.670 nonbonded pdb=" CD GLN F 48 " pdb=" CG GLU G 36 " model vdw 1.147 3.670 nonbonded pdb=" CD GLN I 48 " pdb=" CG GLU J 36 " model vdw 1.156 3.670 nonbonded pdb=" CD GLN A 48 " pdb=" CG GLU B 36 " model vdw 1.157 3.670 nonbonded pdb=" CD GLN E 48 " pdb=" CG GLU F 36 " model vdw 1.165 3.670 ... (remaining 92843 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: 0.04 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 8.170 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5785 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 : 0.009 0.212 11297 Z= 0.398 Angle : 1.125 7.903 15168 Z= 0.657 Chirality : 0.057 0.242 1712 Planarity : 0.006 0.048 1920 Dihedral : 9.867 49.682 4320 Min Nonbonded Distance : 1.147 Molprobity Statistics. All-atom Clashscore : 27.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % 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: -6.04 (0.15), residues: 1328 helix: -4.41 (0.08), residues: 1008 sheet: None (None), residues: 0 loop : -1.36 (0.30), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 9 TYR 0.003 0.001 TYR O 78 PHE 0.018 0.003 PHE I 81 TRP 0.019 0.003 TRP M 30 HIS 0.003 0.001 HIS O 56 Details of bonding type rmsd covalent geometry : bond 0.00858 (11296) covalent geometry : angle 1.12524 (15168) hydrogen bonds : bond 0.32877 ( 560) hydrogen bonds : angle 10.90099 ( 1680) Misc. bond : bond 0.21182 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 487 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 MET cc_start: 0.6847 (mtt) cc_final: 0.6616 (mtt) REVERT: A 76 TRP cc_start: 0.5894 (m100) cc_final: 0.5427 (m100) REVERT: C 26 ASP cc_start: 0.5964 (m-30) cc_final: 0.5429 (m-30) REVERT: D 31 ASN cc_start: 0.7305 (m110) cc_final: 0.7102 (m110) REVERT: F 59 LEU cc_start: 0.8843 (mt) cc_final: 0.8286 (mt) REVERT: I 41 ILE cc_start: 0.7969 (mt) cc_final: 0.7743 (mt) REVERT: K 23 ILE cc_start: 0.6799 (mt) cc_final: 0.6423 (mt) REVERT: K 24 THR cc_start: 0.5636 (p) cc_final: 0.5419 (p) REVERT: M 39 ASN cc_start: 0.8245 (m-40) cc_final: 0.7882 (m-40) REVERT: M 49 ASP cc_start: 0.7176 (m-30) cc_final: 0.6920 (m-30) REVERT: O 15 MET cc_start: 0.4758 (ttt) cc_final: 0.4551 (ttt) REVERT: O 26 ASP cc_start: 0.6343 (m-30) cc_final: 0.6052 (m-30) outliers start: 0 outliers final: 0 residues processed: 487 average time/residue: 0.1116 time to fit residues: 76.9226 Evaluate side-chains 376 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 376 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 124 optimal weight: 0.0170 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN A 67 ASN A 77 ASN ** B 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 ASN ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 ASN ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN ** F 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 77 ASN J 13 GLN ** J 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 77 ASN ** K 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 77 ASN ** N 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN O 22 GLN O 77 ASN O 85 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.146409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.136783 restraints weight = 15943.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.140261 restraints weight = 7501.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.142411 restraints weight = 4041.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.143752 restraints weight = 2365.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.144611 restraints weight = 1463.985| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6447 moved from start: 0.4737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 11297 Z= 0.162 Angle : 0.710 7.492 15168 Z= 0.379 Chirality : 0.042 0.163 1712 Planarity : 0.005 0.042 1920 Dihedral : 5.588 19.537 1424 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.69 % Allowed : 11.16 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.07 (0.18), residues: 1328 helix: -2.58 (0.12), residues: 1168 sheet: None (None), residues: 0 loop : -1.15 (0.36), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 52 TYR 0.012 0.002 TYR B 78 PHE 0.028 0.002 PHE B 81 TRP 0.017 0.002 TRP L 76 HIS 0.002 0.001 HIS E 56 Details of bonding type rmsd covalent geometry : bond 0.00382 (11296) covalent geometry : angle 0.70994 (15168) hydrogen bonds : bond 0.04043 ( 560) hydrogen bonds : angle 4.69471 ( 1680) Misc. bond : bond 0.00114 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 447 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.6142 (tpp) cc_final: 0.5742 (mmm) REVERT: D 1 MET cc_start: 0.7261 (tpp) cc_final: 0.7015 (tpt) REVERT: E 3 PHE cc_start: 0.7328 (t80) cc_final: 0.7038 (t80) REVERT: E 47 GLU cc_start: 0.7251 (pt0) cc_final: 0.6454 (pt0) REVERT: F 17 MET cc_start: 0.7412 (tpt) cc_final: 0.7176 (tpt) REVERT: F 26 ASP cc_start: 0.7127 (m-30) cc_final: 0.6894 (m-30) REVERT: G 38 VAL cc_start: 0.7678 (t) cc_final: 0.7447 (t) REVERT: H 1 MET cc_start: 0.7651 (tpp) cc_final: 0.7359 (tpp) REVERT: J 1 MET cc_start: 0.5995 (tpt) cc_final: 0.5708 (tpt) REVERT: J 37 GLU cc_start: 0.7430 (mt-10) cc_final: 0.6976 (mt-10) REVERT: K 22 GLN cc_start: 0.7265 (tp40) cc_final: 0.6792 (mm110) REVERT: L 20 ILE cc_start: 0.7277 (tt) cc_final: 0.6931 (tt) REVERT: O 85 ASN cc_start: 0.6826 (m-40) cc_final: 0.6599 (m110) REVERT: P 57 MET cc_start: 0.6605 (mmt) cc_final: 0.5909 (mtt) outliers start: 34 outliers final: 16 residues processed: 457 average time/residue: 0.1077 time to fit residues: 70.0470 Evaluate side-chains 411 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 395 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain I residue 39 ASN Chi-restraints excluded: chain I residue 40 ILE Chi-restraints excluded: chain J residue 34 ASN Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain N residue 55 ILE Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 54 ILE Chi-restraints excluded: chain O residue 55 ILE Chi-restraints excluded: chain P residue 15 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 68 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN B 13 GLN B 31 ASN ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 GLN ** F 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 56 HIS I 31 ASN J 39 ASN J 48 GLN ** K 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 ASN L 67 ASN M 22 GLN ** M 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 39 ASN ** O 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.139866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.130894 restraints weight = 16067.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.134131 restraints weight = 7636.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.136107 restraints weight = 4122.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.137345 restraints weight = 2421.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.138177 restraints weight = 1504.688| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.9874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 11297 Z= 0.206 Angle : 0.768 9.739 15168 Z= 0.401 Chirality : 0.045 0.184 1712 Planarity : 0.005 0.042 1920 Dihedral : 5.304 24.649 1424 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.48 % Allowed : 16.22 % Favored : 80.30 % 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: -2.30 (0.22), residues: 1328 helix: -1.41 (0.14), residues: 1152 sheet: None (None), residues: 0 loop : -0.63 (0.48), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 52 TYR 0.008 0.001 TYR A 78 PHE 0.024 0.002 PHE B 81 TRP 0.049 0.002 TRP L 76 HIS 0.005 0.001 HIS B 56 Details of bonding type rmsd covalent geometry : bond 0.00489 (11296) covalent geometry : angle 0.76768 (15168) hydrogen bonds : bond 0.04148 ( 560) hydrogen bonds : angle 4.35607 ( 1680) Misc. bond : bond 0.00024 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 552 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ASP cc_start: 0.8068 (p0) cc_final: 0.7729 (m-30) REVERT: A 26 ASP cc_start: 0.7660 (m-30) cc_final: 0.7042 (m-30) REVERT: B 1 MET cc_start: 0.7151 (tpp) cc_final: 0.6636 (tpp) REVERT: B 20 ILE cc_start: 0.9199 (mm) cc_final: 0.8969 (mm) REVERT: B 46 VAL cc_start: 0.9150 (t) cc_final: 0.8944 (t) REVERT: B 47 GLU cc_start: 0.8173 (pt0) cc_final: 0.7966 (pt0) REVERT: C 19 VAL cc_start: 0.8520 (p) cc_final: 0.8061 (p) REVERT: C 22 GLN cc_start: 0.8282 (mt0) cc_final: 0.7986 (mt0) REVERT: C 30 TRP cc_start: 0.8427 (m-10) cc_final: 0.8216 (m-10) REVERT: E 24 THR cc_start: 0.9338 (p) cc_final: 0.9103 (p) REVERT: E 27 LEU cc_start: 0.9193 (mm) cc_final: 0.8925 (mt) REVERT: E 41 ILE cc_start: 0.8815 (mt) cc_final: 0.7792 (mt) REVERT: E 45 LYS cc_start: 0.7761 (mtmt) cc_final: 0.7471 (mttp) REVERT: E 58 ILE cc_start: 0.8713 (OUTLIER) cc_final: 0.8464 (tp) REVERT: E 84 LEU cc_start: 0.8428 (tp) cc_final: 0.8103 (tp) REVERT: F 59 LEU cc_start: 0.9309 (mt) cc_final: 0.9025 (mt) REVERT: H 1 MET cc_start: 0.8519 (tpp) cc_final: 0.8147 (tpp) REVERT: H 38 VAL cc_start: 0.8978 (t) cc_final: 0.8697 (m) REVERT: H 60 LYS cc_start: 0.8464 (mmtp) cc_final: 0.8072 (mmtm) REVERT: H 85 ASN cc_start: 0.8086 (OUTLIER) cc_final: 0.7882 (m-40) REVERT: I 25 ASP cc_start: 0.7364 (t0) cc_final: 0.7063 (t0) REVERT: I 76 TRP cc_start: 0.7718 (m100) cc_final: 0.7433 (m100) REVERT: J 63 SER cc_start: 0.8728 (p) cc_final: 0.8219 (t) REVERT: J 78 TYR cc_start: 0.8636 (t80) cc_final: 0.8375 (t80) REVERT: J 80 LEU cc_start: 0.8975 (tp) cc_final: 0.8671 (tt) REVERT: K 9 ARG cc_start: 0.8510 (ttp80) cc_final: 0.8098 (mtt-85) REVERT: K 27 LEU cc_start: 0.9153 (mm) cc_final: 0.8826 (mt) REVERT: L 12 ILE cc_start: 0.8769 (mt) cc_final: 0.8428 (mt) REVERT: L 19 VAL cc_start: 0.8263 (p) cc_final: 0.7809 (p) REVERT: L 20 ILE cc_start: 0.8420 (OUTLIER) cc_final: 0.8161 (tt) REVERT: L 36 GLU cc_start: 0.7688 (mm-30) cc_final: 0.6868 (mt-10) REVERT: L 39 ASN cc_start: 0.7894 (m110) cc_final: 0.7522 (m-40) REVERT: N 26 ASP cc_start: 0.8361 (t0) cc_final: 0.8143 (t0) REVERT: N 37 GLU cc_start: 0.8288 (mt-10) cc_final: 0.8086 (mt-10) REVERT: O 8 SER cc_start: 0.9183 (m) cc_final: 0.8919 (m) REVERT: O 23 ILE cc_start: 0.9428 (mt) cc_final: 0.9001 (mp) REVERT: O 60 LYS cc_start: 0.8488 (mtpp) cc_final: 0.7756 (mtmt) REVERT: P 11 LEU cc_start: 0.9060 (mt) cc_final: 0.8540 (mt) REVERT: P 18 THR cc_start: 0.7682 (p) cc_final: 0.7136 (p) REVERT: P 40 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8880 (tt) REVERT: P 71 LYS cc_start: 0.8196 (mttt) cc_final: 0.7874 (mmtt) REVERT: P 73 LEU cc_start: 0.8952 (tp) cc_final: 0.8730 (tp) outliers start: 44 outliers final: 17 residues processed: 569 average time/residue: 0.1058 time to fit residues: 85.7919 Evaluate side-chains 506 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 485 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain H residue 85 ASN Chi-restraints excluded: chain I residue 40 ILE Chi-restraints excluded: chain I residue 43 CYS Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 76 TRP Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 54 ILE Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain P residue 40 ILE Chi-restraints excluded: chain P residue 65 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 81 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 122 optimal weight: 2.9990 chunk 116 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN A 67 ASN B 82 GLN C 7 ASN C 39 ASN ** E 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN F 77 ASN ** H 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 22 GLN ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 13 GLN ** K 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 13 GLN M 13 GLN ** O 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.134816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.125896 restraints weight = 16438.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.128978 restraints weight = 8129.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.130904 restraints weight = 4563.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.132171 restraints weight = 2775.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.132963 restraints weight = 1773.762| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 1.0619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11297 Z= 0.121 Angle : 0.575 7.907 15168 Z= 0.304 Chirality : 0.041 0.167 1712 Planarity : 0.003 0.039 1920 Dihedral : 4.795 23.270 1424 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.48 % Allowed : 19.62 % Favored : 76.90 % 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 (0.23), residues: 1328 helix: -0.68 (0.16), residues: 1136 sheet: None (None), residues: 0 loop : -1.13 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 9 TYR 0.009 0.001 TYR L 78 PHE 0.024 0.002 PHE A 81 TRP 0.015 0.001 TRP L 76 HIS 0.003 0.001 HIS D 56 Details of bonding type rmsd covalent geometry : bond 0.00289 (11296) covalent geometry : angle 0.57479 (15168) hydrogen bonds : bond 0.02750 ( 560) hydrogen bonds : angle 3.75068 ( 1680) Misc. bond : bond 0.00007 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 506 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7953 (tpp) cc_final: 0.7601 (tpp) REVERT: A 15 MET cc_start: 0.8415 (mtp) cc_final: 0.8164 (mtt) REVERT: A 64 GLU cc_start: 0.6071 (mm-30) cc_final: 0.5702 (mm-30) REVERT: B 1 MET cc_start: 0.7182 (tpp) cc_final: 0.6879 (tpp) REVERT: B 46 VAL cc_start: 0.9144 (t) cc_final: 0.8909 (t) REVERT: B 52 ARG cc_start: 0.8685 (ttm-80) cc_final: 0.8383 (ttm110) REVERT: C 21 LYS cc_start: 0.8585 (mmmm) cc_final: 0.8325 (mtmt) REVERT: C 30 TRP cc_start: 0.8685 (m-10) cc_final: 0.7823 (m-10) REVERT: C 71 LYS cc_start: 0.8760 (ttpt) cc_final: 0.8339 (pttt) REVERT: D 78 TYR cc_start: 0.7915 (t80) cc_final: 0.7420 (t80) REVERT: E 24 THR cc_start: 0.9273 (p) cc_final: 0.9005 (p) REVERT: E 27 LEU cc_start: 0.9272 (mm) cc_final: 0.9016 (mt) REVERT: E 64 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7881 (tm-30) REVERT: E 78 TYR cc_start: 0.7835 (t80) cc_final: 0.7451 (t80) REVERT: E 84 LEU cc_start: 0.8389 (tp) cc_final: 0.8186 (mt) REVERT: F 22 GLN cc_start: 0.8799 (mt0) cc_final: 0.8569 (mt0) REVERT: F 59 LEU cc_start: 0.9262 (mt) cc_final: 0.8882 (mt) REVERT: F 60 LYS cc_start: 0.8925 (mtpt) cc_final: 0.8517 (mtpt) REVERT: H 1 MET cc_start: 0.8494 (tpp) cc_final: 0.8258 (tpp) REVERT: H 60 LYS cc_start: 0.8532 (mmtp) cc_final: 0.8170 (mmtm) REVERT: H 81 PHE cc_start: 0.9350 (t80) cc_final: 0.9108 (t80) REVERT: I 75 GLU cc_start: 0.7762 (tt0) cc_final: 0.7450 (tt0) REVERT: J 78 TYR cc_start: 0.8834 (t80) cc_final: 0.8498 (t80) REVERT: K 9 ARG cc_start: 0.8521 (ttp80) cc_final: 0.7970 (mtt-85) REVERT: K 44 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7245 (mt-10) REVERT: K 78 TYR cc_start: 0.8220 (t80) cc_final: 0.7519 (t80) REVERT: L 7 ASN cc_start: 0.8339 (m110) cc_final: 0.8128 (m-40) REVERT: L 84 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7816 (mp) REVERT: M 2 ASN cc_start: 0.7917 (t0) cc_final: 0.7660 (t0) REVERT: M 9 ARG cc_start: 0.8116 (ttp80) cc_final: 0.7616 (ttt-90) REVERT: N 37 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7977 (mt-10) REVERT: O 3 PHE cc_start: 0.8038 (t80) cc_final: 0.7795 (t80) REVERT: O 44 GLU cc_start: 0.7152 (mt-10) cc_final: 0.6555 (mt-10) REVERT: O 49 ASP cc_start: 0.7155 (t0) cc_final: 0.6827 (t0) REVERT: P 18 THR cc_start: 0.8182 (p) cc_final: 0.7761 (p) REVERT: P 37 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7461 (mt-10) REVERT: P 57 MET cc_start: 0.7856 (mtt) cc_final: 0.7549 (mtt) REVERT: P 80 LEU cc_start: 0.8903 (tp) cc_final: 0.8644 (tt) outliers start: 44 outliers final: 24 residues processed: 523 average time/residue: 0.1073 time to fit residues: 79.2315 Evaluate side-chains 492 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 467 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain F residue 58 ILE Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 20 ILE Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain N residue 54 ILE Chi-restraints excluded: chain N residue 64 GLU Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 54 ILE Chi-restraints excluded: chain P residue 15 MET Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 40 ILE Chi-restraints excluded: chain P residue 65 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 110 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 96 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 ASN ** B 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 ASN E 77 ASN F 39 ASN ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 22 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.129348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.120531 restraints weight = 16311.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.123592 restraints weight = 8085.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.125545 restraints weight = 4511.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.126765 restraints weight = 2721.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.127566 restraints weight = 1733.598| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 1.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11297 Z= 0.153 Angle : 0.610 8.988 15168 Z= 0.321 Chirality : 0.043 0.174 1712 Planarity : 0.004 0.043 1920 Dihedral : 4.721 21.559 1424 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 4.11 % Allowed : 18.75 % Favored : 77.14 % 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: -0.67 (0.23), residues: 1328 helix: -0.04 (0.17), residues: 1040 sheet: None (None), residues: 0 loop : -1.50 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 9 TYR 0.008 0.001 TYR L 78 PHE 0.026 0.002 PHE M 69 TRP 0.026 0.001 TRP H 76 HIS 0.004 0.001 HIS M 56 Details of bonding type rmsd covalent geometry : bond 0.00374 (11296) covalent geometry : angle 0.61034 (15168) hydrogen bonds : bond 0.03112 ( 560) hydrogen bonds : angle 3.88862 ( 1680) Misc. bond : bond 0.00055 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 509 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.7141 (tpp) cc_final: 0.6670 (tpp) REVERT: B 21 LYS cc_start: 0.8733 (mtmt) cc_final: 0.8420 (mttm) REVERT: B 46 VAL cc_start: 0.9177 (t) cc_final: 0.8952 (t) REVERT: C 21 LYS cc_start: 0.8670 (mmmm) cc_final: 0.8457 (mtmt) REVERT: C 30 TRP cc_start: 0.8908 (m-10) cc_final: 0.8189 (m-10) REVERT: D 11 LEU cc_start: 0.9485 (mt) cc_final: 0.9202 (mt) REVERT: E 17 MET cc_start: 0.9404 (tpt) cc_final: 0.8912 (tpp) REVERT: E 27 LEU cc_start: 0.9326 (mm) cc_final: 0.8942 (mt) REVERT: E 64 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7998 (tm-30) REVERT: F 14 ARG cc_start: 0.7939 (mtm-85) cc_final: 0.5402 (mmt180) REVERT: F 59 LEU cc_start: 0.9318 (mt) cc_final: 0.9014 (mt) REVERT: G 2 ASN cc_start: 0.8142 (m-40) cc_final: 0.7739 (m110) REVERT: G 6 ASP cc_start: 0.7716 (m-30) cc_final: 0.7515 (m-30) REVERT: G 38 VAL cc_start: 0.9069 (t) cc_final: 0.8805 (m) REVERT: H 1 MET cc_start: 0.8147 (tpp) cc_final: 0.6651 (tpp) REVERT: H 60 LYS cc_start: 0.8767 (mmtp) cc_final: 0.8432 (mmtm) REVERT: H 73 LEU cc_start: 0.9078 (tp) cc_final: 0.8680 (tt) REVERT: J 75 GLU cc_start: 0.7997 (tt0) cc_final: 0.7684 (tt0) REVERT: J 76 TRP cc_start: 0.7712 (m100) cc_final: 0.6665 (m-10) REVERT: K 9 ARG cc_start: 0.8436 (ttp80) cc_final: 0.8127 (mtt-85) REVERT: K 34 ASN cc_start: 0.8361 (p0) cc_final: 0.8144 (p0) REVERT: K 35 ARG cc_start: 0.7489 (mtm110) cc_final: 0.7273 (mtm-85) REVERT: L 26 ASP cc_start: 0.8131 (m-30) cc_final: 0.7440 (m-30) REVERT: L 36 GLU cc_start: 0.7673 (tp30) cc_final: 0.7273 (mt-10) REVERT: L 39 ASN cc_start: 0.8078 (m-40) cc_final: 0.7713 (m-40) REVERT: L 84 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8120 (mp) REVERT: M 9 ARG cc_start: 0.8384 (ttp80) cc_final: 0.7842 (ttp80) REVERT: M 30 TRP cc_start: 0.9271 (m-10) cc_final: 0.9070 (m-10) REVERT: M 52 ARG cc_start: 0.8213 (mtm-85) cc_final: 0.7964 (ttm-80) REVERT: M 78 TYR cc_start: 0.8047 (t80) cc_final: 0.7810 (t80) REVERT: O 80 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8090 (tp) REVERT: P 21 LYS cc_start: 0.8710 (mtpt) cc_final: 0.8236 (mtmm) outliers start: 52 outliers final: 28 residues processed: 523 average time/residue: 0.1062 time to fit residues: 78.3818 Evaluate side-chains 511 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 481 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 58 ILE Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 49 ASP Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 20 ILE Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 57 MET Chi-restraints excluded: chain L residue 76 TRP Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain N residue 54 ILE Chi-restraints excluded: chain N residue 75 GLU Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 40 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 48 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 16 optimal weight: 10.0000 chunk 2 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 ASN ** B 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 ASN G 22 GLN G 39 ASN G 77 ASN H 85 ASN J 22 GLN J 85 ASN K 7 ASN ** K 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 39 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.130704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.121890 restraints weight = 16418.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.124940 restraints weight = 8172.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.126871 restraints weight = 4588.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.128135 restraints weight = 2779.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.128907 restraints weight = 1757.588| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 1.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 11297 Z= 0.124 Angle : 0.587 8.033 15168 Z= 0.309 Chirality : 0.042 0.166 1712 Planarity : 0.003 0.044 1920 Dihedral : 4.632 21.137 1424 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 4.19 % Allowed : 21.76 % Favored : 74.05 % 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: -0.39 (0.23), residues: 1328 helix: 0.23 (0.17), residues: 1024 sheet: None (None), residues: 0 loop : -1.66 (0.31), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 9 TYR 0.014 0.001 TYR B 78 PHE 0.031 0.002 PHE A 81 TRP 0.017 0.001 TRP L 76 HIS 0.002 0.001 HIS H 56 Details of bonding type rmsd covalent geometry : bond 0.00300 (11296) covalent geometry : angle 0.58726 (15168) hydrogen bonds : bond 0.02653 ( 560) hydrogen bonds : angle 3.81490 ( 1680) Misc. bond : bond 0.00039 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 497 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.7230 (tpp) cc_final: 0.6864 (tpp) REVERT: C 30 TRP cc_start: 0.8989 (m-10) cc_final: 0.8316 (m-10) REVERT: E 3 PHE cc_start: 0.7311 (t80) cc_final: 0.6958 (t80) REVERT: E 17 MET cc_start: 0.9404 (tpt) cc_final: 0.8920 (tpp) REVERT: E 27 LEU cc_start: 0.9310 (mm) cc_final: 0.9002 (mt) REVERT: E 81 PHE cc_start: 0.7669 (t80) cc_final: 0.7240 (t80) REVERT: F 14 ARG cc_start: 0.7832 (mtm-85) cc_final: 0.5122 (mmt180) REVERT: F 59 LEU cc_start: 0.9239 (mt) cc_final: 0.8984 (mt) REVERT: G 2 ASN cc_start: 0.8199 (m-40) cc_final: 0.7795 (m110) REVERT: G 15 MET cc_start: 0.8340 (ttp) cc_final: 0.7932 (ttp) REVERT: H 60 LYS cc_start: 0.8620 (mmtp) cc_final: 0.8300 (mmtm) REVERT: H 73 LEU cc_start: 0.8952 (tp) cc_final: 0.8596 (tt) REVERT: J 48 GLN cc_start: 0.8221 (mt0) cc_final: 0.7847 (mp10) REVERT: K 9 ARG cc_start: 0.8454 (ttp80) cc_final: 0.8149 (mtt-85) REVERT: K 78 TYR cc_start: 0.8208 (t80) cc_final: 0.7572 (t80) REVERT: L 36 GLU cc_start: 0.7757 (tp30) cc_final: 0.7320 (mt-10) REVERT: L 52 ARG cc_start: 0.8449 (ttm110) cc_final: 0.8204 (mtm-85) REVERT: L 84 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8165 (mp) REVERT: M 6 ASP cc_start: 0.8045 (m-30) cc_final: 0.7812 (m-30) REVERT: M 9 ARG cc_start: 0.8296 (ttp80) cc_final: 0.7716 (ttp80) REVERT: M 30 TRP cc_start: 0.9217 (m-10) cc_final: 0.8983 (m-10) REVERT: M 43 CYS cc_start: 0.7968 (p) cc_final: 0.7461 (p) REVERT: M 78 TYR cc_start: 0.7889 (t80) cc_final: 0.7614 (t80) REVERT: N 22 GLN cc_start: 0.8518 (mt0) cc_final: 0.8318 (mt0) REVERT: P 1 MET cc_start: 0.7645 (tpt) cc_final: 0.6942 (tpt) REVERT: P 21 LYS cc_start: 0.8357 (mtpt) cc_final: 0.7829 (mtmm) REVERT: P 25 ASP cc_start: 0.7889 (m-30) cc_final: 0.7572 (m-30) outliers start: 53 outliers final: 31 residues processed: 516 average time/residue: 0.1093 time to fit residues: 79.2485 Evaluate side-chains 507 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 475 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 58 ILE Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain J residue 76 TRP Chi-restraints excluded: chain J residue 85 ASN Chi-restraints excluded: chain K residue 57 MET Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain M residue 20 ILE Chi-restraints excluded: chain N residue 54 ILE Chi-restraints excluded: chain N residue 57 MET Chi-restraints excluded: chain N residue 64 GLU Chi-restraints excluded: chain N residue 75 GLU Chi-restraints excluded: chain N residue 76 TRP Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 31 ASN Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 40 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 63 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 116 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 56 optimal weight: 0.0670 chunk 54 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.7522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 ASN ** B 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 ASN F 7 ASN G 77 ASN H 77 ASN ** K 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN ** N 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 39 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.130995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.122552 restraints weight = 16469.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.125561 restraints weight = 8060.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.127440 restraints weight = 4449.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.128600 restraints weight = 2638.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.129366 restraints weight = 1655.617| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 1.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11297 Z= 0.117 Angle : 0.590 8.536 15168 Z= 0.309 Chirality : 0.041 0.164 1712 Planarity : 0.003 0.040 1920 Dihedral : 4.567 21.191 1424 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.32 % Allowed : 23.02 % Favored : 73.66 % 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: -0.15 (0.23), residues: 1328 helix: 0.37 (0.17), residues: 1040 sheet: None (None), residues: 0 loop : -1.50 (0.32), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 9 TYR 0.009 0.001 TYR I 78 PHE 0.027 0.002 PHE M 69 TRP 0.025 0.001 TRP L 76 HIS 0.002 0.000 HIS A 56 Details of bonding type rmsd covalent geometry : bond 0.00279 (11296) covalent geometry : angle 0.58989 (15168) hydrogen bonds : bond 0.02669 ( 560) hydrogen bonds : angle 3.79284 ( 1680) Misc. bond : bond 0.00045 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 501 time to evaluate : 0.468 Fit side-chains REVERT: B 1 MET cc_start: 0.7206 (tpp) cc_final: 0.6865 (tpp) REVERT: B 22 GLN cc_start: 0.9180 (mt0) cc_final: 0.8980 (mt0) REVERT: B 34 ASN cc_start: 0.8913 (p0) cc_final: 0.8637 (p0) REVERT: C 30 TRP cc_start: 0.9027 (m-10) cc_final: 0.8394 (m-10) REVERT: C 35 ARG cc_start: 0.7328 (ttm110) cc_final: 0.6822 (ptp-170) REVERT: C 81 PHE cc_start: 0.7380 (t80) cc_final: 0.7049 (t80) REVERT: D 5 LYS cc_start: 0.8719 (tptm) cc_final: 0.8442 (tttm) REVERT: D 45 LYS cc_start: 0.7957 (mtmm) cc_final: 0.7526 (mtmt) REVERT: E 17 MET cc_start: 0.9388 (tpt) cc_final: 0.9017 (tpp) REVERT: E 27 LEU cc_start: 0.9289 (mm) cc_final: 0.8932 (mt) REVERT: E 85 ASN cc_start: 0.6819 (m-40) cc_final: 0.6551 (m110) REVERT: F 12 ILE cc_start: 0.8559 (OUTLIER) cc_final: 0.8217 (mt) REVERT: F 14 ARG cc_start: 0.8012 (mtm-85) cc_final: 0.5288 (mmt180) REVERT: F 36 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7746 (mt-10) REVERT: F 59 LEU cc_start: 0.9310 (mt) cc_final: 0.9078 (mt) REVERT: G 25 ASP cc_start: 0.6794 (m-30) cc_final: 0.6474 (m-30) REVERT: H 2 ASN cc_start: 0.8276 (t0) cc_final: 0.7858 (t0) REVERT: H 60 LYS cc_start: 0.8737 (mmtp) cc_final: 0.8381 (mmtm) REVERT: H 73 LEU cc_start: 0.8829 (tp) cc_final: 0.8585 (tt) REVERT: J 37 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7922 (mt-10) REVERT: J 48 GLN cc_start: 0.8204 (mt0) cc_final: 0.7817 (mp10) REVERT: K 9 ARG cc_start: 0.8458 (ttp80) cc_final: 0.8109 (mtt-85) REVERT: K 26 ASP cc_start: 0.8351 (m-30) cc_final: 0.8093 (m-30) REVERT: K 78 TYR cc_start: 0.8219 (t80) cc_final: 0.7624 (t80) REVERT: L 9 ARG cc_start: 0.7837 (mtp85) cc_final: 0.7602 (mtp-110) REVERT: L 36 GLU cc_start: 0.7722 (tp30) cc_final: 0.7287 (mt-10) REVERT: M 30 TRP cc_start: 0.9225 (m-10) cc_final: 0.8997 (m-10) REVERT: M 43 CYS cc_start: 0.7999 (p) cc_final: 0.7381 (p) REVERT: M 78 TYR cc_start: 0.7881 (t80) cc_final: 0.7522 (t80) REVERT: P 21 LYS cc_start: 0.8284 (mtpt) cc_final: 0.7656 (mtmm) REVERT: P 22 GLN cc_start: 0.8772 (mt0) cc_final: 0.8450 (mt0) REVERT: P 25 ASP cc_start: 0.8004 (m-30) cc_final: 0.7598 (m-30) outliers start: 42 outliers final: 28 residues processed: 512 average time/residue: 0.1118 time to fit residues: 80.0597 Evaluate side-chains 505 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 476 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 57 MET Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 58 ILE Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain K residue 57 MET Chi-restraints excluded: chain N residue 54 ILE Chi-restraints excluded: chain N residue 57 MET Chi-restraints excluded: chain N residue 75 GLU Chi-restraints excluded: chain N residue 76 TRP Chi-restraints excluded: chain O residue 23 ILE Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 54 ILE Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 31 ASN Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 40 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 107 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 9 optimal weight: 0.0270 chunk 44 optimal weight: 0.0020 chunk 32 optimal weight: 0.4980 chunk 98 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 overall best weight: 0.4246 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 ASN ** B 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 7 ASN G 2 ASN G 77 ASN H 85 ASN I 85 ASN ** K 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN ** N 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 39 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.133852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.125547 restraints weight = 16387.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.128573 restraints weight = 7936.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.130413 restraints weight = 4310.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.131583 restraints weight = 2538.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.132190 restraints weight = 1566.268| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 1.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11297 Z= 0.113 Angle : 0.594 9.337 15168 Z= 0.312 Chirality : 0.041 0.161 1712 Planarity : 0.004 0.050 1920 Dihedral : 4.530 23.742 1424 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.53 % Allowed : 24.37 % Favored : 73.10 % 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: -0.01 (0.23), residues: 1328 helix: 0.50 (0.17), residues: 1040 sheet: None (None), residues: 0 loop : -1.63 (0.31), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG L 52 TYR 0.011 0.001 TYR B 78 PHE 0.030 0.002 PHE H 69 TRP 0.023 0.001 TRP L 76 HIS 0.001 0.000 HIS D 56 Details of bonding type rmsd covalent geometry : bond 0.00258 (11296) covalent geometry : angle 0.59365 (15168) hydrogen bonds : bond 0.02569 ( 560) hydrogen bonds : angle 3.78172 ( 1680) Misc. bond : bond 0.00048 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 500 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.7094 (tpp) cc_final: 0.6823 (tpp) REVERT: B 52 ARG cc_start: 0.8564 (ttm-80) cc_final: 0.8090 (mtt90) REVERT: C 30 TRP cc_start: 0.9045 (m-10) cc_final: 0.8323 (m-10) REVERT: C 35 ARG cc_start: 0.7109 (ttm110) cc_final: 0.6662 (ptp-170) REVERT: D 5 LYS cc_start: 0.8667 (tptm) cc_final: 0.8447 (tttm) REVERT: D 45 LYS cc_start: 0.7917 (mtmm) cc_final: 0.7477 (mtmt) REVERT: E 17 MET cc_start: 0.9400 (tpt) cc_final: 0.9056 (tpp) REVERT: E 27 LEU cc_start: 0.9230 (mm) cc_final: 0.8951 (mt) REVERT: E 48 GLN cc_start: 0.8486 (mm-40) cc_final: 0.8274 (mp10) REVERT: E 52 ARG cc_start: 0.9082 (tpp-160) cc_final: 0.8640 (mtt-85) REVERT: E 85 ASN cc_start: 0.6704 (m-40) cc_final: 0.6473 (m110) REVERT: F 14 ARG cc_start: 0.7934 (mtm-85) cc_final: 0.5135 (mmt180) REVERT: F 36 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7236 (mt-10) REVERT: G 25 ASP cc_start: 0.6799 (m-30) cc_final: 0.6513 (m-30) REVERT: H 2 ASN cc_start: 0.8207 (t0) cc_final: 0.7817 (t0) REVERT: H 60 LYS cc_start: 0.8693 (mmtp) cc_final: 0.8369 (mmtm) REVERT: I 17 MET cc_start: 0.8547 (mmm) cc_final: 0.8325 (tpt) REVERT: J 37 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7525 (mt-10) REVERT: J 48 GLN cc_start: 0.8057 (mt0) cc_final: 0.7712 (mp10) REVERT: J 74 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7848 (mmmm) REVERT: J 75 GLU cc_start: 0.7792 (tt0) cc_final: 0.7275 (tt0) REVERT: J 78 TYR cc_start: 0.8864 (t80) cc_final: 0.8357 (t80) REVERT: K 9 ARG cc_start: 0.8468 (ttp80) cc_final: 0.8029 (mtt-85) REVERT: K 78 TYR cc_start: 0.8159 (t80) cc_final: 0.7606 (t80) REVERT: L 22 GLN cc_start: 0.9252 (mt0) cc_final: 0.8967 (mt0) REVERT: M 1 MET cc_start: 0.7444 (tpp) cc_final: 0.7176 (ttt) REVERT: M 9 ARG cc_start: 0.8037 (ttp80) cc_final: 0.7817 (ttt-90) REVERT: M 21 LYS cc_start: 0.8397 (mtpt) cc_final: 0.7948 (mmtt) REVERT: M 30 TRP cc_start: 0.9234 (m-10) cc_final: 0.8987 (m-10) REVERT: M 43 CYS cc_start: 0.7938 (p) cc_final: 0.7332 (p) REVERT: M 78 TYR cc_start: 0.7876 (t80) cc_final: 0.7478 (t80) REVERT: P 21 LYS cc_start: 0.8018 (mtpt) cc_final: 0.7441 (mttp) REVERT: P 22 GLN cc_start: 0.8779 (mt0) cc_final: 0.8490 (mt0) REVERT: P 25 ASP cc_start: 0.7954 (m-30) cc_final: 0.7521 (m-30) outliers start: 32 outliers final: 22 residues processed: 510 average time/residue: 0.1162 time to fit residues: 81.9185 Evaluate side-chains 503 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 480 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 57 MET Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain E residue 4 ILE Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 49 ASP Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain J residue 74 LYS Chi-restraints excluded: chain J residue 76 TRP Chi-restraints excluded: chain N residue 54 ILE Chi-restraints excluded: chain N residue 57 MET Chi-restraints excluded: chain N residue 76 TRP Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 54 ILE Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 31 ASN Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 40 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 42 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 102 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 31 optimal weight: 0.0270 overall best weight: 2.1844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN ** B 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 2 ASN G 77 ASN I 13 GLN K 13 GLN ** K 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN ** N 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 39 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.122421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.113923 restraints weight = 16642.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.116862 restraints weight = 8263.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.118674 restraints weight = 4614.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.119884 restraints weight = 2802.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.120619 restraints weight = 1778.479| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 1.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 11297 Z= 0.191 Angle : 0.687 9.625 15168 Z= 0.362 Chirality : 0.046 0.178 1712 Planarity : 0.004 0.058 1920 Dihedral : 4.714 22.792 1424 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.32 % Allowed : 24.29 % Favored : 72.39 % 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: -0.46 (0.23), residues: 1328 helix: 0.08 (0.16), residues: 1120 sheet: None (None), residues: 0 loop : -1.81 (0.36), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG L 52 TYR 0.008 0.001 TYR O 78 PHE 0.039 0.002 PHE O 81 TRP 0.026 0.001 TRP L 76 HIS 0.002 0.001 HIS C 56 Details of bonding type rmsd covalent geometry : bond 0.00474 (11296) covalent geometry : angle 0.68740 (15168) hydrogen bonds : bond 0.03286 ( 560) hydrogen bonds : angle 4.20737 ( 1680) Misc. bond : bond 0.00081 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 507 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASN cc_start: 0.7387 (m-40) cc_final: 0.7169 (m110) REVERT: C 21 LYS cc_start: 0.8777 (mmmm) cc_final: 0.8464 (mttt) REVERT: C 30 TRP cc_start: 0.9149 (m-10) cc_final: 0.8429 (m-10) REVERT: C 73 LEU cc_start: 0.9039 (tp) cc_final: 0.8751 (tt) REVERT: C 82 GLN cc_start: 0.7128 (tt0) cc_final: 0.6505 (tt0) REVERT: D 5 LYS cc_start: 0.8773 (tptm) cc_final: 0.8570 (tttm) REVERT: E 17 MET cc_start: 0.9372 (tpt) cc_final: 0.9081 (tpp) REVERT: E 27 LEU cc_start: 0.9316 (mm) cc_final: 0.8906 (mt) REVERT: F 1 MET cc_start: 0.7470 (ttm) cc_final: 0.7151 (ttm) REVERT: F 14 ARG cc_start: 0.8360 (mtm-85) cc_final: 0.5499 (mmt180) REVERT: F 60 LYS cc_start: 0.8487 (mttt) cc_final: 0.8207 (mttt) REVERT: G 52 ARG cc_start: 0.8678 (ttm-80) cc_final: 0.8311 (ttp-110) REVERT: H 1 MET cc_start: 0.8009 (tpp) cc_final: 0.7461 (tpp) REVERT: H 2 ASN cc_start: 0.8214 (t0) cc_final: 0.7804 (t0) REVERT: H 60 LYS cc_start: 0.8888 (mmtp) cc_final: 0.8351 (mmtm) REVERT: J 48 GLN cc_start: 0.8218 (mt0) cc_final: 0.7848 (mp10) REVERT: K 9 ARG cc_start: 0.8564 (ttp80) cc_final: 0.7973 (mtt90) REVERT: M 20 ILE cc_start: 0.8894 (OUTLIER) cc_final: 0.8552 (mm) REVERT: M 43 CYS cc_start: 0.8210 (p) cc_final: 0.7741 (p) REVERT: O 75 GLU cc_start: 0.7587 (tt0) cc_final: 0.7375 (tt0) REVERT: P 15 MET cc_start: 0.7482 (ttm) cc_final: 0.7256 (ttm) REVERT: P 21 LYS cc_start: 0.8518 (mtpt) cc_final: 0.7937 (mtmm) REVERT: P 22 GLN cc_start: 0.8904 (mt0) cc_final: 0.8628 (mt0) REVERT: P 25 ASP cc_start: 0.7934 (m-30) cc_final: 0.7566 (m-30) outliers start: 42 outliers final: 29 residues processed: 526 average time/residue: 0.1173 time to fit residues: 85.1049 Evaluate side-chains 517 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 487 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 57 MET Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain G residue 15 MET Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 49 ASP Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain L residue 57 MET Chi-restraints excluded: chain M residue 20 ILE Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain N residue 54 ILE Chi-restraints excluded: chain N residue 57 MET Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 54 ILE Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 40 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 65 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 chunk 115 optimal weight: 5.9990 chunk 35 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 ASN D 85 ASN E 22 GLN ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 22 GLN G 2 ASN G 77 ASN ** K 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 22 GLN N 31 ASN ** N 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 39 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.125326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.116849 restraints weight = 16460.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.119784 restraints weight = 8057.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.121651 restraints weight = 4486.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.122811 restraints weight = 2687.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.123565 restraints weight = 1702.197| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 1.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11297 Z= 0.150 Angle : 0.674 11.049 15168 Z= 0.354 Chirality : 0.044 0.169 1712 Planarity : 0.004 0.073 1920 Dihedral : 4.773 21.922 1424 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.09 % Allowed : 26.03 % Favored : 70.89 % 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: -0.60 (0.23), residues: 1328 helix: -0.05 (0.16), residues: 1136 sheet: None (None), residues: 0 loop : -1.72 (0.38), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 35 TYR 0.013 0.001 TYR B 78 PHE 0.045 0.002 PHE E 81 TRP 0.024 0.001 TRP L 76 HIS 0.002 0.001 HIS P 56 Details of bonding type rmsd covalent geometry : bond 0.00369 (11296) covalent geometry : angle 0.67416 (15168) hydrogen bonds : bond 0.03054 ( 560) hydrogen bonds : angle 4.27950 ( 1680) Misc. bond : bond 0.00057 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 511 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 21 LYS cc_start: 0.8748 (mmmm) cc_final: 0.8424 (mttt) REVERT: C 30 TRP cc_start: 0.9143 (m-10) cc_final: 0.8518 (m-10) REVERT: C 54 ILE cc_start: 0.9204 (tt) cc_final: 0.8920 (tt) REVERT: C 73 LEU cc_start: 0.9007 (tp) cc_final: 0.8748 (tt) REVERT: C 82 GLN cc_start: 0.7271 (tt0) cc_final: 0.6645 (tt0) REVERT: D 45 LYS cc_start: 0.8219 (mtmm) cc_final: 0.7763 (mtmt) REVERT: D 85 ASN cc_start: 0.7360 (m-40) cc_final: 0.7026 (m-40) REVERT: E 17 MET cc_start: 0.9367 (tpt) cc_final: 0.9161 (tpp) REVERT: E 27 LEU cc_start: 0.9251 (mm) cc_final: 0.8877 (mt) REVERT: F 1 MET cc_start: 0.7575 (ttm) cc_final: 0.7312 (ttm) REVERT: F 14 ARG cc_start: 0.8218 (mtm-85) cc_final: 0.5420 (mmt180) REVERT: F 60 LYS cc_start: 0.8515 (mttt) cc_final: 0.8265 (mttt) REVERT: H 1 MET cc_start: 0.7996 (tpp) cc_final: 0.7504 (ttp) REVERT: H 2 ASN cc_start: 0.8206 (t0) cc_final: 0.7946 (m-40) REVERT: H 60 LYS cc_start: 0.8852 (mmtp) cc_final: 0.8354 (mmtm) REVERT: I 37 GLU cc_start: 0.8347 (tt0) cc_final: 0.8134 (tt0) REVERT: J 48 GLN cc_start: 0.8203 (mt0) cc_final: 0.7963 (mp10) REVERT: K 9 ARG cc_start: 0.8548 (ttp80) cc_final: 0.7952 (mtt90) REVERT: K 78 TYR cc_start: 0.8181 (t80) cc_final: 0.7644 (t80) REVERT: M 43 CYS cc_start: 0.8168 (p) cc_final: 0.7708 (p) REVERT: N 36 GLU cc_start: 0.7540 (mp0) cc_final: 0.7331 (mp0) REVERT: P 21 LYS cc_start: 0.8412 (mtpt) cc_final: 0.7747 (mtmm) REVERT: P 22 GLN cc_start: 0.8912 (mt0) cc_final: 0.8649 (mt0) REVERT: P 25 ASP cc_start: 0.7938 (m-30) cc_final: 0.7521 (m-30) REVERT: P 65 SER cc_start: 0.9292 (p) cc_final: 0.8950 (p) outliers start: 39 outliers final: 28 residues processed: 525 average time/residue: 0.1160 time to fit residues: 84.9483 Evaluate side-chains 518 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 490 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 57 MET Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 49 ASP Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain J residue 74 LYS Chi-restraints excluded: chain J residue 76 TRP Chi-restraints excluded: chain M residue 20 ILE Chi-restraints excluded: chain M residue 22 GLN Chi-restraints excluded: chain N residue 57 MET Chi-restraints excluded: chain O residue 4 ILE Chi-restraints excluded: chain O residue 54 ILE Chi-restraints excluded: chain O residue 57 MET Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 40 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 112 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 72 optimal weight: 10.0000 chunk 7 optimal weight: 0.0010 chunk 61 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 116 optimal weight: 0.0010 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 ASN G 2 ASN H 85 ASN ** J 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 85 ASN ** K 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 22 GLN ** N 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN ** N 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 85 ASN P 39 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.129255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.121034 restraints weight = 16568.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.123958 restraints weight = 8015.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.125771 restraints weight = 4398.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.126922 restraints weight = 2598.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.127670 restraints weight = 1602.938| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 1.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11297 Z= 0.130 Angle : 0.655 8.860 15168 Z= 0.343 Chirality : 0.043 0.163 1712 Planarity : 0.004 0.062 1920 Dihedral : 4.748 20.964 1424 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.93 % Allowed : 26.42 % Favored : 70.65 % 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: -0.55 (0.23), residues: 1328 helix: 0.00 (0.16), residues: 1136 sheet: None (None), residues: 0 loop : -1.84 (0.37), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 35 TYR 0.006 0.001 TYR O 78 PHE 0.043 0.002 PHE O 81 TRP 0.020 0.001 TRP L 76 HIS 0.002 0.000 HIS F 56 Details of bonding type rmsd covalent geometry : bond 0.00302 (11296) covalent geometry : angle 0.65460 (15168) hydrogen bonds : bond 0.02852 ( 560) hydrogen bonds : angle 4.23208 ( 1680) Misc. bond : bond 0.00080 ( 1) =============================================================================== Job complete usr+sys time: 2042.23 seconds wall clock time: 36 minutes 13.93 seconds (2173.93 seconds total)