Starting phenix.real_space_refine on Fri Feb 14 19:30:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6n1i_8903/02_2025/6n1i_8903.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n1i_8903/02_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_8903/02_2025/6n1i_8903.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n1i_8903/02_2025/6n1i_8903.map" model { file = "/net/cci-nas-00/data/ceres_data/6n1i_8903/02_2025/6n1i_8903.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n1i_8903/02_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-5592/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: 3.22, per 1000 atoms: 0.29 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: 3.08 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: 1.16 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: 3.20 Time building geometry restraints manager: 3.42 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: 0.600 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: 0.000 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 23.550 Find NCS groups from input model: 0.220 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.880 ------------------------------------------------------------------------------- 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 0.072 11296 Z= 0.542 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 *********************** 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 : 1.333 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: 0.2419 time to fit residues: 164.9893 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 : 1.405 ------------------------------------------------------------------------------- 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 = 33)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.135327 restraints weight = 15778.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.138813 restraints weight = 7440.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.140914 restraints weight = 3996.992| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6528 moved from start: 0.4753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 11296 Z= 0.239 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 *********************** 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 : 1.357 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: 0.6183 (tpp) cc_final: 0.5833 (mmm) REVERT: D 1 MET cc_start: 0.7294 (tpp) cc_final: 0.7054 (tpt) REVERT: E 3 PHE cc_start: 0.7456 (t80) cc_final: 0.7131 (t80) REVERT: E 47 GLU cc_start: 0.7300 (pt0) cc_final: 0.6526 (pt0) REVERT: F 26 ASP cc_start: 0.7084 (m-30) cc_final: 0.6809 (m-30) REVERT: G 38 VAL cc_start: 0.7764 (t) cc_final: 0.7541 (t) REVERT: H 1 MET cc_start: 0.7663 (tpp) cc_final: 0.7355 (tpp) REVERT: H 6 ASP cc_start: 0.7275 (m-30) cc_final: 0.7068 (m-30) REVERT: I 2 ASN cc_start: 0.6690 (t0) cc_final: 0.6419 (p0) REVERT: J 1 MET cc_start: 0.6183 (tpt) cc_final: 0.5882 (tpt) REVERT: J 22 GLN cc_start: 0.7415 (mt0) cc_final: 0.7180 (mt0) REVERT: K 22 GLN cc_start: 0.7332 (tp40) cc_final: 0.6945 (mm-40) REVERT: K 47 GLU cc_start: 0.7710 (pt0) cc_final: 0.7418 (pt0) REVERT: L 20 ILE cc_start: 0.7312 (tt) cc_final: 0.6935 (tt) REVERT: M 36 GLU cc_start: 0.5640 (mp0) cc_final: 0.5122 (mp0) REVERT: M 49 ASP cc_start: 0.7321 (m-30) cc_final: 0.7058 (m-30) REVERT: O 85 ASN cc_start: 0.6903 (m-40) cc_final: 0.6694 (m110) REVERT: P 57 MET cc_start: 0.6655 (mmt) cc_final: 0.5952 (mtt) outliers start: 34 outliers final: 16 residues processed: 459 average time/residue: 0.2392 time to fit residues: 155.4078 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 : 1.318 ------------------------------------------------------------------------------- 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: 4.9990 chunk 99 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 chunk 76 optimal weight: 0.0040 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 ASN C 39 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 O 13 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.143888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.134569 restraints weight = 16122.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.137897 restraints weight = 7811.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.139945 restraints weight = 4274.507| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.6581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11296 Z= 0.188 Angle : 0.615 8.338 15168 Z= 0.322 Chirality : 0.040 0.161 1712 Planarity : 0.004 0.035 1920 Dihedral : 5.000 25.395 1424 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.09 % Allowed : 15.82 % Favored : 81.09 % 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: -2.04 (0.22), residues: 1328 helix: -1.17 (0.15), residues: 1136 sheet: None (None), residues: 0 loop : -1.11 (0.42), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP L 76 HIS 0.002 0.000 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 E 35 *********************** 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 493 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 454 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.6926 (m-30) cc_final: 0.6447 (m-30) REVERT: B 64 GLU cc_start: 0.8026 (pp20) cc_final: 0.7776 (tm-30) REVERT: C 21 LYS cc_start: 0.7895 (mttm) cc_final: 0.7618 (mtmt) REVERT: C 25 ASP cc_start: 0.7286 (t0) cc_final: 0.6997 (t0) REVERT: D 11 LEU cc_start: 0.8588 (mt) cc_final: 0.8230 (mt) REVERT: D 57 MET cc_start: 0.7379 (mpp) cc_final: 0.6688 (mtt) REVERT: E 34 ASN cc_start: 0.7282 (p0) cc_final: 0.6777 (p0) REVERT: H 1 MET cc_start: 0.8248 (tpp) cc_final: 0.8010 (tpp) REVERT: I 12 ILE cc_start: 0.9063 (pt) cc_final: 0.8667 (mt) REVERT: I 37 GLU cc_start: 0.7650 (mt-10) cc_final: 0.6814 (mt-10) REVERT: I 76 TRP cc_start: 0.5694 (m100) cc_final: 0.4881 (m100) REVERT: K 9 ARG cc_start: 0.8154 (ttp80) cc_final: 0.7621 (mtt-85) REVERT: K 22 GLN cc_start: 0.7853 (tp40) cc_final: 0.7516 (mm110) REVERT: K 47 GLU cc_start: 0.8224 (pt0) cc_final: 0.7850 (pt0) REVERT: K 64 GLU cc_start: 0.8392 (pp20) cc_final: 0.8155 (pp20) REVERT: L 36 GLU cc_start: 0.7439 (mm-30) cc_final: 0.6526 (mt-10) REVERT: L 39 ASN cc_start: 0.7176 (m110) cc_final: 0.6824 (m-40) REVERT: L 76 TRP cc_start: 0.6172 (OUTLIER) cc_final: 0.5234 (m100) REVERT: N 26 ASP cc_start: 0.8233 (t0) cc_final: 0.7896 (t0) REVERT: O 23 ILE cc_start: 0.8877 (mt) cc_final: 0.8516 (mt) REVERT: O 82 GLN cc_start: 0.5902 (OUTLIER) cc_final: 0.4882 (mt0) outliers start: 39 outliers final: 23 residues processed: 465 average time/residue: 0.2409 time to fit residues: 159.7128 Evaluate side-chains 444 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 419 time to evaluate : 1.326 ------------------------------------------------------------------------------- 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 20 ILE 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 40 ILE Chi-restraints excluded: chain I residue 43 CYS Chi-restraints excluded: chain K residue 58 ILE 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 55 ILE Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 82 GLN 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: 0.3980 chunk 58 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 92 optimal weight: 0.0970 chunk 86 optimal weight: 5.9990 chunk 111 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 13 GLN B 39 ASN E 48 GLN E 67 ASN 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 48 GLN O 39 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.144636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.135657 restraints weight = 16144.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.138888 restraints weight = 7700.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.140882 restraints weight = 4189.362| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.7730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11296 Z= 0.166 Angle : 0.573 6.471 15168 Z= 0.303 Chirality : 0.041 0.208 1712 Planarity : 0.003 0.035 1920 Dihedral : 4.711 23.333 1424 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.24 % Allowed : 17.64 % Favored : 79.11 % 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: -1.29 (0.23), residues: 1328 helix: -0.64 (0.16), residues: 1136 sheet: None (None), residues: 0 loop : -1.06 (0.41), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP M 76 HIS 0.003 0.001 HIS M 56 PHE 0.028 0.002 PHE B 81 TYR 0.011 0.001 TYR O 78 ARG 0.005 0.000 ARG A 35 *********************** 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 499 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 458 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.8469 (m-30) cc_final: 0.8220 (m-30) REVERT: B 26 ASP cc_start: 0.8082 (OUTLIER) cc_final: 0.7832 (m-30) REVERT: B 64 GLU cc_start: 0.8134 (pp20) cc_final: 0.7861 (tm-30) REVERT: C 21 LYS cc_start: 0.8359 (mttm) cc_final: 0.7940 (mtmt) REVERT: C 22 GLN cc_start: 0.7588 (OUTLIER) cc_final: 0.7223 (mt0) REVERT: C 30 TRP cc_start: 0.8342 (m-10) cc_final: 0.8018 (m-10) REVERT: E 1 MET cc_start: 0.6800 (tpp) cc_final: 0.6252 (tmm) REVERT: E 49 ASP cc_start: 0.7887 (m-30) cc_final: 0.7542 (m-30) REVERT: E 76 TRP cc_start: 0.7628 (m100) cc_final: 0.7358 (m100) REVERT: F 17 MET cc_start: 0.7862 (tpt) cc_final: 0.7519 (tpt) REVERT: G 36 GLU cc_start: 0.7714 (tp30) cc_final: 0.7509 (tp30) REVERT: G 39 ASN cc_start: 0.8762 (t0) cc_final: 0.8270 (t0) REVERT: H 1 MET cc_start: 0.8591 (tpp) cc_final: 0.8150 (tpp) REVERT: H 3 PHE cc_start: 0.8129 (t80) cc_final: 0.7814 (t80) REVERT: I 12 ILE cc_start: 0.9175 (pt) cc_final: 0.8918 (mt) REVERT: I 76 TRP cc_start: 0.5834 (m100) cc_final: 0.5294 (m100) REVERT: J 37 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7712 (mt-10) REVERT: K 9 ARG cc_start: 0.8203 (ttp80) cc_final: 0.7754 (mtt-85) REVERT: K 47 GLU cc_start: 0.8185 (pt0) cc_final: 0.7849 (pt0) REVERT: K 49 ASP cc_start: 0.8468 (t0) cc_final: 0.8222 (t0) REVERT: L 26 ASP cc_start: 0.7511 (m-30) cc_final: 0.6953 (m-30) REVERT: L 39 ASN cc_start: 0.7595 (m110) cc_final: 0.7021 (m-40) REVERT: L 76 TRP cc_start: 0.5959 (m-10) cc_final: 0.5475 (m-10) REVERT: O 23 ILE cc_start: 0.9077 (mt) cc_final: 0.8786 (mp) REVERT: O 44 GLU cc_start: 0.6986 (mt-10) cc_final: 0.6148 (mt-10) REVERT: O 49 ASP cc_start: 0.7945 (t0) cc_final: 0.7475 (t0) REVERT: O 82 GLN cc_start: 0.5925 (OUTLIER) cc_final: 0.4837 (mt0) REVERT: P 81 PHE cc_start: 0.8200 (t80) cc_final: 0.7943 (t80) outliers start: 41 outliers final: 21 residues processed: 474 average time/residue: 0.2293 time to fit residues: 154.0317 Evaluate side-chains 453 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 429 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 27 LEU Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain E residue 73 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 24 THR Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 76 TRP Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain N residue 58 ILE 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 80 LEU Chi-restraints excluded: chain O residue 82 GLN 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: 1.9990 chunk 106 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 98 optimal weight: 0.6980 chunk 102 optimal weight: 9.9990 chunk 127 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 26 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 ASN F 13 GLN ** J 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 22 GLN ** M 34 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 = 0.3567 r_free = 0.3567 target = 0.142582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.133481 restraints weight = 16026.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.136725 restraints weight = 7685.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.138685 restraints weight = 4206.735| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.8871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11296 Z= 0.182 Angle : 0.576 9.924 15168 Z= 0.303 Chirality : 0.041 0.162 1712 Planarity : 0.003 0.035 1920 Dihedral : 4.536 22.700 1424 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.88 % Allowed : 19.22 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.87 (0.23), residues: 1328 helix: -0.33 (0.16), residues: 1136 sheet: None (None), residues: 0 loop : -1.08 (0.41), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP M 76 HIS 0.004 0.001 HIS M 56 PHE 0.026 0.002 PHE B 81 TYR 0.017 0.001 TYR A 78 ARG 0.005 0.000 ARG N 52 *********************** 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 535 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 486 time to evaluate : 1.296 Fit side-chains revert: symmetry clash REVERT: A 15 MET cc_start: 0.8208 (mtp) cc_final: 0.7904 (mmm) REVERT: A 35 ARG cc_start: 0.7138 (mtm110) cc_final: 0.6937 (mtm110) REVERT: C 21 LYS cc_start: 0.8620 (mttm) cc_final: 0.8278 (mtmt) REVERT: C 30 TRP cc_start: 0.8483 (m-10) cc_final: 0.7854 (m-10) REVERT: E 49 ASP cc_start: 0.8047 (m-30) cc_final: 0.7722 (m-30) REVERT: F 27 LEU cc_start: 0.9128 (mm) cc_final: 0.8581 (mt) REVERT: G 39 ASN cc_start: 0.8898 (t0) cc_final: 0.8573 (t0) REVERT: H 1 MET cc_start: 0.8564 (tpp) cc_final: 0.8094 (tpp) REVERT: H 3 PHE cc_start: 0.8364 (t80) cc_final: 0.8091 (t80) REVERT: H 45 LYS cc_start: 0.7811 (mtmm) cc_final: 0.7543 (mtpp) REVERT: I 37 GLU cc_start: 0.8477 (tt0) cc_final: 0.8143 (tt0) REVERT: J 1 MET cc_start: 0.7370 (tpp) cc_final: 0.7113 (tpp) REVERT: K 9 ARG cc_start: 0.8206 (ttp80) cc_final: 0.7872 (mtt-85) REVERT: L 26 ASP cc_start: 0.7658 (m-30) cc_final: 0.7349 (m-30) REVERT: L 36 GLU cc_start: 0.7493 (tp30) cc_final: 0.7277 (mt-10) REVERT: L 39 ASN cc_start: 0.7852 (m110) cc_final: 0.7557 (m-40) REVERT: L 76 TRP cc_start: 0.6476 (OUTLIER) cc_final: 0.5948 (m-10) REVERT: M 1 MET cc_start: 0.7674 (tpp) cc_final: 0.7235 (tpp) REVERT: O 23 ILE cc_start: 0.9282 (mt) cc_final: 0.8848 (mp) REVERT: O 44 GLU cc_start: 0.7229 (mt-10) cc_final: 0.6954 (mt-10) REVERT: P 1 MET cc_start: 0.6828 (tpt) cc_final: 0.6542 (tpt) outliers start: 49 outliers final: 25 residues processed: 499 average time/residue: 0.2242 time to fit residues: 158.3734 Evaluate side-chains 472 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 446 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 76 TRP Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain L residue 76 TRP Chi-restraints excluded: chain M residue 54 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 58 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: 0.6980 chunk 56 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 127 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 87 optimal weight: 0.6980 chunk 44 optimal weight: 6.9990 chunk 97 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 31 ASN A 82 GLN E 48 GLN F 48 GLN G 39 ASN J 13 GLN K 22 GLN L 13 GLN L 67 ASN ** N 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.134266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.126088 restraints weight = 16376.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.128958 restraints weight = 8147.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.130746 restraints weight = 4559.468| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 1.0411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11296 Z= 0.241 Angle : 0.646 10.396 15168 Z= 0.337 Chirality : 0.043 0.264 1712 Planarity : 0.004 0.036 1920 Dihedral : 4.619 23.106 1424 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.64 % Allowed : 19.46 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.72 (0.23), residues: 1328 helix: -0.22 (0.16), residues: 1136 sheet: None (None), residues: 0 loop : -1.14 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 76 HIS 0.004 0.001 HIS P 56 PHE 0.026 0.002 PHE M 69 TYR 0.017 0.002 TYR A 78 ARG 0.006 0.001 ARG M 35 *********************** 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 558 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 512 time to evaluate : 1.399 Fit side-chains REVERT: A 64 GLU cc_start: 0.6104 (mm-30) cc_final: 0.5802 (mm-30) REVERT: B 1 MET cc_start: 0.7170 (tpp) cc_final: 0.6931 (tpp) REVERT: B 20 ILE cc_start: 0.9258 (mm) cc_final: 0.8979 (mm) REVERT: B 44 GLU cc_start: 0.7337 (mt-10) cc_final: 0.7119 (mt-10) REVERT: C 8 SER cc_start: 0.9377 (t) cc_final: 0.9081 (m) REVERT: C 15 MET cc_start: 0.8369 (ttp) cc_final: 0.8148 (ttm) REVERT: C 21 LYS cc_start: 0.8944 (mttm) cc_final: 0.8309 (mtmt) REVERT: C 22 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7958 (mt0) REVERT: E 24 THR cc_start: 0.9224 (p) cc_final: 0.9016 (p) REVERT: E 49 ASP cc_start: 0.8204 (m-30) cc_final: 0.7808 (m-30) REVERT: E 84 LEU cc_start: 0.8382 (tp) cc_final: 0.8153 (tp) REVERT: F 14 ARG cc_start: 0.7294 (mtm-85) cc_final: 0.4813 (mmt180) REVERT: F 22 GLN cc_start: 0.8138 (mt0) cc_final: 0.7516 (mt0) REVERT: F 23 ILE cc_start: 0.9452 (mt) cc_final: 0.9222 (mp) REVERT: F 57 MET cc_start: 0.8478 (ttm) cc_final: 0.8110 (ttm) REVERT: G 5 LYS cc_start: 0.8291 (tptp) cc_final: 0.8030 (tmtt) REVERT: G 38 VAL cc_start: 0.8979 (t) cc_final: 0.8774 (m) REVERT: H 3 PHE cc_start: 0.8448 (t80) cc_final: 0.8205 (t80) REVERT: H 37 GLU cc_start: 0.7503 (mt-10) cc_final: 0.7115 (tt0) REVERT: H 38 VAL cc_start: 0.9097 (t) cc_final: 0.8857 (m) REVERT: H 60 LYS cc_start: 0.8288 (mmtp) cc_final: 0.7949 (mmtm) REVERT: I 37 GLU cc_start: 0.8385 (mt-10) cc_final: 0.7849 (tt0) REVERT: J 1 MET cc_start: 0.7462 (tpp) cc_final: 0.7166 (tpp) REVERT: J 48 GLN cc_start: 0.8804 (mp10) cc_final: 0.8267 (mp-120) REVERT: J 75 GLU cc_start: 0.8088 (tt0) cc_final: 0.7860 (tt0) REVERT: K 9 ARG cc_start: 0.8367 (ttp80) cc_final: 0.8039 (mtt-85) REVERT: K 64 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8447 (tm-30) REVERT: L 39 ASN cc_start: 0.8057 (m110) cc_final: 0.7606 (m-40) REVERT: M 1 MET cc_start: 0.7896 (tpp) cc_final: 0.7184 (tpp) REVERT: O 3 PHE cc_start: 0.8052 (t80) cc_final: 0.7632 (t80) REVERT: P 2 ASN cc_start: 0.8168 (m-40) cc_final: 0.7653 (m-40) REVERT: P 11 LEU cc_start: 0.8782 (mt) cc_final: 0.8504 (mt) REVERT: P 36 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7698 (tm-30) REVERT: P 81 PHE cc_start: 0.8558 (t80) cc_final: 0.8315 (t80) outliers start: 46 outliers final: 21 residues processed: 533 average time/residue: 0.2304 time to fit residues: 176.4205 Evaluate side-chains 487 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 464 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain C residue 22 GLN Chi-restraints excluded: chain C residue 46 VAL 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 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 63 SER Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 76 TRP Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 64 GLU 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 80 LEU 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: 4.9990 chunk 14 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN B 22 GLN ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 HIS C 7 ASN E 39 ASN G 22 GLN H 85 ASN ** J 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 13 GLN K 22 GLN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 ASN ** N 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 22 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.132269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.123639 restraints weight = 16328.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.126660 restraints weight = 8118.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.128523 restraints weight = 4541.064| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 1.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11296 Z= 0.230 Angle : 0.628 9.761 15168 Z= 0.332 Chirality : 0.043 0.169 1712 Planarity : 0.004 0.049 1920 Dihedral : 4.588 21.522 1424 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.40 % Allowed : 21.12 % Favored : 75.47 % 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: -0.58 (0.23), residues: 1328 helix: -0.08 (0.16), residues: 1136 sheet: None (None), residues: 0 loop : -1.36 (0.41), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 76 HIS 0.003 0.001 HIS M 56 PHE 0.027 0.002 PHE M 69 TYR 0.014 0.002 TYR B 78 ARG 0.006 0.001 ARG K 35 *********************** 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 536 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 493 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.6249 (mm-30) cc_final: 0.5832 (mm-30) REVERT: B 1 MET cc_start: 0.7114 (tpp) cc_final: 0.6869 (tpp) REVERT: C 8 SER cc_start: 0.9471 (t) cc_final: 0.9197 (m) REVERT: C 15 MET cc_start: 0.8505 (ttp) cc_final: 0.8303 (ttm) REVERT: C 21 LYS cc_start: 0.8825 (mttm) cc_final: 0.7874 (mtmt) REVERT: C 30 TRP cc_start: 0.8909 (m-10) cc_final: 0.8464 (m-10) REVERT: D 37 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8186 (mt-10) REVERT: D 76 TRP cc_start: 0.8255 (m100) cc_final: 0.8042 (m100) REVERT: E 24 THR cc_start: 0.9294 (p) cc_final: 0.9084 (p) REVERT: E 49 ASP cc_start: 0.8056 (m-30) cc_final: 0.7851 (m-30) REVERT: E 75 GLU cc_start: 0.8275 (tp30) cc_final: 0.8073 (tp30) REVERT: F 14 ARG cc_start: 0.7731 (mtm-85) cc_final: 0.5126 (mmt180) REVERT: F 22 GLN cc_start: 0.8277 (mt0) cc_final: 0.8074 (mt0) REVERT: F 23 ILE cc_start: 0.9427 (mt) cc_final: 0.9122 (mp) REVERT: F 34 ASN cc_start: 0.8548 (p0) cc_final: 0.8255 (p0) REVERT: F 39 ASN cc_start: 0.7836 (m-40) cc_final: 0.7382 (m-40) REVERT: F 57 MET cc_start: 0.8473 (ttm) cc_final: 0.8043 (ttm) REVERT: H 38 VAL cc_start: 0.9195 (t) cc_final: 0.8919 (m) REVERT: H 60 LYS cc_start: 0.8551 (mmtp) cc_final: 0.8215 (mmtm) REVERT: H 63 SER cc_start: 0.8239 (OUTLIER) cc_final: 0.8025 (p) REVERT: J 48 GLN cc_start: 0.8863 (mp10) cc_final: 0.8341 (mp-120) REVERT: K 9 ARG cc_start: 0.8477 (ttp80) cc_final: 0.8036 (mtt-85) REVERT: K 78 TYR cc_start: 0.8219 (t80) cc_final: 0.7498 (t80) REVERT: L 30 TRP cc_start: 0.8703 (m-10) cc_final: 0.8487 (m-10) REVERT: L 39 ASN cc_start: 0.8067 (m110) cc_final: 0.7644 (m-40) REVERT: M 9 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.6940 (ttp80) REVERT: M 78 TYR cc_start: 0.7876 (t80) cc_final: 0.7421 (t80) REVERT: O 3 PHE cc_start: 0.8075 (t80) cc_final: 0.7741 (t80) REVERT: P 1 MET cc_start: 0.7775 (tpt) cc_final: 0.7425 (tpt) REVERT: P 81 PHE cc_start: 0.8626 (t80) cc_final: 0.8411 (t80) outliers start: 43 outliers final: 22 residues processed: 512 average time/residue: 0.2380 time to fit residues: 173.4377 Evaluate side-chains 488 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 464 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 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 46 VAL 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 63 SER Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain M residue 9 ARG 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 32 VAL 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: 0.9990 chunk 102 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 96 optimal weight: 10.0000 chunk 119 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 123 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 ASN G 22 GLN ** J 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 85 ASN K 7 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.132469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.123854 restraints weight = 16340.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.126857 restraints weight = 8080.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.128750 restraints weight = 4514.186| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 1.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11296 Z= 0.198 Angle : 0.625 10.408 15168 Z= 0.327 Chirality : 0.042 0.165 1712 Planarity : 0.004 0.044 1920 Dihedral : 4.573 21.861 1424 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.06 % Allowed : 23.02 % Favored : 74.92 % 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: -0.46 (0.23), residues: 1328 helix: 0.01 (0.16), residues: 1136 sheet: None (None), residues: 0 loop : -1.41 (0.40), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP L 76 HIS 0.002 0.001 HIS F 56 PHE 0.033 0.002 PHE A 81 TYR 0.011 0.001 TYR A 78 ARG 0.009 0.000 ARG A 9 *********************** 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 523 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 497 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.6275 (mm-30) cc_final: 0.5891 (mm-30) REVERT: B 1 MET cc_start: 0.7158 (tpp) cc_final: 0.6642 (tpp) REVERT: B 84 LEU cc_start: 0.8812 (mt) cc_final: 0.8559 (mt) REVERT: C 8 SER cc_start: 0.9477 (t) cc_final: 0.9201 (m) REVERT: C 15 MET cc_start: 0.8574 (ttp) cc_final: 0.8249 (ttm) REVERT: C 21 LYS cc_start: 0.8642 (mttm) cc_final: 0.8175 (mtmt) REVERT: C 30 TRP cc_start: 0.8868 (m-10) cc_final: 0.8141 (m-10) REVERT: D 1 MET cc_start: 0.6921 (tpp) cc_final: 0.6679 (tpp) REVERT: F 14 ARG cc_start: 0.7622 (mtm-85) cc_final: 0.4996 (mmt180) REVERT: F 57 MET cc_start: 0.8300 (ttm) cc_final: 0.7950 (ttm) REVERT: G 2 ASN cc_start: 0.8050 (m110) cc_final: 0.7797 (t0) REVERT: H 38 VAL cc_start: 0.9281 (t) cc_final: 0.9000 (m) REVERT: H 60 LYS cc_start: 0.8571 (mmtp) cc_final: 0.8256 (mmtm) REVERT: H 73 LEU cc_start: 0.9020 (tp) cc_final: 0.8733 (tt) REVERT: K 9 ARG cc_start: 0.8459 (ttp80) cc_final: 0.8046 (mtt-85) REVERT: K 39 ASN cc_start: 0.8479 (m-40) cc_final: 0.7961 (m-40) REVERT: K 78 TYR cc_start: 0.8215 (t80) cc_final: 0.7585 (t80) REVERT: L 26 ASP cc_start: 0.7784 (m-30) cc_final: 0.7467 (m-30) REVERT: L 39 ASN cc_start: 0.8021 (m110) cc_final: 0.7559 (m-40) REVERT: M 1 MET cc_start: 0.7961 (tpp) cc_final: 0.7619 (tpp) REVERT: M 78 TYR cc_start: 0.7803 (t80) cc_final: 0.7380 (t80) outliers start: 26 outliers final: 21 residues processed: 505 average time/residue: 0.2501 time to fit residues: 176.5250 Evaluate side-chains 495 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 474 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain F residue 54 ILE 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 I residue 58 ILE Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 85 ASN Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain L residue 4 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 32 VAL 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: 0.7980 chunk 89 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 80 optimal weight: 10.0000 chunk 124 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 85 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 GLN E 77 ASN F 7 ASN ** J 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.130780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.122189 restraints weight = 16275.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.125169 restraints weight = 8113.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.127085 restraints weight = 4551.318| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 1.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11296 Z= 0.217 Angle : 0.644 10.167 15168 Z= 0.339 Chirality : 0.043 0.168 1712 Planarity : 0.004 0.048 1920 Dihedral : 4.620 21.863 1424 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.69 % Allowed : 23.10 % 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: -0.20 (0.23), residues: 1328 helix: 0.38 (0.17), residues: 1040 sheet: None (None), residues: 0 loop : -1.75 (0.31), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP L 76 HIS 0.002 0.001 HIS A 56 PHE 0.035 0.002 PHE A 81 TYR 0.015 0.001 TYR J 78 ARG 0.008 0.001 ARG P 9 *********************** 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 522 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 488 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.8301 (mt-10) cc_final: 0.8096 (mt-10) REVERT: A 64 GLU cc_start: 0.6223 (mm-30) cc_final: 0.5871 (mm-30) REVERT: A 84 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8346 (mt) REVERT: B 1 MET cc_start: 0.7138 (tpp) cc_final: 0.6803 (tpp) REVERT: C 15 MET cc_start: 0.8657 (ttp) cc_final: 0.8422 (ttm) REVERT: C 21 LYS cc_start: 0.8619 (mttm) cc_final: 0.8141 (mtmt) REVERT: D 65 SER cc_start: 0.7979 (OUTLIER) cc_final: 0.7497 (m) REVERT: E 41 ILE cc_start: 0.8985 (mt) cc_final: 0.8713 (mp) REVERT: F 14 ARG cc_start: 0.7903 (mtm-85) cc_final: 0.5315 (tpt170) REVERT: F 57 MET cc_start: 0.8196 (ttm) cc_final: 0.7907 (ttm) REVERT: G 2 ASN cc_start: 0.8325 (m110) cc_final: 0.8070 (m110) REVERT: H 1 MET cc_start: 0.7992 (tpp) cc_final: 0.7521 (ttp) REVERT: H 38 VAL cc_start: 0.9322 (t) cc_final: 0.9044 (m) REVERT: H 60 LYS cc_start: 0.8665 (mmtp) cc_final: 0.8236 (mmtm) REVERT: H 73 LEU cc_start: 0.9018 (tp) cc_final: 0.8739 (tt) REVERT: K 9 ARG cc_start: 0.8417 (ttp80) cc_final: 0.8063 (mtt-85) REVERT: K 78 TYR cc_start: 0.8217 (t80) cc_final: 0.7618 (t80) REVERT: L 26 ASP cc_start: 0.7940 (m-30) cc_final: 0.7581 (m-30) REVERT: L 39 ASN cc_start: 0.8010 (m110) cc_final: 0.7596 (m-40) REVERT: M 1 MET cc_start: 0.8118 (tpp) cc_final: 0.7840 (tpp) REVERT: M 9 ARG cc_start: 0.8299 (mmm-85) cc_final: 0.7948 (mtp85) REVERT: M 78 TYR cc_start: 0.7829 (t80) cc_final: 0.7509 (t80) REVERT: P 5 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8526 (tmtt) outliers start: 34 outliers final: 25 residues processed: 502 average time/residue: 0.2422 time to fit residues: 169.2756 Evaluate side-chains 491 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 463 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 37 GLU Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 76 TRP Chi-restraints excluded: chain K residue 20 ILE Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain O residue 38 VAL 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 5 LYS Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 40 ILE Chi-restraints excluded: chain P residue 65 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 22 optimal weight: 0.0870 chunk 82 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 111 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 ASN F 7 ASN ** J 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 85 ASN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 39 ASN P 39 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.132310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.123714 restraints weight = 16314.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.126756 restraints weight = 8067.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.128654 restraints weight = 4506.611| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 1.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11296 Z= 0.190 Angle : 0.639 10.645 15168 Z= 0.337 Chirality : 0.042 0.176 1712 Planarity : 0.004 0.081 1920 Dihedral : 4.603 21.809 1424 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.22 % Allowed : 24.53 % Favored : 73.26 % 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: -0.17 (0.23), residues: 1328 helix: 0.43 (0.17), residues: 1040 sheet: None (None), residues: 0 loop : -1.84 (0.30), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP L 76 HIS 0.002 0.000 HIS A 56 PHE 0.038 0.002 PHE J 81 TYR 0.010 0.001 TYR A 78 ARG 0.009 0.001 ARG K 35 ********************** 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 524 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 496 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.6131 (mm-30) cc_final: 0.5773 (mm-30) REVERT: B 1 MET cc_start: 0.7096 (tpp) cc_final: 0.6861 (tpp) REVERT: B 22 GLN cc_start: 0.8968 (mt0) cc_final: 0.8581 (mp10) REVERT: C 8 SER cc_start: 0.9511 (t) cc_final: 0.9248 (m) REVERT: C 9 ARG cc_start: 0.8373 (tmm160) cc_final: 0.8050 (ttt-90) REVERT: C 15 MET cc_start: 0.8620 (ttp) cc_final: 0.8387 (ttm) REVERT: C 21 LYS cc_start: 0.8560 (mttm) cc_final: 0.8118 (mtmt) REVERT: D 1 MET cc_start: 0.7256 (tpp) cc_final: 0.6919 (tpp) REVERT: D 65 SER cc_start: 0.8060 (OUTLIER) cc_final: 0.7604 (m) REVERT: F 1 MET cc_start: 0.6981 (mmm) cc_final: 0.6777 (mtt) REVERT: F 14 ARG cc_start: 0.7812 (mtm-85) cc_final: 0.5369 (tpt170) REVERT: G 2 ASN cc_start: 0.8245 (m110) cc_final: 0.7886 (t0) REVERT: G 36 GLU cc_start: 0.7932 (tp30) cc_final: 0.7721 (tp30) REVERT: H 1 MET cc_start: 0.7835 (tpp) cc_final: 0.7444 (ttp) REVERT: H 15 MET cc_start: 0.7164 (ptp) cc_final: 0.6836 (mtp) REVERT: H 38 VAL cc_start: 0.9332 (t) cc_final: 0.9073 (m) REVERT: H 60 LYS cc_start: 0.8608 (mmtp) cc_final: 0.8220 (mmtm) REVERT: H 73 LEU cc_start: 0.8884 (tp) cc_final: 0.8636 (tt) REVERT: J 57 MET cc_start: 0.7916 (mtm) cc_final: 0.7585 (mtm) REVERT: K 9 ARG cc_start: 0.8434 (ttp80) cc_final: 0.8076 (mtt-85) REVERT: K 55 ILE cc_start: 0.9216 (mm) cc_final: 0.8970 (mt) REVERT: K 78 TYR cc_start: 0.8115 (t80) cc_final: 0.7670 (t80) REVERT: L 39 ASN cc_start: 0.8025 (m110) cc_final: 0.7545 (m-40) REVERT: M 1 MET cc_start: 0.7866 (tpp) cc_final: 0.7591 (tpp) REVERT: M 78 TYR cc_start: 0.7871 (t80) cc_final: 0.7533 (t80) REVERT: N 27 LEU cc_start: 0.9374 (mm) cc_final: 0.9126 (mt) REVERT: P 2 ASN cc_start: 0.8004 (m-40) cc_final: 0.7785 (m110) outliers start: 28 outliers final: 22 residues processed: 506 average time/residue: 0.2435 time to fit residues: 171.5267 Evaluate side-chains 500 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 477 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 37 GLU Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 76 TRP Chi-restraints excluded: chain J residue 85 ASN Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain O residue 46 VAL 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 24 THR Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 40 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 44 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 17 optimal weight: 0.2980 chunk 68 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 96 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 8 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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** D 22 GLN ** J 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 22 GLN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 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 = 0.3437 r_free = 0.3437 target = 0.131690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.123213 restraints weight = 16149.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.126174 restraints weight = 8006.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.128044 restraints weight = 4462.229| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 1.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11296 Z= 0.212 Angle : 0.661 10.352 15168 Z= 0.349 Chirality : 0.043 0.301 1712 Planarity : 0.004 0.057 1920 Dihedral : 4.637 21.325 1424 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.45 % Allowed : 25.87 % Favored : 71.68 % 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: -0.47 (0.23), residues: 1328 helix: 0.04 (0.16), residues: 1136 sheet: None (None), residues: 0 loop : -1.70 (0.37), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP L 76 HIS 0.002 0.001 HIS N 56 PHE 0.044 0.003 PHE J 81 TYR 0.034 0.002 TYR J 78 ARG 0.011 0.001 ARG K 35 =============================================================================== Job complete usr+sys time: 3597.12 seconds wall clock time: 65 minutes 18.82 seconds (3918.82 seconds total)