Starting phenix.real_space_refine on Mon Jul 28 17:59:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6n1i_8903/07_2025/6n1i_8903.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n1i_8903/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6n1i_8903/07_2025/6n1i_8903.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n1i_8903/07_2025/6n1i_8903.map" model { file = "/net/cci-nas-00/data/ceres_data/6n1i_8903/07_2025/6n1i_8903.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n1i_8903/07_2025/6n1i_8903.cif" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: C, B, E, D, G, F, I, H, K, J, M, L, O, N, P Time building chain proxies: 3.50, per 1000 atoms: 0.31 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: 2.80 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.08 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: 2.63 Time building geometry restraints manager: 3.30 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' selection = chain 'O' selection = chain 'N' 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: 0.780 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: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 23.770 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.170 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.019 0.003 TRP M 30 HIS 0.003 0.001 HIS O 56 PHE 0.018 0.003 PHE I 81 TYR 0.003 0.001 TYR O 78 ARG 0.003 0.001 ARG G 9 Details of bonding type rmsd hydrogen bonds : bond 0.32877 ( 560) hydrogen bonds : angle 10.90099 ( 1680) covalent geometry : bond 0.00858 (11296) covalent geometry : angle 1.12524 (15168) 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 : 1.246 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: 0.6619 (mtt) REVERT: A 76 TRP cc_start: 0.5894 (m100) cc_final: 0.5428 (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: 0.7101 (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: 0.6424 (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: 0.4550 (ttt) REVERT: O 26 ASP cc_start: 0.6343 (m-30) cc_final: 0.6053 (m-30) outliers start: 0 outliers final: 0 residues processed: 487 average time/residue: 0.2426 time to fit residues: 165.1952 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 : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.1980 chunk 74 optimal weight: 0.7980 chunk 116 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 G 31 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 34 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 ** P 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.144869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.135334 restraints weight = 15778.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.138814 restraints weight = 7427.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.140944 restraints weight = 3994.249| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6520 moved from start: 0.4752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 11297 Z= 0.167 Angle : 0.708 7.522 15168 Z= 0.381 Chirality : 0.042 0.161 1712 Planarity : 0.005 0.042 1920 Dihedral : 5.559 19.308 1424 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.69 % Allowed : 10.92 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.11 (0.18), residues: 1328 helix: -2.61 (0.12), residues: 1168 sheet: None (None), residues: 0 loop : -1.17 (0.36), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 76 HIS 0.002 0.001 HIS E 56 PHE 0.029 0.002 PHE B 81 TYR 0.012 0.002 TYR B 78 ARG 0.008 0.001 ARG M 52 Details of bonding type rmsd hydrogen bonds : bond 0.04174 ( 560) hydrogen bonds : angle 4.68604 ( 1680) covalent geometry : bond 0.00387 (11296) covalent geometry : angle 0.70843 (15168) Misc. bond : bond 0.00140 ( 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 483 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 449 time to evaluate : 1.281 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: B 1 MET cc_start: 0.6184 (tpp) cc_final: 0.5846 (mmm) REVERT: D 1 MET cc_start: 0.7283 (tpp) cc_final: 0.7038 (tpt) REVERT: E 3 PHE cc_start: 0.7391 (t80) cc_final: 0.7083 (t80) REVERT: E 47 GLU cc_start: 0.7268 (pt0) cc_final: 0.6506 (pt0) REVERT: F 26 ASP cc_start: 0.7046 (m-30) cc_final: 0.6779 (m-30) REVERT: G 38 VAL cc_start: 0.7738 (t) cc_final: 0.7517 (t) REVERT: H 1 MET cc_start: 0.7671 (tpp) cc_final: 0.7380 (tpp) REVERT: I 2 ASN cc_start: 0.6604 (t0) cc_final: 0.6382 (p0) REVERT: J 1 MET cc_start: 0.6205 (tpt) cc_final: 0.5920 (tpt) REVERT: J 22 GLN cc_start: 0.7403 (mt0) cc_final: 0.7170 (mt0) REVERT: K 22 GLN cc_start: 0.7310 (tp40) cc_final: 0.6929 (mm-40) REVERT: K 47 GLU cc_start: 0.7701 (pt0) cc_final: 0.7427 (pt0) REVERT: L 20 ILE cc_start: 0.7334 (tt) cc_final: 0.6951 (tt) REVERT: M 36 GLU cc_start: 0.5645 (mp0) cc_final: 0.5137 (mp0) REVERT: M 49 ASP cc_start: 0.7298 (m-30) cc_final: 0.7043 (m-30) REVERT: O 85 ASN cc_start: 0.6907 (m-40) cc_final: 0.6692 (m110) REVERT: P 57 MET cc_start: 0.6587 (mmt) cc_final: 0.5919 (mtt) outliers start: 34 outliers final: 16 residues processed: 459 average time/residue: 0.2338 time to fit residues: 150.6042 Evaluate side-chains 416 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 400 time to evaluate : 1.466 ------------------------------------------------------------------------------- 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 L residue 11 LEU 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 P residue 15 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 19 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 127 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 37 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN B 31 ASN F 56 HIS ** J 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 ASN M 22 GLN ** N 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 13 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.143338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.134183 restraints weight = 16146.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.137476 restraints weight = 7753.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.139502 restraints weight = 4219.520| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.7003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11297 Z= 0.140 Angle : 0.637 8.591 15168 Z= 0.332 Chirality : 0.041 0.164 1712 Planarity : 0.004 0.036 1920 Dihedral : 4.994 25.952 1424 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.24 % Allowed : 16.06 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.22), residues: 1328 helix: -1.14 (0.15), residues: 1136 sheet: None (None), residues: 0 loop : -1.09 (0.42), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 76 HIS 0.002 0.001 HIS M 56 PHE 0.028 0.002 PHE B 81 TYR 0.008 0.001 TYR B 78 ARG 0.004 0.000 ARG K 35 Details of bonding type rmsd hydrogen bonds : bond 0.03284 ( 560) hydrogen bonds : angle 3.93062 ( 1680) covalent geometry : bond 0.00327 (11296) covalent geometry : angle 0.63656 (15168) Misc. bond : bond 0.00037 ( 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 502 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 461 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7077 (m-30) cc_final: 0.6829 (m-30) REVERT: B 64 GLU cc_start: 0.8046 (pp20) cc_final: 0.7754 (tm-30) REVERT: C 21 LYS cc_start: 0.8100 (mttm) cc_final: 0.7765 (mtmt) REVERT: C 25 ASP cc_start: 0.7246 (t0) cc_final: 0.7028 (t0) REVERT: D 11 LEU cc_start: 0.8762 (mt) cc_final: 0.8445 (mt) REVERT: D 41 ILE cc_start: 0.6866 (mm) cc_final: 0.6657 (mm) REVERT: D 57 MET cc_start: 0.7435 (mpp) cc_final: 0.6951 (mtt) REVERT: E 34 ASN cc_start: 0.7487 (p0) cc_final: 0.7283 (p0) REVERT: E 41 ILE cc_start: 0.8052 (mt) cc_final: 0.7702 (mt) REVERT: H 55 ILE cc_start: 0.7773 (tt) cc_final: 0.7211 (mt) REVERT: I 3 PHE cc_start: 0.7518 (t80) cc_final: 0.7292 (t80) REVERT: I 12 ILE cc_start: 0.9101 (pt) cc_final: 0.8790 (mt) REVERT: I 37 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7057 (mt-10) REVERT: I 76 TRP cc_start: 0.5736 (m100) cc_final: 0.4978 (m100) REVERT: J 22 GLN cc_start: 0.8284 (mt0) cc_final: 0.8058 (mt0) REVERT: J 37 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7467 (mt-10) REVERT: K 9 ARG cc_start: 0.8227 (ttp80) cc_final: 0.7684 (mtt-85) REVERT: K 22 GLN cc_start: 0.8085 (tp40) cc_final: 0.7724 (mm-40) REVERT: K 47 GLU cc_start: 0.8270 (pt0) cc_final: 0.7897 (pt0) REVERT: L 26 ASP cc_start: 0.7459 (m-30) cc_final: 0.7023 (m-30) REVERT: L 36 GLU cc_start: 0.7374 (mm-30) cc_final: 0.6564 (mt-10) REVERT: L 39 ASN cc_start: 0.7441 (m110) cc_final: 0.7138 (m-40) REVERT: L 76 TRP cc_start: 0.6189 (OUTLIER) cc_final: 0.5362 (m100) REVERT: M 20 ILE cc_start: 0.7696 (mm) cc_final: 0.7492 (mm) REVERT: N 26 ASP cc_start: 0.8379 (t0) cc_final: 0.8066 (t0) REVERT: N 57 MET cc_start: 0.7097 (mtm) cc_final: 0.6864 (mtm) REVERT: O 23 ILE cc_start: 0.8966 (mt) cc_final: 0.8759 (mt) REVERT: O 60 LYS cc_start: 0.8264 (mtpp) cc_final: 0.7787 (mtmm) REVERT: P 1 MET cc_start: 0.6788 (tpp) cc_final: 0.6552 (tpt) outliers start: 41 outliers final: 23 residues processed: 472 average time/residue: 0.2816 time to fit residues: 188.5906 Evaluate side-chains 449 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 425 time to evaluate : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain H residue 85 ASN Chi-restraints excluded: chain I residue 24 THR 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 L residue 24 THR Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 76 TRP Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain P residue 31 ASN 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 10 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 36 optimal weight: 8.9990 chunk 33 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 92 optimal weight: 0.5980 chunk 86 optimal weight: 0.1980 chunk 111 optimal weight: 3.9990 chunk 53 optimal weight: 0.0570 chunk 0 optimal weight: 10.0000 overall best weight: 0.5702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 ASN C 13 GLN C 39 ASN E 48 GLN F 13 GLN F 39 ASN I 31 ASN ** J 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 13 GLN ** L 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 48 GLN O 39 ASN O 48 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.143443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.134508 restraints weight = 16087.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.137739 restraints weight = 7664.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.139675 restraints weight = 4123.066| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.8035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11297 Z= 0.117 Angle : 0.568 6.340 15168 Z= 0.299 Chirality : 0.041 0.198 1712 Planarity : 0.003 0.036 1920 Dihedral : 4.678 23.985 1424 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.93 % Allowed : 18.12 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.23), residues: 1328 helix: -0.62 (0.16), residues: 1136 sheet: None (None), residues: 0 loop : -0.99 (0.42), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP M 76 HIS 0.003 0.001 HIS M 56 PHE 0.028 0.002 PHE B 81 TYR 0.010 0.001 TYR O 78 ARG 0.005 0.000 ARG A 35 Details of bonding type rmsd hydrogen bonds : bond 0.02798 ( 560) hydrogen bonds : angle 3.60107 ( 1680) covalent geometry : bond 0.00277 (11296) covalent geometry : angle 0.56767 (15168) Misc. bond : bond 0.00009 ( 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 509 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 472 time to evaluate : 1.592 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 26 ASP cc_start: 0.7934 (OUTLIER) cc_final: 0.7672 (m-30) REVERT: B 47 GLU cc_start: 0.8007 (pt0) cc_final: 0.7378 (pt0) REVERT: B 64 GLU cc_start: 0.8107 (pp20) cc_final: 0.7897 (tm-30) REVERT: C 21 LYS cc_start: 0.8428 (mttm) cc_final: 0.8094 (mtmt) REVERT: C 22 GLN cc_start: 0.7629 (OUTLIER) cc_final: 0.7415 (mt0) REVERT: C 30 TRP cc_start: 0.8408 (m-10) cc_final: 0.8075 (m-10) REVERT: E 17 MET cc_start: 0.8224 (tpt) cc_final: 0.7980 (tpt) REVERT: E 49 ASP cc_start: 0.7963 (m-30) cc_final: 0.7614 (m-30) REVERT: G 39 ASN cc_start: 0.8917 (t0) cc_final: 0.8528 (t0) REVERT: H 1 MET cc_start: 0.8583 (tpp) cc_final: 0.8142 (tpp) REVERT: H 3 PHE cc_start: 0.8238 (t80) cc_final: 0.7975 (t80) REVERT: I 37 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7405 (tt0) REVERT: I 76 TRP cc_start: 0.5999 (m100) cc_final: 0.5525 (m100) REVERT: J 1 MET cc_start: 0.7165 (tpp) cc_final: 0.6925 (tpp) REVERT: K 9 ARG cc_start: 0.8215 (ttp80) cc_final: 0.7754 (mtt-85) REVERT: K 47 GLU cc_start: 0.8212 (pt0) cc_final: 0.7918 (pt0) REVERT: L 26 ASP cc_start: 0.7503 (m-30) cc_final: 0.6712 (m-30) REVERT: L 39 ASN cc_start: 0.7783 (m110) cc_final: 0.7292 (m-40) REVERT: M 20 ILE cc_start: 0.8091 (mm) cc_final: 0.7845 (mm) REVERT: N 17 MET cc_start: 0.8477 (mmm) cc_final: 0.8206 (mmm) REVERT: O 23 ILE cc_start: 0.9251 (mt) cc_final: 0.8977 (mt) REVERT: O 44 GLU cc_start: 0.7206 (mt-10) cc_final: 0.6505 (mt-10) REVERT: O 49 ASP cc_start: 0.7549 (t0) cc_final: 0.7220 (t0) REVERT: P 81 PHE cc_start: 0.8227 (t80) cc_final: 0.7952 (t80) outliers start: 37 outliers final: 18 residues processed: 485 average time/residue: 0.2554 time to fit residues: 178.6220 Evaluate side-chains 454 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 434 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 MET Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain C residue 22 GLN Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain N residue 64 GLU Chi-restraints excluded: chain O residue 54 ILE Chi-restraints excluded: chain O residue 55 ILE Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain P residue 31 ASN 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 48 optimal weight: 9.9990 chunk 106 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 127 optimal weight: 0.9990 chunk 121 optimal weight: 5.9990 chunk 58 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 GLN F 48 GLN ** G 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 67 ASN ** M 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.135539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.127250 restraints weight = 16078.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.130158 restraints weight = 8040.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.131942 restraints weight = 4525.538| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 1.0181 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= 0.157 Angle : 0.643 10.450 15168 Z= 0.337 Chirality : 0.043 0.172 1712 Planarity : 0.004 0.036 1920 Dihedral : 4.730 22.504 1424 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.88 % Allowed : 19.62 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.23), residues: 1328 helix: -0.37 (0.16), residues: 1120 sheet: None (None), residues: 0 loop : -1.30 (0.40), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP L 76 HIS 0.004 0.001 HIS M 56 PHE 0.046 0.002 PHE A 81 TYR 0.011 0.001 TYR O 78 ARG 0.006 0.001 ARG D 9 Details of bonding type rmsd hydrogen bonds : bond 0.03382 ( 560) hydrogen bonds : angle 3.78361 ( 1680) covalent geometry : bond 0.00382 (11296) covalent geometry : angle 0.64343 (15168) Misc. bond : bond 0.00050 ( 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 569 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 520 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 LEU cc_start: 0.9043 (tp) cc_final: 0.8826 (tp) REVERT: B 1 MET cc_start: 0.7250 (tpp) cc_final: 0.6977 (tpp) REVERT: B 22 GLN cc_start: 0.9177 (mt0) cc_final: 0.8659 (mt0) REVERT: B 27 LEU cc_start: 0.9407 (mm) cc_final: 0.9195 (mp) REVERT: B 84 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8233 (mp) REVERT: C 21 LYS cc_start: 0.8970 (mttm) cc_final: 0.8642 (mtmt) REVERT: C 30 TRP cc_start: 0.8721 (m-10) cc_final: 0.8030 (m-10) REVERT: D 78 TYR cc_start: 0.7924 (t80) cc_final: 0.7554 (t80) REVERT: E 17 MET cc_start: 0.8992 (tpt) cc_final: 0.8497 (tpt) REVERT: E 20 ILE cc_start: 0.8686 (mm) cc_final: 0.8441 (mm) REVERT: E 24 THR cc_start: 0.9291 (p) cc_final: 0.9080 (p) REVERT: E 45 LYS cc_start: 0.7689 (mtmt) cc_final: 0.7477 (mttp) REVERT: E 47 GLU cc_start: 0.7486 (pt0) cc_final: 0.7013 (pt0) REVERT: E 49 ASP cc_start: 0.8178 (m-30) cc_final: 0.7904 (m-30) REVERT: E 84 LEU cc_start: 0.8276 (tp) cc_final: 0.7680 (mt) REVERT: F 22 GLN cc_start: 0.8309 (mt0) cc_final: 0.7781 (mt0) REVERT: F 49 ASP cc_start: 0.8254 (t0) cc_final: 0.8017 (t0) REVERT: F 57 MET cc_start: 0.8424 (ttm) cc_final: 0.8111 (ttm) REVERT: H 1 MET cc_start: 0.8722 (tpp) cc_final: 0.8161 (tpp) REVERT: H 60 LYS cc_start: 0.8254 (mmtp) cc_final: 0.8000 (mmtm) REVERT: H 73 LEU cc_start: 0.8896 (tp) cc_final: 0.8598 (tt) REVERT: I 61 LYS cc_start: 0.7518 (mttt) cc_final: 0.5863 (mmtt) REVERT: I 80 LEU cc_start: 0.8700 (tp) cc_final: 0.8181 (tp) REVERT: J 1 MET cc_start: 0.7588 (tpp) cc_final: 0.7154 (tpp) REVERT: J 48 GLN cc_start: 0.8835 (mp10) cc_final: 0.8555 (mp10) REVERT: J 75 GLU cc_start: 0.8130 (tt0) cc_final: 0.7387 (tt0) REVERT: J 78 TYR cc_start: 0.8117 (t80) cc_final: 0.7502 (t80) REVERT: J 80 LEU cc_start: 0.9048 (tp) cc_final: 0.8680 (tt) REVERT: J 82 GLN cc_start: 0.8325 (tp40) cc_final: 0.7460 (mp10) REVERT: K 9 ARG cc_start: 0.8320 (ttp80) cc_final: 0.7995 (mtt-85) REVERT: K 26 ASP cc_start: 0.8554 (m-30) cc_final: 0.8314 (m-30) REVERT: K 27 LEU cc_start: 0.9254 (mm) cc_final: 0.8948 (mt) REVERT: L 26 ASP cc_start: 0.7760 (m-30) cc_final: 0.7476 (m-30) REVERT: M 1 MET cc_start: 0.8031 (tpp) cc_final: 0.7515 (tpp) REVERT: M 2 ASN cc_start: 0.8063 (t0) cc_final: 0.7749 (t0) REVERT: M 9 ARG cc_start: 0.7938 (ttp80) cc_final: 0.7303 (ttp80) REVERT: N 11 LEU cc_start: 0.8980 (mt) cc_final: 0.8749 (mt) REVERT: O 3 PHE cc_start: 0.7962 (t80) cc_final: 0.7648 (t80) REVERT: P 1 MET cc_start: 0.7190 (tpt) cc_final: 0.6890 (tpt) REVERT: P 2 ASN cc_start: 0.8193 (m-40) cc_final: 0.7526 (m-40) REVERT: P 19 VAL cc_start: 0.8919 (p) cc_final: 0.8674 (m) outliers start: 49 outliers final: 24 residues processed: 539 average time/residue: 0.2203 time to fit residues: 167.7713 Evaluate side-chains 496 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 471 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain G residue 15 MET Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 76 TRP Chi-restraints excluded: chain N residue 54 ILE Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 55 ILE Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain P residue 31 ASN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 47 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 127 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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** C 7 ASN D 77 ASN E 48 GLN F 77 ASN G 22 GLN ** G 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 85 ASN K 7 ASN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 ASN ** M 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 22 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.136140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.127115 restraints weight = 16224.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.130201 restraints weight = 8194.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.132146 restraints weight = 4629.864| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 1.0846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11297 Z= 0.125 Angle : 0.600 9.469 15168 Z= 0.315 Chirality : 0.042 0.198 1712 Planarity : 0.003 0.037 1920 Dihedral : 4.572 22.326 1424 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.32 % Allowed : 20.89 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.23), residues: 1328 helix: -0.17 (0.16), residues: 1136 sheet: None (None), residues: 0 loop : -1.12 (0.42), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 76 HIS 0.003 0.001 HIS H 56 PHE 0.032 0.002 PHE J 81 TYR 0.011 0.001 TYR L 78 ARG 0.006 0.000 ARG K 35 Details of bonding type rmsd hydrogen bonds : bond 0.02834 ( 560) hydrogen bonds : angle 3.67182 ( 1680) covalent geometry : bond 0.00302 (11296) covalent geometry : angle 0.60030 (15168) Misc. bond : bond 0.00035 ( 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 535 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 493 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ASP cc_start: 0.7286 (OUTLIER) cc_final: 0.7023 (m-30) REVERT: A 64 GLU cc_start: 0.6096 (mm-30) cc_final: 0.5840 (mm-30) REVERT: A 80 LEU cc_start: 0.9004 (tp) cc_final: 0.8671 (tp) REVERT: B 1 MET cc_start: 0.7265 (tpp) cc_final: 0.6747 (tpp) REVERT: B 22 GLN cc_start: 0.8998 (mt0) cc_final: 0.8097 (mt0) REVERT: C 21 LYS cc_start: 0.8891 (mttm) cc_final: 0.8302 (mtmt) REVERT: E 24 THR cc_start: 0.9283 (p) cc_final: 0.9065 (p) REVERT: E 27 LEU cc_start: 0.9293 (mm) cc_final: 0.9043 (mt) REVERT: E 45 LYS cc_start: 0.7688 (mtmt) cc_final: 0.7456 (mttp) REVERT: E 47 GLU cc_start: 0.7506 (pt0) cc_final: 0.7268 (pt0) REVERT: E 49 ASP cc_start: 0.8136 (m-30) cc_final: 0.7927 (m-30) REVERT: E 84 LEU cc_start: 0.8080 (tp) cc_final: 0.7876 (tp) REVERT: F 27 LEU cc_start: 0.9467 (mm) cc_final: 0.9072 (mt) REVERT: F 57 MET cc_start: 0.8325 (ttm) cc_final: 0.8073 (ttm) REVERT: H 1 MET cc_start: 0.8622 (tpp) cc_final: 0.8277 (tpp) REVERT: H 60 LYS cc_start: 0.8288 (mmtp) cc_final: 0.8056 (mmtm) REVERT: H 73 LEU cc_start: 0.9048 (tp) cc_final: 0.8742 (tt) REVERT: J 48 GLN cc_start: 0.8961 (mp10) cc_final: 0.8418 (mp10) REVERT: J 75 GLU cc_start: 0.7885 (tt0) cc_final: 0.7535 (tt0) REVERT: J 76 TRP cc_start: 0.8025 (m100) cc_final: 0.7800 (m100) REVERT: J 78 TYR cc_start: 0.8481 (t80) cc_final: 0.8146 (t80) REVERT: K 9 ARG cc_start: 0.8458 (ttp80) cc_final: 0.8135 (mtt-85) REVERT: K 26 ASP cc_start: 0.8545 (m-30) cc_final: 0.8341 (m-30) REVERT: K 35 ARG cc_start: 0.7109 (ttm110) cc_final: 0.6867 (mtm-85) REVERT: K 60 LYS cc_start: 0.5397 (tptt) cc_final: 0.5153 (tptm) REVERT: K 78 TYR cc_start: 0.8151 (t80) cc_final: 0.7635 (t80) REVERT: M 1 MET cc_start: 0.7956 (tpp) cc_final: 0.7329 (tpp) REVERT: M 2 ASN cc_start: 0.8031 (t0) cc_final: 0.7802 (t0) REVERT: M 20 ILE cc_start: 0.8961 (mm) cc_final: 0.8615 (mt) REVERT: M 69 PHE cc_start: 0.8781 (t80) cc_final: 0.8575 (t80) REVERT: M 78 TYR cc_start: 0.7704 (t80) cc_final: 0.7476 (t80) REVERT: N 59 LEU cc_start: 0.9255 (mt) cc_final: 0.9052 (mt) REVERT: O 3 PHE cc_start: 0.8054 (t80) cc_final: 0.7688 (t80) REVERT: P 2 ASN cc_start: 0.8322 (m-40) cc_final: 0.7809 (m-40) REVERT: P 36 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7708 (tm-30) REVERT: P 81 PHE cc_start: 0.8555 (t80) cc_final: 0.8286 (t80) outliers start: 42 outliers final: 24 residues processed: 510 average time/residue: 0.2485 time to fit residues: 179.0145 Evaluate side-chains 481 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 456 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain F residue 15 MET Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain G residue 15 MET Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain H residue 37 GLU Chi-restraints excluded: chain I residue 20 ILE Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 85 ASN Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain N residue 54 ILE Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 55 ILE Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain P residue 15 MET Chi-restraints excluded: chain P residue 18 THR Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 40 ILE Chi-restraints excluded: chain P residue 65 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 6 optimal weight: 0.8980 chunk 14 optimal weight: 9.9990 chunk 33 optimal weight: 0.0050 chunk 29 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 73 optimal weight: 0.3980 chunk 127 optimal weight: 0.8980 overall best weight: 0.5994 ------------------------------------------------------------------------------- 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** C 7 ASN D 48 GLN E 39 ASN E 77 ASN G 22 GLN ** J 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 7 ASN K 13 GLN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 ASN ** N 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 34 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 = 0.3481 r_free = 0.3481 target = 0.135431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.126298 restraints weight = 16319.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.129238 restraints weight = 8271.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.131247 restraints weight = 4858.413| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 1.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11297 Z= 0.118 Angle : 0.609 8.934 15168 Z= 0.318 Chirality : 0.042 0.167 1712 Planarity : 0.003 0.036 1920 Dihedral : 4.517 20.817 1424 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.29 % Allowed : 23.50 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.23), residues: 1328 helix: 0.03 (0.16), residues: 1136 sheet: None (None), residues: 0 loop : -1.20 (0.41), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP L 76 HIS 0.002 0.000 HIS I 56 PHE 0.036 0.002 PHE J 81 TYR 0.011 0.001 TYR A 78 ARG 0.005 0.000 ARG K 35 Details of bonding type rmsd hydrogen bonds : bond 0.02795 ( 560) hydrogen bonds : angle 3.64202 ( 1680) covalent geometry : bond 0.00278 (11296) covalent geometry : angle 0.60853 (15168) 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 513 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 484 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ASP cc_start: 0.7206 (OUTLIER) cc_final: 0.6965 (m-30) REVERT: A 64 GLU cc_start: 0.6204 (mm-30) cc_final: 0.5822 (mm-30) REVERT: B 1 MET cc_start: 0.7220 (tpp) cc_final: 0.6648 (tpp) REVERT: B 17 MET cc_start: 0.8824 (tpp) cc_final: 0.8604 (mmm) REVERT: C 21 LYS cc_start: 0.8684 (mttm) cc_final: 0.7905 (mtmt) REVERT: C 30 TRP cc_start: 0.8883 (m-10) cc_final: 0.8495 (m-10) REVERT: C 35 ARG cc_start: 0.7107 (ttm110) cc_final: 0.6666 (ptp-110) REVERT: E 17 MET cc_start: 0.9320 (tpt) cc_final: 0.9094 (tpp) REVERT: E 24 THR cc_start: 0.9248 (p) cc_final: 0.9035 (p) REVERT: E 27 LEU cc_start: 0.9336 (mm) cc_final: 0.9062 (mt) REVERT: F 27 LEU cc_start: 0.9457 (mm) cc_final: 0.9169 (mt) REVERT: H 1 MET cc_start: 0.8489 (tpp) cc_final: 0.8055 (tpp) REVERT: H 60 LYS cc_start: 0.8344 (mmtp) cc_final: 0.8071 (mmtm) REVERT: H 73 LEU cc_start: 0.8961 (tp) cc_final: 0.8689 (tt) REVERT: J 48 GLN cc_start: 0.8840 (mp10) cc_final: 0.8442 (mp-120) REVERT: J 78 TYR cc_start: 0.8526 (t80) cc_final: 0.8188 (t80) REVERT: K 9 ARG cc_start: 0.8463 (ttp80) cc_final: 0.8096 (mtt-85) REVERT: K 26 ASP cc_start: 0.8534 (m-30) cc_final: 0.8303 (m-30) REVERT: K 78 TYR cc_start: 0.8074 (t80) cc_final: 0.7494 (t80) REVERT: L 22 GLN cc_start: 0.9265 (mt0) cc_final: 0.8769 (mp10) REVERT: M 1 MET cc_start: 0.7848 (tpp) cc_final: 0.7162 (tpp) REVERT: M 69 PHE cc_start: 0.8743 (t80) cc_final: 0.8536 (t80) REVERT: M 78 TYR cc_start: 0.7681 (t80) cc_final: 0.7420 (t80) REVERT: N 59 LEU cc_start: 0.9316 (mt) cc_final: 0.9083 (mt) REVERT: O 3 PHE cc_start: 0.8060 (t80) cc_final: 0.7637 (t80) outliers start: 29 outliers final: 18 residues processed: 497 average time/residue: 0.2814 time to fit residues: 198.8086 Evaluate side-chains 478 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 459 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain F residue 15 MET Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain H residue 37 GLU Chi-restraints excluded: chain I residue 20 ILE Chi-restraints excluded: chain N residue 54 ILE Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 55 ILE Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 27 LEU Chi-restraints excluded: chain P residue 40 ILE Chi-restraints excluded: chain P residue 65 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 20 optimal weight: 5.9990 chunk 102 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 85 ASN ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 7 ASN I 22 GLN J 13 GLN J 85 ASN K 22 GLN ** K 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 34 ASN ** N 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 22 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.130079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.121130 restraints weight = 16306.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.124169 restraints weight = 8221.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.126110 restraints weight = 4655.534| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 1.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11297 Z= 0.154 Angle : 0.649 8.927 15168 Z= 0.342 Chirality : 0.044 0.174 1712 Planarity : 0.003 0.037 1920 Dihedral : 4.610 21.558 1424 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.01 % Allowed : 22.71 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.23), residues: 1328 helix: 0.05 (0.16), residues: 1136 sheet: None (None), residues: 0 loop : -1.39 (0.40), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP L 76 HIS 0.003 0.001 HIS F 56 PHE 0.027 0.002 PHE P 3 TYR 0.011 0.001 TYR A 78 ARG 0.005 0.001 ARG P 9 Details of bonding type rmsd hydrogen bonds : bond 0.03102 ( 560) hydrogen bonds : angle 3.85280 ( 1680) covalent geometry : bond 0.00383 (11296) covalent geometry : angle 0.64887 (15168) Misc. bond : bond 0.00076 ( 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 534 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 496 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.6262 (mm-30) cc_final: 0.5861 (mm-30) REVERT: B 1 MET cc_start: 0.7215 (tpp) cc_final: 0.6596 (tpp) REVERT: B 22 GLN cc_start: 0.8996 (mt0) cc_final: 0.8412 (mt0) REVERT: C 9 ARG cc_start: 0.8395 (tmm160) cc_final: 0.8178 (ttt-90) REVERT: C 21 LYS cc_start: 0.8626 (mttm) cc_final: 0.8175 (mtmt) REVERT: C 30 TRP cc_start: 0.8952 (m-10) cc_final: 0.8221 (m-10) REVERT: C 35 ARG cc_start: 0.7345 (ttm110) cc_final: 0.6593 (ptp-170) REVERT: D 1 MET cc_start: 0.7226 (tpp) cc_final: 0.7002 (tpp) REVERT: D 65 SER cc_start: 0.7966 (OUTLIER) cc_final: 0.7471 (m) REVERT: E 27 LEU cc_start: 0.9397 (mm) cc_final: 0.9072 (mt) REVERT: F 14 ARG cc_start: 0.8049 (mtm-85) cc_final: 0.5317 (mmt180) REVERT: G 1 MET cc_start: 0.7793 (tpt) cc_final: 0.6859 (tpp) REVERT: G 78 TYR cc_start: 0.8472 (t80) cc_final: 0.8259 (t80) REVERT: H 2 ASN cc_start: 0.8234 (t0) cc_final: 0.7995 (m-40) REVERT: H 60 LYS cc_start: 0.8653 (mmtp) cc_final: 0.8319 (mmtm) REVERT: H 73 LEU cc_start: 0.9016 (tp) cc_final: 0.8667 (tt) REVERT: I 81 PHE cc_start: 0.8972 (t80) cc_final: 0.8711 (t80) REVERT: J 37 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7852 (mt-10) REVERT: J 48 GLN cc_start: 0.9005 (mp10) cc_final: 0.8586 (mp10) REVERT: J 77 ASN cc_start: 0.9209 (t0) cc_final: 0.8767 (t0) REVERT: J 78 TYR cc_start: 0.8650 (t80) cc_final: 0.8353 (t80) REVERT: K 7 ASN cc_start: 0.8634 (m110) cc_final: 0.8398 (m-40) REVERT: K 9 ARG cc_start: 0.8466 (ttp80) cc_final: 0.8137 (mtt-85) REVERT: K 20 ILE cc_start: 0.9291 (mm) cc_final: 0.8995 (mm) REVERT: K 26 ASP cc_start: 0.8579 (m-30) cc_final: 0.8373 (m-30) REVERT: K 35 ARG cc_start: 0.8007 (mmm160) cc_final: 0.7790 (mmm160) REVERT: K 39 ASN cc_start: 0.8661 (m-40) cc_final: 0.8164 (m-40) REVERT: K 78 TYR cc_start: 0.8318 (t80) cc_final: 0.7644 (t80) REVERT: L 39 ASN cc_start: 0.8403 (m-40) cc_final: 0.8164 (m-40) REVERT: M 1 MET cc_start: 0.7964 (tpp) cc_final: 0.7653 (tpp) REVERT: M 78 TYR cc_start: 0.7880 (t80) cc_final: 0.7611 (t80) REVERT: O 3 PHE cc_start: 0.8167 (t80) cc_final: 0.7808 (t80) REVERT: O 8 SER cc_start: 0.9092 (m) cc_final: 0.8828 (m) REVERT: P 15 MET cc_start: 0.8062 (mtm) cc_final: 0.7586 (ttm) outliers start: 38 outliers final: 22 residues processed: 511 average time/residue: 0.3373 time to fit residues: 240.6875 Evaluate side-chains 493 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 470 time to evaluate : 2.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain G residue 15 MET Chi-restraints excluded: chain G residue 24 THR 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 20 ILE Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain N residue 54 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 19 VAL Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 40 ILE Chi-restraints excluded: chain P residue 65 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 71 optimal weight: 0.0270 chunk 89 optimal weight: 5.9990 chunk 70 optimal weight: 0.5980 chunk 90 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 chunk 80 optimal weight: 10.0000 chunk 124 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.6238 ------------------------------------------------------------------------------- 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** ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 7 ASN G 77 ASN H 7 ASN I 22 GLN ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 7 ASN K 22 GLN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.134404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.125805 restraints weight = 16247.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.128823 restraints weight = 8125.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.130711 restraints weight = 4568.860| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 1.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11297 Z= 0.124 Angle : 0.627 10.252 15168 Z= 0.330 Chirality : 0.042 0.177 1712 Planarity : 0.004 0.044 1920 Dihedral : 4.598 21.129 1424 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.06 % Allowed : 24.13 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.23), residues: 1328 helix: 0.08 (0.16), residues: 1136 sheet: None (None), residues: 0 loop : -1.56 (0.38), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP J 76 HIS 0.001 0.000 HIS O 56 PHE 0.031 0.002 PHE A 81 TYR 0.014 0.001 TYR B 78 ARG 0.010 0.000 ARG L 35 Details of bonding type rmsd hydrogen bonds : bond 0.02910 ( 560) hydrogen bonds : angle 3.85588 ( 1680) covalent geometry : bond 0.00290 (11296) covalent geometry : angle 0.62683 (15168) Misc. bond : bond 0.00033 ( 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 531 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 505 time to evaluate : 2.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ASN cc_start: 0.8154 (t0) cc_final: 0.7457 (p0) REVERT: A 64 GLU cc_start: 0.6177 (mm-30) cc_final: 0.5800 (mm-30) REVERT: B 1 MET cc_start: 0.7238 (tpp) cc_final: 0.6838 (tpp) REVERT: B 52 ARG cc_start: 0.8436 (ttm110) cc_final: 0.8090 (mtt90) REVERT: C 9 ARG cc_start: 0.8386 (tmm160) cc_final: 0.8124 (ttt-90) REVERT: C 21 LYS cc_start: 0.8543 (mttm) cc_final: 0.7950 (mtmt) REVERT: C 29 VAL cc_start: 0.9290 (t) cc_final: 0.9086 (m) REVERT: C 35 ARG cc_start: 0.7052 (ttm110) cc_final: 0.6509 (ptp-170) REVERT: D 1 MET cc_start: 0.7209 (tpp) cc_final: 0.6974 (tpp) REVERT: D 5 LYS cc_start: 0.8590 (tptm) cc_final: 0.8382 (tttm) REVERT: D 45 LYS cc_start: 0.7967 (mtmm) cc_final: 0.7491 (mtmt) REVERT: E 27 LEU cc_start: 0.9424 (mm) cc_final: 0.9167 (mt) REVERT: E 64 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7950 (tm-30) REVERT: F 14 ARG cc_start: 0.7801 (mtm-85) cc_final: 0.4957 (mmt180) REVERT: F 39 ASN cc_start: 0.7474 (m110) cc_final: 0.7120 (m-40) REVERT: G 36 GLU cc_start: 0.7961 (tp30) cc_final: 0.7743 (tp30) REVERT: G 78 TYR cc_start: 0.8439 (t80) cc_final: 0.8222 (t80) REVERT: H 2 ASN cc_start: 0.8249 (t0) cc_final: 0.7893 (m-40) REVERT: H 37 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7409 (mt-10) REVERT: H 60 LYS cc_start: 0.8604 (mmtp) cc_final: 0.8272 (mmtm) REVERT: H 73 LEU cc_start: 0.8878 (tp) cc_final: 0.8610 (tt) REVERT: I 75 GLU cc_start: 0.7660 (tt0) cc_final: 0.7201 (tt0) REVERT: I 85 ASN cc_start: 0.5985 (m-40) cc_final: 0.5503 (m-40) REVERT: J 13 GLN cc_start: 0.7928 (mm-40) cc_final: 0.7460 (mm-40) REVERT: J 48 GLN cc_start: 0.8960 (mp10) cc_final: 0.8466 (mp10) REVERT: J 78 TYR cc_start: 0.8602 (t80) cc_final: 0.8314 (t80) REVERT: K 9 ARG cc_start: 0.8439 (ttp80) cc_final: 0.8143 (mtt-85) REVERT: K 26 ASP cc_start: 0.8548 (m-30) cc_final: 0.8310 (m-30) REVERT: K 35 ARG cc_start: 0.7761 (mmm160) cc_final: 0.7458 (mmm160) REVERT: K 39 ASN cc_start: 0.8585 (m-40) cc_final: 0.8008 (m-40) REVERT: K 78 TYR cc_start: 0.8250 (t80) cc_final: 0.7697 (t80) REVERT: M 1 MET cc_start: 0.7663 (tpp) cc_final: 0.7329 (tpp) REVERT: M 43 CYS cc_start: 0.7925 (p) cc_final: 0.7342 (p) REVERT: M 78 TYR cc_start: 0.7851 (t80) cc_final: 0.7442 (t80) REVERT: N 22 GLN cc_start: 0.8024 (mt0) cc_final: 0.7728 (mt0) REVERT: O 3 PHE cc_start: 0.8302 (t80) cc_final: 0.7975 (t80) REVERT: O 8 SER cc_start: 0.8929 (m) cc_final: 0.8673 (m) REVERT: P 15 MET cc_start: 0.7972 (mtm) cc_final: 0.7612 (ttm) REVERT: P 81 PHE cc_start: 0.8459 (t80) cc_final: 0.8175 (t80) outliers start: 26 outliers final: 18 residues processed: 509 average time/residue: 0.3491 time to fit residues: 242.8758 Evaluate side-chains 501 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 482 time to evaluate : 2.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain E residue 4 ILE Chi-restraints excluded: chain G residue 15 MET Chi-restraints excluded: chain G residue 24 THR 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 H residue 19 VAL Chi-restraints excluded: chain H residue 37 GLU Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain J residue 76 TRP Chi-restraints excluded: chain N residue 54 ILE Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 55 ILE Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 24 THR 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 22 optimal weight: 0.0020 chunk 82 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 100 optimal weight: 0.5980 chunk 122 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 chunk 111 optimal weight: 1.9990 chunk 47 optimal weight: 0.0060 overall best weight: 0.7006 ------------------------------------------------------------------------------- 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 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 7 ASN ** J 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 85 ASN K 22 GLN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.134407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.125788 restraints weight = 16282.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.128765 restraints weight = 8105.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.130642 restraints weight = 4561.658| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 1.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11297 Z= 0.130 Angle : 0.645 8.401 15168 Z= 0.342 Chirality : 0.043 0.179 1712 Planarity : 0.004 0.037 1920 Dihedral : 4.605 20.758 1424 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.14 % Allowed : 25.08 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.23), residues: 1328 helix: 0.15 (0.16), residues: 1120 sheet: None (None), residues: 0 loop : -1.84 (0.34), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP J 76 HIS 0.001 0.000 HIS O 56 PHE 0.039 0.002 PHE J 81 TYR 0.010 0.001 TYR O 78 ARG 0.008 0.001 ARG L 35 Details of bonding type rmsd hydrogen bonds : bond 0.02928 ( 560) hydrogen bonds : angle 3.98819 ( 1680) covalent geometry : bond 0.00306 (11296) covalent geometry : angle 0.64527 (15168) Misc. bond : bond 0.00062 ( 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 521 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 494 time to evaluate : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 ASN cc_start: 0.8070 (t0) cc_final: 0.7433 (p0) REVERT: A 22 GLN cc_start: 0.8306 (mt0) cc_final: 0.8082 (mt0) REVERT: A 64 GLU cc_start: 0.6164 (mm-30) cc_final: 0.5762 (mm-30) REVERT: B 1 MET cc_start: 0.7115 (tpp) cc_final: 0.6751 (tpp) REVERT: B 76 TRP cc_start: 0.7777 (m100) cc_final: 0.7464 (m-90) REVERT: C 35 ARG cc_start: 0.7004 (ttm110) cc_final: 0.6437 (ptp-170) REVERT: C 81 PHE cc_start: 0.7327 (t80) cc_final: 0.7069 (t80) REVERT: D 1 MET cc_start: 0.7210 (tpp) cc_final: 0.6996 (tpp) REVERT: D 45 LYS cc_start: 0.7855 (mtmm) cc_final: 0.7468 (mtmt) REVERT: D 48 GLN cc_start: 0.7697 (mp10) cc_final: 0.7123 (mp10) REVERT: D 65 SER cc_start: 0.8044 (OUTLIER) cc_final: 0.7643 (m) REVERT: E 27 LEU cc_start: 0.9372 (mm) cc_final: 0.9009 (mt) REVERT: F 14 ARG cc_start: 0.7883 (mtm-85) cc_final: 0.5031 (mmt180) REVERT: F 39 ASN cc_start: 0.7051 (m110) cc_final: 0.6714 (m-40) REVERT: G 78 TYR cc_start: 0.8475 (t80) cc_final: 0.8260 (t80) REVERT: H 1 MET cc_start: 0.7920 (tpp) cc_final: 0.7526 (ttp) REVERT: H 2 ASN cc_start: 0.8284 (t0) cc_final: 0.7985 (m-40) REVERT: H 60 LYS cc_start: 0.8593 (mmtp) cc_final: 0.8152 (mmtm) REVERT: H 73 LEU cc_start: 0.8848 (tp) cc_final: 0.8603 (tt) REVERT: I 85 ASN cc_start: 0.6641 (m-40) cc_final: 0.6414 (m110) REVERT: J 13 GLN cc_start: 0.7773 (mm-40) cc_final: 0.7558 (mm-40) REVERT: J 38 VAL cc_start: 0.9227 (t) cc_final: 0.8989 (t) REVERT: J 48 GLN cc_start: 0.8978 (mp10) cc_final: 0.8592 (mp10) REVERT: J 78 TYR cc_start: 0.8516 (t80) cc_final: 0.8297 (t80) REVERT: K 9 ARG cc_start: 0.8456 (ttp80) cc_final: 0.8150 (mtt90) REVERT: K 26 ASP cc_start: 0.8494 (m-30) cc_final: 0.8194 (m-30) REVERT: K 35 ARG cc_start: 0.7848 (mmm160) cc_final: 0.7307 (mmm160) REVERT: K 39 ASN cc_start: 0.8632 (m-40) cc_final: 0.8276 (m-40) REVERT: K 78 TYR cc_start: 0.8294 (t80) cc_final: 0.7830 (t80) REVERT: L 26 ASP cc_start: 0.7660 (m-30) cc_final: 0.7160 (m-30) REVERT: M 78 TYR cc_start: 0.7851 (t80) cc_final: 0.7416 (t80) REVERT: O 8 SER cc_start: 0.9020 (m) cc_final: 0.8804 (m) REVERT: P 15 MET cc_start: 0.8212 (mtm) cc_final: 0.7836 (ttm) REVERT: P 81 PHE cc_start: 0.8428 (t80) cc_final: 0.8191 (t80) outliers start: 27 outliers final: 20 residues processed: 500 average time/residue: 0.2953 time to fit residues: 204.8359 Evaluate side-chains 499 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 478 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain F residue 57 MET Chi-restraints excluded: chain G residue 15 MET Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 24 THR 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 H residue 19 VAL Chi-restraints excluded: chain H residue 37 GLU Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain N residue 54 ILE Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 24 THR 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 44 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 68 optimal weight: 0.2980 chunk 99 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 97 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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** ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 77 ASN ** J 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 22 GLN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 39 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.134171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.125592 restraints weight = 16126.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.128560 restraints weight = 8020.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.130454 restraints weight = 4510.375| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 1.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11297 Z= 0.138 Angle : 0.656 8.628 15168 Z= 0.349 Chirality : 0.044 0.224 1712 Planarity : 0.004 0.037 1920 Dihedral : 4.648 24.157 1424 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.06 % Allowed : 26.34 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.23), residues: 1328 helix: 0.10 (0.16), residues: 1120 sheet: None (None), residues: 0 loop : -1.86 (0.34), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP J 76 HIS 0.001 0.000 HIS M 56 PHE 0.048 0.002 PHE E 81 TYR 0.021 0.001 TYR B 78 ARG 0.012 0.001 ARG A 52 Details of bonding type rmsd hydrogen bonds : bond 0.02968 ( 560) hydrogen bonds : angle 4.07235 ( 1680) covalent geometry : bond 0.00331 (11296) covalent geometry : angle 0.65609 (15168) Misc. bond : bond 0.00047 ( 1) =============================================================================== Job complete usr+sys time: 4512.31 seconds wall clock time: 85 minutes 20.01 seconds (5120.01 seconds total)