Starting phenix.real_space_refine on Wed Sep 25 14:53:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n1i_8903/09_2024/6n1i_8903.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n1i_8903/09_2024/6n1i_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n1i_8903/09_2024/6n1i_8903.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n1i_8903/09_2024/6n1i_8903.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n1i_8903/09_2024/6n1i_8903.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n1i_8903/09_2024/6n1i_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-5461/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: 3.10, per 1000 atoms: 0.28 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=0, symmetry=0 Time building additional restraints: 2.69 Conformation dependent library (CDL) restraints added in 1.2 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: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 1 through 7 removed outlier: 3.592A pdb=" N LYS A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 7 through 12 Processing helix chain 'A' and resid 16 through 30 removed outlier: 4.153A pdb=" N GLN A 22 " --> pdb=" O THR A 18 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP A 25 " --> pdb=" O LYS A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 43 removed outlier: 3.898A pdb=" N ILE A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS A 43 " --> pdb=" O ASN A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 59 removed outlier: 3.511A pdb=" N ILE A 55 " --> pdb=" O ALA A 51 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET A 57 " --> pdb=" O GLY A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.832A pdb=" N ASN A 67 " --> pdb=" O SER A 63 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU A 68 " --> pdb=" O GLU A 64 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE A 69 " --> pdb=" O SER A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 85 removed outlier: 3.662A pdb=" N PHE A 81 " --> pdb=" O ASN A 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 7 Processing helix chain 'B' and resid 7 through 12 Processing helix chain 'B' and resid 16 through 30 removed outlier: 4.153A pdb=" N GLN B 22 " --> pdb=" O THR B 18 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP B 25 " --> pdb=" O LYS B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 43 removed outlier: 3.897A pdb=" N ILE B 41 " --> pdb=" O GLU B 37 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS B 43 " --> pdb=" O ASN B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 59 removed outlier: 3.510A pdb=" N ILE B 55 " --> pdb=" O ALA B 51 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET B 57 " --> pdb=" O GLY B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 76 removed outlier: 3.833A pdb=" N ASN B 67 " --> pdb=" O SER B 63 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU B 68 " --> pdb=" O GLU B 64 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N PHE B 69 " --> pdb=" O SER B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 85 removed outlier: 3.662A pdb=" N PHE B 81 " --> pdb=" O ASN B 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 7 Processing helix chain 'C' and resid 7 through 12 Processing helix chain 'C' and resid 16 through 30 removed outlier: 4.153A pdb=" N GLN C 22 " --> pdb=" O THR C 18 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP C 25 " --> pdb=" O LYS C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 43 removed outlier: 3.897A pdb=" N ILE C 41 " --> pdb=" O GLU C 37 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS C 43 " --> pdb=" O ASN C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 59 removed outlier: 3.510A pdb=" N ILE C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET C 57 " --> pdb=" O GLY C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 76 removed outlier: 3.833A pdb=" N ASN C 67 " --> pdb=" O SER C 63 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU C 68 " --> pdb=" O GLU C 64 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE C 69 " --> pdb=" O SER C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 85 removed outlier: 3.662A pdb=" N PHE C 81 " --> pdb=" O ASN C 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 7 Processing helix chain 'D' and resid 7 through 12 Processing helix chain 'D' and resid 16 through 30 removed outlier: 4.153A pdb=" N GLN D 22 " --> pdb=" O THR D 18 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP D 25 " --> pdb=" O LYS D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 43 removed outlier: 3.897A pdb=" N ILE D 41 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS D 43 " --> pdb=" O ASN D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 59 removed outlier: 3.510A pdb=" N ILE D 55 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET D 57 " --> pdb=" O GLY D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 76 removed outlier: 3.833A pdb=" N ASN D 67 " --> pdb=" O SER D 63 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU D 68 " --> pdb=" O GLU D 64 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE D 69 " --> pdb=" O SER D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 85 removed outlier: 3.662A pdb=" N PHE D 81 " --> pdb=" O ASN D 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 7 Processing helix chain 'E' and resid 7 through 12 Processing helix chain 'E' and resid 16 through 30 removed outlier: 4.153A pdb=" N GLN E 22 " --> pdb=" O THR E 18 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP E 25 " --> pdb=" O LYS E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 43 removed outlier: 3.898A pdb=" N ILE E 41 " --> pdb=" O GLU E 37 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS E 43 " --> pdb=" O ASN E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 59 removed outlier: 3.510A pdb=" N ILE E 55 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET E 57 " --> pdb=" O GLY E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.833A pdb=" N ASN E 67 " --> pdb=" O SER E 63 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU E 68 " --> pdb=" O GLU E 64 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N PHE E 69 " --> pdb=" O SER E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 85 removed outlier: 3.661A pdb=" N PHE E 81 " --> pdb=" O ASN E 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 7 Processing helix chain 'F' and resid 7 through 12 Processing helix chain 'F' and resid 16 through 30 removed outlier: 4.154A pdb=" N GLN F 22 " --> pdb=" O THR F 18 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP F 25 " --> pdb=" O LYS F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 43 removed outlier: 3.897A pdb=" N ILE F 41 " --> pdb=" O GLU F 37 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS F 43 " --> pdb=" O ASN F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 59 removed outlier: 3.510A pdb=" N ILE F 55 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET F 57 " --> pdb=" O GLY F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 76 removed outlier: 3.833A pdb=" N ASN F 67 " --> pdb=" O SER F 63 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU F 68 " --> pdb=" O GLU F 64 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE F 69 " --> pdb=" O SER F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 85 removed outlier: 3.662A pdb=" N PHE F 81 " --> pdb=" O ASN F 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 7 Processing helix chain 'G' and resid 7 through 12 Processing helix chain 'G' and resid 16 through 30 removed outlier: 4.154A pdb=" N GLN G 22 " --> pdb=" O THR G 18 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP G 25 " --> pdb=" O LYS G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 43 removed outlier: 3.897A pdb=" N ILE G 41 " --> pdb=" O GLU G 37 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS G 43 " --> pdb=" O ASN G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 59 removed outlier: 3.510A pdb=" N ILE G 55 " --> pdb=" O ALA G 51 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET G 57 " --> pdb=" O GLY G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 76 removed outlier: 3.832A pdb=" N ASN G 67 " --> pdb=" O SER G 63 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU G 68 " --> pdb=" O GLU G 64 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N PHE G 69 " --> pdb=" O SER G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 85 removed outlier: 3.662A pdb=" N PHE G 81 " --> pdb=" O ASN G 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 7 Processing helix chain 'H' and resid 7 through 12 Processing helix chain 'H' and resid 16 through 30 removed outlier: 4.153A pdb=" N GLN H 22 " --> pdb=" O THR H 18 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP H 25 " --> pdb=" O LYS H 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 43 removed outlier: 3.897A pdb=" N ILE H 41 " --> pdb=" O GLU H 37 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS H 43 " --> pdb=" O ASN H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 59 removed outlier: 3.510A pdb=" N ILE H 55 " --> pdb=" O ALA H 51 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET H 57 " --> pdb=" O GLY H 53 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 76 removed outlier: 3.833A pdb=" N ASN H 67 " --> pdb=" O SER H 63 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU H 68 " --> pdb=" O GLU H 64 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE H 69 " --> pdb=" O SER H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 85 removed outlier: 3.663A pdb=" N PHE H 81 " --> pdb=" O ASN H 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 7 Processing helix chain 'I' and resid 7 through 12 Processing helix chain 'I' and resid 16 through 30 removed outlier: 4.153A pdb=" N GLN I 22 " --> pdb=" O THR I 18 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP I 25 " --> pdb=" O LYS I 21 " (cutoff:3.500A) Processing helix chain 'I' and resid 35 through 43 removed outlier: 3.897A pdb=" N ILE I 41 " --> pdb=" O GLU I 37 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS I 43 " --> pdb=" O ASN I 39 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 59 removed outlier: 3.511A pdb=" N ILE I 55 " --> pdb=" O ALA I 51 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET I 57 " --> pdb=" O GLY I 53 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 76 removed outlier: 3.833A pdb=" N ASN I 67 " --> pdb=" O SER I 63 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU I 68 " --> pdb=" O GLU I 64 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE I 69 " --> pdb=" O SER I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 77 through 85 removed outlier: 3.662A pdb=" N PHE I 81 " --> pdb=" O ASN I 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 7 Processing helix chain 'J' and resid 7 through 12 Processing helix chain 'J' and resid 16 through 30 removed outlier: 4.153A pdb=" N GLN J 22 " --> pdb=" O THR J 18 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP J 25 " --> pdb=" O LYS J 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 35 through 43 removed outlier: 3.897A pdb=" N ILE J 41 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS J 43 " --> pdb=" O ASN J 39 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 59 removed outlier: 3.510A pdb=" N ILE J 55 " --> pdb=" O ALA J 51 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET J 57 " --> pdb=" O GLY J 53 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 76 removed outlier: 3.833A pdb=" N ASN J 67 " --> pdb=" O SER J 63 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU J 68 " --> pdb=" O GLU J 64 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE J 69 " --> pdb=" O SER J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 85 removed outlier: 3.662A pdb=" N PHE J 81 " --> pdb=" O ASN J 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 7 Processing helix chain 'K' and resid 7 through 12 Processing helix chain 'K' and resid 16 through 30 removed outlier: 4.153A pdb=" N GLN K 22 " --> pdb=" O THR K 18 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP K 25 " --> pdb=" O LYS K 21 " (cutoff:3.500A) Processing helix chain 'K' and resid 35 through 43 removed outlier: 3.897A pdb=" N ILE K 41 " --> pdb=" O GLU K 37 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS K 43 " --> pdb=" O ASN K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 59 removed outlier: 3.510A pdb=" N ILE K 55 " --> pdb=" O ALA K 51 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET K 57 " --> pdb=" O GLY K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 76 removed outlier: 3.834A pdb=" N ASN K 67 " --> pdb=" O SER K 63 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU K 68 " --> pdb=" O GLU K 64 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE K 69 " --> pdb=" O SER K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 85 removed outlier: 3.662A pdb=" N PHE K 81 " --> pdb=" O ASN K 77 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 7 Processing helix chain 'L' and resid 7 through 12 Processing helix chain 'L' and resid 16 through 30 removed outlier: 4.154A pdb=" N GLN L 22 " --> pdb=" O THR L 18 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP L 25 " --> pdb=" O LYS L 21 " (cutoff:3.500A) Processing helix chain 'L' and resid 35 through 43 removed outlier: 3.898A pdb=" N ILE L 41 " --> pdb=" O GLU L 37 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS L 43 " --> pdb=" O ASN L 39 " (cutoff:3.500A) Processing helix chain 'L' and resid 46 through 59 removed outlier: 3.510A pdb=" N ILE L 55 " --> pdb=" O ALA L 51 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET L 57 " --> pdb=" O GLY L 53 " (cutoff:3.500A) Processing helix chain 'L' and resid 63 through 76 removed outlier: 3.833A pdb=" N ASN L 67 " --> pdb=" O SER L 63 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU L 68 " --> pdb=" O GLU L 64 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N PHE L 69 " --> pdb=" O SER L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 85 removed outlier: 3.661A pdb=" N PHE L 81 " --> pdb=" O ASN L 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 7 Processing helix chain 'M' and resid 7 through 12 Processing helix chain 'M' and resid 16 through 30 removed outlier: 4.152A pdb=" N GLN M 22 " --> pdb=" O THR M 18 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP M 25 " --> pdb=" O LYS M 21 " (cutoff:3.500A) Processing helix chain 'M' and resid 35 through 43 removed outlier: 3.898A pdb=" N ILE M 41 " --> pdb=" O GLU M 37 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS M 43 " --> pdb=" O ASN M 39 " (cutoff:3.500A) Processing helix chain 'M' and resid 46 through 59 removed outlier: 3.510A pdb=" N ILE M 55 " --> pdb=" O ALA M 51 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET M 57 " --> pdb=" O GLY M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 76 removed outlier: 3.834A pdb=" N ASN M 67 " --> pdb=" O SER M 63 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU M 68 " --> pdb=" O GLU M 64 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N PHE M 69 " --> pdb=" O SER M 65 " (cutoff:3.500A) Processing helix chain 'M' and resid 77 through 85 removed outlier: 3.661A pdb=" N PHE M 81 " --> pdb=" O ASN M 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 7 Processing helix chain 'N' and resid 7 through 12 Processing helix chain 'N' and resid 16 through 30 removed outlier: 4.153A pdb=" N GLN N 22 " --> pdb=" O THR N 18 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP N 25 " --> pdb=" O LYS N 21 " (cutoff:3.500A) Processing helix chain 'N' and resid 35 through 43 removed outlier: 3.897A pdb=" N ILE N 41 " --> pdb=" O GLU N 37 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS N 43 " --> pdb=" O ASN N 39 " (cutoff:3.500A) Processing helix chain 'N' and resid 46 through 59 removed outlier: 3.510A pdb=" N ILE N 55 " --> pdb=" O ALA N 51 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET N 57 " --> pdb=" O GLY N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 63 through 76 removed outlier: 3.833A pdb=" N ASN N 67 " --> pdb=" O SER N 63 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU N 68 " --> pdb=" O GLU N 64 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE N 69 " --> pdb=" O SER N 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 77 through 85 removed outlier: 3.662A pdb=" N PHE N 81 " --> pdb=" O ASN N 77 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 7 Processing helix chain 'O' and resid 7 through 12 Processing helix chain 'O' and resid 16 through 30 removed outlier: 4.154A pdb=" N GLN O 22 " --> pdb=" O THR O 18 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP O 25 " --> pdb=" O LYS O 21 " (cutoff:3.500A) Processing helix chain 'O' and resid 35 through 43 removed outlier: 3.896A pdb=" N ILE O 41 " --> pdb=" O GLU O 37 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS O 43 " --> pdb=" O ASN O 39 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 59 removed outlier: 3.510A pdb=" N ILE O 55 " --> pdb=" O ALA O 51 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET O 57 " --> pdb=" O GLY O 53 " (cutoff:3.500A) Processing helix chain 'O' and resid 63 through 76 removed outlier: 3.832A pdb=" N ASN O 67 " --> pdb=" O SER O 63 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU O 68 " --> pdb=" O GLU O 64 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE O 69 " --> pdb=" O SER O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 77 through 85 removed outlier: 3.663A pdb=" N PHE O 81 " --> pdb=" O ASN O 77 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 7 Processing helix chain 'P' and resid 7 through 12 Processing helix chain 'P' and resid 16 through 30 removed outlier: 4.153A pdb=" N GLN P 22 " --> pdb=" O THR P 18 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP P 25 " --> pdb=" O LYS P 21 " (cutoff:3.500A) Processing helix chain 'P' and resid 35 through 43 removed outlier: 3.896A pdb=" N ILE P 41 " --> pdb=" O GLU P 37 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS P 43 " --> pdb=" O ASN P 39 " (cutoff:3.500A) Processing helix chain 'P' and resid 46 through 59 removed outlier: 3.511A pdb=" N ILE P 55 " --> pdb=" O ALA P 51 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET P 57 " --> pdb=" O GLY P 53 " (cutoff:3.500A) Processing helix chain 'P' and resid 63 through 76 removed outlier: 3.833A pdb=" N ASN P 67 " --> pdb=" O SER P 63 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU P 68 " --> pdb=" O GLU P 64 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE P 69 " --> pdb=" O SER P 65 " (cutoff:3.500A) Processing helix chain 'P' and resid 77 through 85 removed outlier: 3.663A pdb=" N PHE P 81 " --> pdb=" O ASN P 77 " (cutoff:3.500A) 560 hydrogen bonds defined for protein. 1680 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.74 Time building geometry restraints manager: 3.12 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: 157 1.90 - 2.65: 327 2.65 - 3.40: 15715 3.40 - 4.15: 26803 4.15 - 4.90: 49850 Nonbonded interactions: 92852 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 92847 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 22.240 Find NCS groups from input model: 0.410 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.930 ------------------------------------------------------------------------------- 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= 0.541 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 fitting. rotamer outliers: 0 poor density : 487 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 MET cc_start: 0.6847 (mtt) cc_final: 0.6619 (mtt) REVERT: A 76 TRP cc_start: 0.5894 (m100) cc_final: 0.5428 (m100) REVERT: C 26 ASP cc_start: 0.5964 (m-30) cc_final: 0.5429 (m-30) REVERT: D 31 ASN cc_start: 0.7305 (m110) cc_final: 0.7101 (m110) REVERT: F 59 LEU cc_start: 0.8843 (mt) cc_final: 0.8286 (mt) REVERT: I 41 ILE cc_start: 0.7969 (mt) cc_final: 0.7743 (mt) REVERT: K 23 ILE cc_start: 0.6799 (mt) cc_final: 0.6424 (mt) REVERT: K 24 THR cc_start: 0.5636 (p) cc_final: 0.5419 (p) REVERT: M 39 ASN cc_start: 0.8245 (m-40) cc_final: 0.7882 (m-40) REVERT: M 49 ASP cc_start: 0.7176 (m-30) cc_final: 0.6920 (m-30) REVERT: O 15 MET cc_start: 0.4758 (ttt) cc_final: 0.4550 (ttt) REVERT: O 26 ASP cc_start: 0.6343 (m-30) cc_final: 0.6053 (m-30) outliers start: 0 outliers final: 0 residues processed: 487 average time/residue: 0.2308 time to fit residues: 157.2483 Evaluate side-chains 376 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 376 time to evaluate : 1.240 ------------------------------------------------------------------------------- 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 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 ASN A 77 ASN ** B 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 ASN C 77 ASN ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN ** F 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 56 HIS F 77 ASN G 31 ASN H 85 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 22 GLN ** 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 Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6557 moved from start: 0.5031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 11296 Z= 0.251 Angle : 0.716 7.986 15168 Z= 0.384 Chirality : 0.043 0.158 1712 Planarity : 0.005 0.042 1920 Dihedral : 5.554 19.209 1424 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.61 % Allowed : 11.55 % Favored : 85.84 % 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: -3.71 (0.19), residues: 1328 helix: -2.62 (0.12), residues: 1120 sheet: None (None), residues: 0 loop : 0.34 (0.42), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 76 HIS 0.002 0.001 HIS N 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 491 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 458 time to evaluate : 1.162 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: B 1 MET cc_start: 0.6259 (tpp) cc_final: 0.5899 (mmm) REVERT: C 49 ASP cc_start: 0.7481 (t0) cc_final: 0.7151 (t0) REVERT: D 1 MET cc_start: 0.7279 (tpp) cc_final: 0.6663 (tpt) REVERT: E 3 PHE cc_start: 0.7318 (t80) cc_final: 0.7023 (t80) REVERT: E 47 GLU cc_start: 0.7266 (pt0) cc_final: 0.6554 (pt0) REVERT: F 17 MET cc_start: 0.7507 (tpt) cc_final: 0.7280 (tpt) REVERT: F 26 ASP cc_start: 0.7023 (m-30) cc_final: 0.6804 (m-30) REVERT: G 38 VAL cc_start: 0.7759 (t) cc_final: 0.7483 (t) REVERT: H 1 MET cc_start: 0.7938 (tpp) cc_final: 0.7682 (tpp) REVERT: K 22 GLN cc_start: 0.7374 (tp40) cc_final: 0.6937 (mm-40) REVERT: L 20 ILE cc_start: 0.7324 (tt) cc_final: 0.6953 (tt) REVERT: O 85 ASN cc_start: 0.6940 (m-40) cc_final: 0.6715 (m110) REVERT: P 57 MET cc_start: 0.6766 (mmt) cc_final: 0.6193 (mtt) outliers start: 33 outliers final: 14 residues processed: 469 average time/residue: 0.2369 time to fit residues: 155.4977 Evaluate side-chains 414 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 400 time to evaluate : 1.235 ------------------------------------------------------------------------------- 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 F residue 20 ILE 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 J residue 34 ASN Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain N residue 55 ILE Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 54 ILE Chi-restraints excluded: chain O residue 55 ILE Chi-restraints excluded: chain P residue 15 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 125 optimal weight: 0.5980 chunk 103 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN B 34 ASN F 13 GLN H 85 ASN I 31 ASN J 39 ASN K 13 GLN ** L 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 67 ASN ** N 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 13 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.9363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 11296 Z= 0.287 Angle : 0.757 16.023 15168 Z= 0.391 Chirality : 0.044 0.184 1712 Planarity : 0.005 0.040 1920 Dihedral : 5.161 25.918 1424 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.64 % Allowed : 16.22 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.13 (0.22), residues: 1328 helix: -1.26 (0.15), residues: 1136 sheet: None (None), residues: 0 loop : -0.96 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP L 76 HIS 0.006 0.001 HIS D 56 PHE 0.026 0.002 PHE B 81 TYR 0.008 0.001 TYR L 78 ARG 0.006 0.001 ARG B 52 *********************** 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 567 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 521 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ASP cc_start: 0.8017 (p0) cc_final: 0.7786 (m-30) REVERT: A 35 ARG cc_start: 0.7266 (mtm110) cc_final: 0.7046 (mtm110) REVERT: A 52 ARG cc_start: 0.8375 (ttm110) cc_final: 0.7863 (mtt-85) REVERT: A 80 LEU cc_start: 0.9189 (tp) cc_final: 0.8894 (tp) REVERT: B 47 GLU cc_start: 0.8132 (pt0) cc_final: 0.7901 (pt0) REVERT: B 76 TRP cc_start: 0.8061 (OUTLIER) cc_final: 0.7625 (m100) REVERT: C 21 LYS cc_start: 0.8883 (mttm) cc_final: 0.8543 (mtmt) REVERT: C 22 GLN cc_start: 0.8181 (mt0) cc_final: 0.7927 (mt0) REVERT: C 44 GLU cc_start: 0.7344 (tp30) cc_final: 0.7108 (tp30) REVERT: E 27 LEU cc_start: 0.9297 (mm) cc_final: 0.9061 (mt) REVERT: E 41 ILE cc_start: 0.8791 (mt) cc_final: 0.8349 (mt) REVERT: E 45 LYS cc_start: 0.7725 (mtmt) cc_final: 0.7446 (mttp) REVERT: E 84 LEU cc_start: 0.8418 (tp) cc_final: 0.7991 (tp) REVERT: F 17 MET cc_start: 0.8432 (tpt) cc_final: 0.8227 (tpt) REVERT: F 27 LEU cc_start: 0.9338 (mm) cc_final: 0.9016 (mt) REVERT: F 49 ASP cc_start: 0.8666 (t0) cc_final: 0.8369 (t0) REVERT: F 59 LEU cc_start: 0.9323 (mt) cc_final: 0.9024 (mt) REVERT: H 1 MET cc_start: 0.8377 (tpp) cc_final: 0.7977 (tpp) REVERT: H 38 VAL cc_start: 0.8905 (t) cc_final: 0.8592 (m) REVERT: H 60 LYS cc_start: 0.8593 (mmtp) cc_final: 0.8170 (mmtm) REVERT: J 37 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7725 (mt-10) REVERT: J 61 LYS cc_start: 0.8343 (mttm) cc_final: 0.8135 (mttm) REVERT: J 75 GLU cc_start: 0.7917 (tt0) cc_final: 0.7446 (tt0) REVERT: J 78 TYR cc_start: 0.8469 (t80) cc_final: 0.8116 (t80) REVERT: K 9 ARG cc_start: 0.8543 (ttp80) cc_final: 0.8060 (mtt-85) REVERT: K 26 ASP cc_start: 0.8375 (m-30) cc_final: 0.8160 (m-30) REVERT: K 27 LEU cc_start: 0.9178 (mm) cc_final: 0.8833 (mt) REVERT: L 7 ASN cc_start: 0.8490 (m-40) cc_final: 0.8279 (m110) REVERT: L 17 MET cc_start: 0.8105 (tpp) cc_final: 0.7861 (tpp) REVERT: L 20 ILE cc_start: 0.8516 (OUTLIER) cc_final: 0.8257 (tt) REVERT: L 36 GLU cc_start: 0.7678 (mm-30) cc_final: 0.6693 (mt-10) REVERT: M 9 ARG cc_start: 0.7802 (ttp80) cc_final: 0.7526 (ttp80) REVERT: N 11 LEU cc_start: 0.8615 (mt) cc_final: 0.8392 (mt) REVERT: N 26 ASP cc_start: 0.8252 (t0) cc_final: 0.8004 (t70) REVERT: N 27 LEU cc_start: 0.9230 (mm) cc_final: 0.8980 (mt) REVERT: O 23 ILE cc_start: 0.9437 (mt) cc_final: 0.9004 (mp) REVERT: O 49 ASP cc_start: 0.7646 (t0) cc_final: 0.7137 (t0) REVERT: P 1 MET cc_start: 0.7453 (tpp) cc_final: 0.7041 (tpt) REVERT: P 11 LEU cc_start: 0.9138 (mt) cc_final: 0.8725 (mt) outliers start: 46 outliers final: 19 residues processed: 540 average time/residue: 0.2257 time to fit residues: 172.5590 Evaluate side-chains 478 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 457 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 TRP Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 43 CYS Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain I residue 40 ILE Chi-restraints excluded: chain I residue 43 CYS Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain O residue 54 ILE Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 76 TRP Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain P residue 31 ASN Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 40 ILE Chi-restraints excluded: chain P residue 65 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 12 optimal weight: 0.0970 chunk 55 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 116 optimal weight: 0.2980 chunk 123 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 ASN B 22 GLN C 7 ASN C 39 ASN ** E 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN F 77 ASN G 39 ASN ** N 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 48 GLN O 39 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 1.0062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11296 Z= 0.167 Angle : 0.564 7.644 15168 Z= 0.301 Chirality : 0.041 0.157 1712 Planarity : 0.004 0.053 1920 Dihedral : 4.731 21.636 1424 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.40 % Allowed : 18.35 % Favored : 78.24 % 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: -1.24 (0.23), residues: 1328 helix: -0.62 (0.16), residues: 1136 sheet: None (None), residues: 0 loop : -0.94 (0.44), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 76 HIS 0.007 0.001 HIS O 56 PHE 0.025 0.002 PHE L 69 TYR 0.010 0.001 TYR L 78 ARG 0.008 0.001 ARG D 9 *********************** 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 537 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 494 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 MET cc_start: 0.8222 (mtp) cc_final: 0.7917 (mtt) REVERT: A 80 LEU cc_start: 0.9211 (tp) cc_final: 0.8900 (tp) REVERT: B 34 ASN cc_start: 0.7887 (p0) cc_final: 0.7547 (p0) REVERT: B 52 ARG cc_start: 0.8711 (ttm-80) cc_final: 0.8322 (mtt90) REVERT: B 76 TRP cc_start: 0.8194 (OUTLIER) cc_final: 0.7880 (m100) REVERT: C 21 LYS cc_start: 0.8821 (mttm) cc_final: 0.8330 (mtmt) REVERT: C 30 TRP cc_start: 0.8662 (m-10) cc_final: 0.8234 (m-10) REVERT: E 17 MET cc_start: 0.9087 (tpt) cc_final: 0.8819 (tpt) REVERT: E 22 GLN cc_start: 0.8324 (mt0) cc_final: 0.8063 (mt0) REVERT: E 27 LEU cc_start: 0.9335 (mm) cc_final: 0.9125 (mt) REVERT: E 41 ILE cc_start: 0.9086 (mt) cc_final: 0.8229 (mt) REVERT: E 45 LYS cc_start: 0.7429 (mtmt) cc_final: 0.7138 (mttp) REVERT: E 47 GLU cc_start: 0.7333 (pt0) cc_final: 0.6975 (pt0) REVERT: E 64 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7903 (tm-30) REVERT: E 84 LEU cc_start: 0.8232 (tp) cc_final: 0.8032 (tp) REVERT: F 27 LEU cc_start: 0.9339 (mm) cc_final: 0.9075 (mt) REVERT: F 60 LYS cc_start: 0.8818 (mtpt) cc_final: 0.8395 (mtmt) REVERT: H 1 MET cc_start: 0.8505 (tpp) cc_final: 0.8058 (tpp) REVERT: H 60 LYS cc_start: 0.8500 (mmtp) cc_final: 0.8228 (mmtm) REVERT: H 85 ASN cc_start: 0.8113 (m-40) cc_final: 0.7825 (m-40) REVERT: I 37 GLU cc_start: 0.8346 (tt0) cc_final: 0.8087 (tt0) REVERT: J 37 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7826 (mt-10) REVERT: J 48 GLN cc_start: 0.8632 (mp10) cc_final: 0.8260 (mp-120) REVERT: J 78 TYR cc_start: 0.8658 (t80) cc_final: 0.8289 (t80) REVERT: K 9 ARG cc_start: 0.8496 (ttp80) cc_final: 0.7916 (mtt-85) REVERT: K 78 TYR cc_start: 0.7937 (t80) cc_final: 0.7540 (t80) REVERT: L 26 ASP cc_start: 0.7688 (m-30) cc_final: 0.7003 (m-30) REVERT: L 36 GLU cc_start: 0.7816 (mm-30) cc_final: 0.6885 (mt-10) REVERT: M 2 ASN cc_start: 0.7963 (t0) cc_final: 0.7688 (t0) REVERT: M 9 ARG cc_start: 0.8005 (ttp80) cc_final: 0.7664 (ttp80) REVERT: N 22 GLN cc_start: 0.8320 (mt0) cc_final: 0.7881 (mt0) REVERT: N 37 GLU cc_start: 0.7259 (mt-10) cc_final: 0.6925 (mt-10) REVERT: N 81 PHE cc_start: 0.8442 (t80) cc_final: 0.8194 (t80) REVERT: O 44 GLU cc_start: 0.7039 (mt-10) cc_final: 0.6077 (mt-10) REVERT: O 49 ASP cc_start: 0.7133 (t0) cc_final: 0.6763 (t0) REVERT: P 1 MET cc_start: 0.7642 (tpp) cc_final: 0.7226 (tpt) REVERT: P 80 LEU cc_start: 0.8972 (tp) cc_final: 0.8637 (tt) outliers start: 43 outliers final: 23 residues processed: 511 average time/residue: 0.2129 time to fit residues: 154.7465 Evaluate side-chains 483 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 459 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 TRP Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 57 MET Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain N residue 54 ILE Chi-restraints excluded: chain N residue 64 GLU Chi-restraints excluded: chain O residue 21 LYS Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 54 ILE Chi-restraints excluded: chain P residue 15 MET Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 40 ILE Chi-restraints excluded: chain P residue 65 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 0.9980 chunk 70 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 63 optimal weight: 3.9990 chunk 111 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 ASN J 13 GLN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 ASN ** L 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 48 GLN ** O 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 1.1124 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= 0.232 Angle : 0.615 10.013 15168 Z= 0.323 Chirality : 0.042 0.175 1712 Planarity : 0.003 0.038 1920 Dihedral : 4.652 22.329 1424 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.16 % Allowed : 19.86 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.85 (0.24), residues: 1328 helix: -0.38 (0.16), residues: 1152 sheet: None (None), residues: 0 loop : -0.58 (0.47), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP H 76 HIS 0.004 0.001 HIS D 56 PHE 0.022 0.002 PHE L 69 TYR 0.010 0.001 TYR A 78 ARG 0.006 0.001 ARG L 35 *********************** 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 537 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 497 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.8537 (mm110) cc_final: 0.8290 (mm110) REVERT: C 21 LYS cc_start: 0.8877 (mttm) cc_final: 0.8446 (mtmt) REVERT: D 11 LEU cc_start: 0.9335 (mt) cc_final: 0.9102 (mt) REVERT: D 19 VAL cc_start: 0.8272 (p) cc_final: 0.8068 (p) REVERT: D 48 GLN cc_start: 0.8592 (mp10) cc_final: 0.8329 (mp10) REVERT: E 1 MET cc_start: 0.7351 (tpp) cc_final: 0.7068 (tpp) REVERT: E 17 MET cc_start: 0.9374 (tpt) cc_final: 0.8981 (tpp) REVERT: E 27 LEU cc_start: 0.9391 (mm) cc_final: 0.9118 (mt) REVERT: E 64 GLU cc_start: 0.8276 (tm-30) cc_final: 0.8016 (tm-30) REVERT: F 23 ILE cc_start: 0.9428 (mt) cc_final: 0.9206 (mp) REVERT: F 57 MET cc_start: 0.8566 (ttm) cc_final: 0.8203 (ttm) REVERT: G 2 ASN cc_start: 0.8075 (m-40) cc_final: 0.7714 (m110) REVERT: G 6 ASP cc_start: 0.7714 (m-30) cc_final: 0.7495 (m-30) REVERT: H 1 MET cc_start: 0.8360 (tpp) cc_final: 0.7211 (tpp) REVERT: H 60 LYS cc_start: 0.8624 (mmtp) cc_final: 0.8347 (mmtm) REVERT: H 73 LEU cc_start: 0.9067 (tp) cc_final: 0.8787 (tt) REVERT: H 85 ASN cc_start: 0.8385 (m-40) cc_final: 0.8071 (m-40) REVERT: I 69 PHE cc_start: 0.8797 (t80) cc_final: 0.8394 (t80) REVERT: J 34 ASN cc_start: 0.8144 (p0) cc_final: 0.7646 (p0) REVERT: J 78 TYR cc_start: 0.8849 (t80) cc_final: 0.8501 (t80) REVERT: K 9 ARG cc_start: 0.8413 (ttp80) cc_final: 0.7969 (mtt-85) REVERT: M 9 ARG cc_start: 0.8346 (ttp80) cc_final: 0.7839 (ttt-90) REVERT: M 78 TYR cc_start: 0.7930 (t80) cc_final: 0.7585 (t80) REVERT: N 11 LEU cc_start: 0.9015 (mt) cc_final: 0.8813 (mt) REVERT: N 27 LEU cc_start: 0.9393 (mm) cc_final: 0.9149 (mt) REVERT: O 44 GLU cc_start: 0.7490 (mt-10) cc_final: 0.6438 (mt-10) REVERT: O 49 ASP cc_start: 0.7128 (t0) cc_final: 0.6875 (t0) REVERT: P 37 GLU cc_start: 0.8300 (mt-10) cc_final: 0.7665 (mt-10) REVERT: P 57 MET cc_start: 0.8167 (mtt) cc_final: 0.7797 (mtt) outliers start: 40 outliers final: 30 residues processed: 512 average time/residue: 0.2220 time to fit residues: 161.6930 Evaluate side-chains 488 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 458 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain C residue 46 VAL 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 F residue 58 ILE Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 49 ASP Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 76 TRP Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain K residue 57 MET Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain M residue 37 GLU 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 12 ILE Chi-restraints excluded: chain P residue 15 MET Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 40 ILE Chi-restraints excluded: chain P residue 65 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 72 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 7 ASN J 13 GLN K 22 GLN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 ASN L 22 GLN ** N 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 39 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 1.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11296 Z= 0.220 Angle : 0.610 8.967 15168 Z= 0.323 Chirality : 0.042 0.169 1712 Planarity : 0.003 0.039 1920 Dihedral : 4.569 20.237 1424 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 12.21 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: -0.84 (0.23), residues: 1328 helix: -0.21 (0.15), residues: 1184 sheet: None (None), residues: 0 loop : -2.26 (0.44), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 76 HIS 0.004 0.001 HIS O 56 PHE 0.028 0.002 PHE M 69 TYR 0.014 0.001 TYR B 78 ARG 0.006 0.000 ARG K 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 564 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 521 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 34 ASN cc_start: 0.8771 (p0) cc_final: 0.8451 (p0) REVERT: C 21 LYS cc_start: 0.8786 (mttm) cc_final: 0.8376 (mtmt) REVERT: C 30 TRP cc_start: 0.8960 (m-10) cc_final: 0.8392 (m-10) REVERT: D 1 MET cc_start: 0.7024 (tpp) cc_final: 0.6701 (tpp) REVERT: D 65 SER cc_start: 0.7898 (OUTLIER) cc_final: 0.7331 (m) REVERT: E 1 MET cc_start: 0.7169 (tpp) cc_final: 0.6853 (tpp) REVERT: E 3 PHE cc_start: 0.7274 (t80) cc_final: 0.7055 (t80) REVERT: E 22 GLN cc_start: 0.8739 (mt0) cc_final: 0.8515 (mt0) REVERT: E 27 LEU cc_start: 0.9376 (mm) cc_final: 0.9173 (mt) REVERT: F 14 ARG cc_start: 0.8042 (mtm-85) cc_final: 0.5340 (mmt180) REVERT: F 23 ILE cc_start: 0.9457 (mt) cc_final: 0.9153 (mp) REVERT: F 57 MET cc_start: 0.8532 (ttm) cc_final: 0.8228 (ttm) REVERT: G 2 ASN cc_start: 0.8287 (m-40) cc_final: 0.7822 (m110) REVERT: H 1 MET cc_start: 0.8264 (tpp) cc_final: 0.6707 (tpt) REVERT: H 60 LYS cc_start: 0.8721 (mmtp) cc_final: 0.8351 (mmtm) REVERT: H 73 LEU cc_start: 0.9127 (tp) cc_final: 0.8775 (tt) REVERT: J 78 TYR cc_start: 0.8923 (t80) cc_final: 0.8509 (t80) REVERT: K 9 ARG cc_start: 0.8509 (ttp80) cc_final: 0.8087 (mtt90) REVERT: K 78 TYR cc_start: 0.8207 (t80) cc_final: 0.7568 (t80) REVERT: L 26 ASP cc_start: 0.7900 (m-30) cc_final: 0.7312 (m-30) REVERT: L 36 GLU cc_start: 0.7892 (tp30) cc_final: 0.7352 (mt-10) REVERT: M 6 ASP cc_start: 0.8155 (m-30) cc_final: 0.7885 (m-30) REVERT: M 43 CYS cc_start: 0.7987 (p) cc_final: 0.7550 (p) REVERT: M 78 TYR cc_start: 0.7921 (t80) cc_final: 0.7602 (t80) REVERT: N 22 GLN cc_start: 0.8415 (mt0) cc_final: 0.8052 (mt0) REVERT: N 27 LEU cc_start: 0.9396 (mm) cc_final: 0.9144 (mt) REVERT: O 44 GLU cc_start: 0.7312 (mt-10) cc_final: 0.6152 (mt-10) REVERT: P 37 GLU cc_start: 0.8376 (mt-10) cc_final: 0.7569 (mt-10) REVERT: P 57 MET cc_start: 0.8089 (mtt) cc_final: 0.7573 (mtm) REVERT: P 70 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8662 (mm) outliers start: 43 outliers final: 26 residues processed: 537 average time/residue: 0.2333 time to fit residues: 174.9818 Evaluate side-chains 514 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 486 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain F residue 15 MET Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 58 ILE Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 57 MET Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain M residue 20 ILE Chi-restraints excluded: chain N residue 54 ILE Chi-restraints excluded: chain N residue 64 GLU Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain P residue 15 MET Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 40 ILE Chi-restraints excluded: chain P residue 65 SER Chi-restraints excluded: chain P residue 70 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 7.9990 chunk 13 optimal weight: 0.5980 chunk 70 optimal weight: 0.0670 chunk 90 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 123 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 overall best weight: 0.6518 ------------------------------------------------------------------------------- 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 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 ASN G 77 ASN H 7 ASN K 7 ASN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 ASN P 22 GLN P 39 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 1.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11296 Z= 0.171 Angle : 0.589 9.569 15168 Z= 0.311 Chirality : 0.041 0.171 1712 Planarity : 0.003 0.039 1920 Dihedral : 4.593 23.340 1424 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.01 % Allowed : 22.55 % Favored : 74.45 % 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: -0.50 (0.23), residues: 1328 helix: -0.04 (0.16), residues: 1136 sheet: None (None), residues: 0 loop : -1.25 (0.41), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP L 76 HIS 0.003 0.001 HIS O 56 PHE 0.025 0.002 PHE J 81 TYR 0.009 0.001 TYR I 78 ARG 0.007 0.000 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 541 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 503 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASN cc_start: 0.6569 (m110) cc_final: 0.6324 (m110) REVERT: B 34 ASN cc_start: 0.8663 (p0) cc_final: 0.8325 (p0) REVERT: C 21 LYS cc_start: 0.8710 (mttm) cc_final: 0.8229 (mtmt) REVERT: C 30 TRP cc_start: 0.8968 (m-10) cc_final: 0.8453 (m-10) REVERT: D 1 MET cc_start: 0.7243 (tpp) cc_final: 0.7036 (tpp) REVERT: D 45 LYS cc_start: 0.7825 (mtmm) cc_final: 0.7387 (mtmt) REVERT: D 65 SER cc_start: 0.7997 (OUTLIER) cc_final: 0.7455 (m) REVERT: E 1 MET cc_start: 0.7161 (tpp) cc_final: 0.6883 (tpp) REVERT: E 3 PHE cc_start: 0.7236 (t80) cc_final: 0.7016 (t80) REVERT: E 27 LEU cc_start: 0.9302 (mm) cc_final: 0.9056 (mt) REVERT: F 14 ARG cc_start: 0.8020 (mtm-85) cc_final: 0.5205 (mmt180) REVERT: G 25 ASP cc_start: 0.6896 (m-30) cc_final: 0.6639 (m-30) REVERT: H 60 LYS cc_start: 0.8722 (mmtp) cc_final: 0.8314 (mmtm) REVERT: H 73 LEU cc_start: 0.9077 (tp) cc_final: 0.8771 (tt) REVERT: I 85 ASN cc_start: 0.6241 (m-40) cc_final: 0.5867 (m110) REVERT: J 78 TYR cc_start: 0.8854 (t80) cc_final: 0.8399 (t80) REVERT: K 9 ARG cc_start: 0.8497 (ttp80) cc_final: 0.8081 (mtt90) REVERT: K 35 ARG cc_start: 0.7885 (mmm160) cc_final: 0.7357 (mmm160) REVERT: K 39 ASN cc_start: 0.8504 (m-40) cc_final: 0.7696 (m-40) REVERT: K 78 TYR cc_start: 0.8152 (t80) cc_final: 0.7545 (t80) REVERT: L 22 GLN cc_start: 0.9118 (mt0) cc_final: 0.8787 (mt0) REVERT: L 26 ASP cc_start: 0.7768 (m-30) cc_final: 0.7174 (m-30) REVERT: M 20 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8363 (mt) REVERT: M 43 CYS cc_start: 0.7940 (p) cc_final: 0.7612 (p) REVERT: M 78 TYR cc_start: 0.7912 (t80) cc_final: 0.7487 (t80) REVERT: N 22 GLN cc_start: 0.8379 (mt0) cc_final: 0.7929 (mt0) REVERT: N 27 LEU cc_start: 0.9365 (mm) cc_final: 0.9156 (mt) REVERT: N 36 GLU cc_start: 0.8445 (mm-30) cc_final: 0.7951 (mm-30) REVERT: O 44 GLU cc_start: 0.6845 (mt-10) cc_final: 0.6283 (mt-10) REVERT: O 49 ASP cc_start: 0.7308 (t0) cc_final: 0.6378 (t0) REVERT: P 37 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7499 (mt-10) REVERT: P 70 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8586 (mm) outliers start: 38 outliers final: 24 residues processed: 520 average time/residue: 0.2138 time to fit residues: 157.7178 Evaluate side-chains 514 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 487 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain E residue 4 ILE Chi-restraints excluded: chain F residue 15 MET Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain G residue 49 ASP Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain H residue 37 GLU Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain I residue 17 MET Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 76 TRP Chi-restraints excluded: chain K residue 57 MET Chi-restraints excluded: chain K residue 76 TRP Chi-restraints excluded: chain M residue 20 ILE Chi-restraints excluded: chain N residue 54 ILE Chi-restraints excluded: chain N residue 64 GLU Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain P residue 15 MET Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 40 ILE Chi-restraints excluded: chain P residue 70 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 84 optimal weight: 0.0050 chunk 60 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 22 GLN ** G 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 77 ASN ** K 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 39 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 1.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11296 Z= 0.183 Angle : 0.609 9.051 15168 Z= 0.324 Chirality : 0.041 0.162 1712 Planarity : 0.003 0.039 1920 Dihedral : 4.539 22.782 1424 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.37 % Allowed : 23.66 % Favored : 73.97 % 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: -0.33 (0.23), residues: 1328 helix: 0.09 (0.16), residues: 1136 sheet: None (None), residues: 0 loop : -1.30 (0.40), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 76 HIS 0.002 0.001 HIS O 56 PHE 0.048 0.002 PHE A 81 TYR 0.013 0.001 TYR B 78 ARG 0.009 0.001 ARG P 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 527 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 497 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 34 ASN cc_start: 0.8589 (p0) cc_final: 0.8303 (p0) REVERT: B 52 ARG cc_start: 0.8657 (ttm-80) cc_final: 0.8314 (mtt90) REVERT: C 21 LYS cc_start: 0.8655 (mttm) cc_final: 0.8278 (mtmt) REVERT: C 30 TRP cc_start: 0.8987 (m-10) cc_final: 0.8400 (m-10) REVERT: D 45 LYS cc_start: 0.7790 (mtmm) cc_final: 0.7468 (mtmt) REVERT: D 65 SER cc_start: 0.8051 (OUTLIER) cc_final: 0.7637 (m) REVERT: E 1 MET cc_start: 0.7115 (tpp) cc_final: 0.6868 (tpp) REVERT: E 27 LEU cc_start: 0.9317 (mm) cc_final: 0.9040 (mt) REVERT: E 85 ASN cc_start: 0.6324 (m-40) cc_final: 0.6123 (m-40) REVERT: F 14 ARG cc_start: 0.8158 (mtm-85) cc_final: 0.5237 (tpt170) REVERT: F 34 ASN cc_start: 0.8802 (p0) cc_final: 0.8556 (p0) REVERT: G 25 ASP cc_start: 0.6881 (m-30) cc_final: 0.6651 (m-30) REVERT: H 60 LYS cc_start: 0.8682 (mmtp) cc_final: 0.8302 (mmtm) REVERT: H 73 LEU cc_start: 0.8957 (tp) cc_final: 0.8727 (tt) REVERT: J 78 TYR cc_start: 0.8786 (t80) cc_final: 0.8505 (t80) REVERT: K 9 ARG cc_start: 0.8533 (ttp80) cc_final: 0.8066 (mtt90) REVERT: K 35 ARG cc_start: 0.7758 (mmm160) cc_final: 0.7065 (mmm160) REVERT: K 39 ASN cc_start: 0.8662 (m-40) cc_final: 0.8167 (m-40) REVERT: K 78 TYR cc_start: 0.8139 (t80) cc_final: 0.7574 (t80) REVERT: L 22 GLN cc_start: 0.9174 (mt0) cc_final: 0.8873 (mt0) REVERT: L 26 ASP cc_start: 0.7761 (m-30) cc_final: 0.7367 (m-30) REVERT: M 20 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8486 (mm) REVERT: M 21 LYS cc_start: 0.8261 (mtpt) cc_final: 0.7809 (mmtt) REVERT: M 43 CYS cc_start: 0.7972 (p) cc_final: 0.7561 (p) REVERT: M 78 TYR cc_start: 0.7900 (t80) cc_final: 0.7422 (t80) REVERT: N 22 GLN cc_start: 0.8354 (mt0) cc_final: 0.7972 (mt0) REVERT: O 44 GLU cc_start: 0.6958 (mt-10) cc_final: 0.6289 (mt-10) REVERT: O 49 ASP cc_start: 0.7333 (t0) cc_final: 0.6339 (t0) REVERT: O 74 LYS cc_start: 0.8301 (ttpt) cc_final: 0.8098 (tttt) REVERT: P 70 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8531 (mm) outliers start: 30 outliers final: 22 residues processed: 508 average time/residue: 0.2403 time to fit residues: 168.5600 Evaluate side-chains 504 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 479 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain F residue 15 MET Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain H residue 37 GLU Chi-restraints excluded: chain I residue 17 MET Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 57 MET Chi-restraints excluded: chain J residue 76 TRP Chi-restraints excluded: chain K residue 57 MET Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain M residue 20 ILE Chi-restraints excluded: chain N residue 54 ILE Chi-restraints excluded: chain N residue 64 GLU Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain P residue 15 MET Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 40 ILE Chi-restraints excluded: chain P residue 70 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 108 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 GLN F 13 GLN F 48 GLN G 2 ASN ** G 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 56 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 1.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 11296 Z= 0.317 Angle : 0.704 12.242 15168 Z= 0.370 Chirality : 0.046 0.185 1712 Planarity : 0.004 0.039 1920 Dihedral : 4.754 21.259 1424 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.77 % Allowed : 23.89 % Favored : 73.34 % 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: -0.50 (0.23), residues: 1328 helix: -0.01 (0.16), residues: 1136 sheet: None (None), residues: 0 loop : -1.47 (0.39), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP L 76 HIS 0.003 0.001 HIS C 56 PHE 0.036 0.003 PHE J 81 TYR 0.008 0.001 TYR O 78 ARG 0.006 0.001 ARG B 35 *********************** 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 542 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 507 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 34 ASN cc_start: 0.8500 (p0) cc_final: 0.8281 (p0) REVERT: B 48 GLN cc_start: 0.8224 (mp10) cc_final: 0.7660 (mt0) REVERT: C 21 LYS cc_start: 0.8938 (mttm) cc_final: 0.8592 (mtmt) REVERT: C 82 GLN cc_start: 0.7309 (tt0) cc_final: 0.6697 (tt0) REVERT: D 2 ASN cc_start: 0.6529 (t0) cc_final: 0.6222 (t0) REVERT: D 65 SER cc_start: 0.8223 (OUTLIER) cc_final: 0.7975 (m) REVERT: E 1 MET cc_start: 0.7090 (tpp) cc_final: 0.6791 (tpp) REVERT: E 27 LEU cc_start: 0.9349 (mm) cc_final: 0.9005 (mt) REVERT: E 85 ASN cc_start: 0.6408 (m-40) cc_final: 0.5865 (m110) REVERT: F 14 ARG cc_start: 0.8456 (mtm-85) cc_final: 0.5578 (tpt170) REVERT: G 39 ASN cc_start: 0.8839 (t0) cc_final: 0.8565 (t0) REVERT: H 1 MET cc_start: 0.8083 (tpp) cc_final: 0.7666 (ttp) REVERT: H 2 ASN cc_start: 0.7908 (m-40) cc_final: 0.7606 (m-40) REVERT: H 60 LYS cc_start: 0.8869 (mmtp) cc_final: 0.8294 (mmtm) REVERT: H 73 LEU cc_start: 0.9098 (tp) cc_final: 0.8863 (tt) REVERT: K 9 ARG cc_start: 0.8561 (ttp80) cc_final: 0.7994 (mtt90) REVERT: M 43 CYS cc_start: 0.8245 (p) cc_final: 0.7790 (p) REVERT: N 22 GLN cc_start: 0.8377 (mt0) cc_final: 0.7997 (mt0) REVERT: N 59 LEU cc_start: 0.9314 (mt) cc_final: 0.9064 (mt) REVERT: O 44 GLU cc_start: 0.7047 (mt-10) cc_final: 0.6430 (mt-10) REVERT: O 49 ASP cc_start: 0.7521 (t0) cc_final: 0.6623 (t0) REVERT: O 85 ASN cc_start: 0.8039 (m-40) cc_final: 0.7797 (m110) REVERT: P 70 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8678 (mm) outliers start: 35 outliers final: 26 residues processed: 521 average time/residue: 0.2329 time to fit residues: 168.1035 Evaluate side-chains 519 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 491 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain E residue 36 GLU Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain G residue 15 MET Chi-restraints excluded: chain G residue 37 GLU Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 49 ASP Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain H residue 37 GLU Chi-restraints excluded: chain I residue 17 MET Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 57 MET Chi-restraints excluded: chain J residue 76 TRP Chi-restraints excluded: chain K residue 57 MET 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 15 MET Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 40 ILE Chi-restraints excluded: chain P residue 70 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 0.9990 chunk 57 optimal weight: 8.9990 chunk 84 optimal weight: 8.9990 chunk 127 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 78 optimal weight: 0.3980 chunk 62 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 chunk 108 optimal weight: 5.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 ASN E 22 GLN G 2 ASN ** J 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 1.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11296 Z= 0.212 Angle : 0.657 9.386 15168 Z= 0.349 Chirality : 0.043 0.179 1712 Planarity : 0.004 0.047 1920 Dihedral : 4.759 21.384 1424 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.45 % Allowed : 25.79 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.23), residues: 1328 helix: 0.08 (0.16), residues: 1136 sheet: None (None), residues: 0 loop : -1.58 (0.38), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 76 HIS 0.002 0.001 HIS O 56 PHE 0.038 0.002 PHE O 81 TYR 0.020 0.001 TYR B 78 ARG 0.008 0.001 ARG D 9 ********************** 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 531 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 500 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLN cc_start: 0.8525 (mt0) cc_final: 0.8225 (mt0) REVERT: B 22 GLN cc_start: 0.8801 (mt0) cc_final: 0.8578 (mt0) REVERT: B 34 ASN cc_start: 0.8181 (p0) cc_final: 0.7832 (p0) REVERT: B 48 GLN cc_start: 0.8186 (mp10) cc_final: 0.7747 (mt0) REVERT: B 52 ARG cc_start: 0.8652 (ttm-80) cc_final: 0.8267 (mtt90) REVERT: C 21 LYS cc_start: 0.8728 (mttm) cc_final: 0.8402 (mtmt) REVERT: C 30 TRP cc_start: 0.9063 (m-10) cc_final: 0.8572 (m-10) REVERT: C 82 GLN cc_start: 0.7005 (tt0) cc_final: 0.6469 (tt0) REVERT: D 2 ASN cc_start: 0.6577 (t0) cc_final: 0.6312 (t0) REVERT: D 5 LYS cc_start: 0.8739 (tptm) cc_final: 0.8496 (tttm) REVERT: E 1 MET cc_start: 0.6990 (tpp) cc_final: 0.6730 (tpp) REVERT: E 27 LEU cc_start: 0.9290 (mm) cc_final: 0.9015 (mt) REVERT: F 14 ARG cc_start: 0.8338 (mtm-85) cc_final: 0.5489 (tpt170) REVERT: F 36 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7550 (mp0) REVERT: F 75 GLU cc_start: 0.8423 (tt0) cc_final: 0.8035 (tt0) REVERT: H 1 MET cc_start: 0.7923 (tpp) cc_final: 0.7646 (ttp) REVERT: H 2 ASN cc_start: 0.7851 (m-40) cc_final: 0.7599 (m-40) REVERT: H 60 LYS cc_start: 0.8791 (mmtp) cc_final: 0.8253 (mmtm) REVERT: I 19 VAL cc_start: 0.9220 (OUTLIER) cc_final: 0.8986 (p) REVERT: K 9 ARG cc_start: 0.8632 (ttp80) cc_final: 0.7959 (mtt90) REVERT: K 35 ARG cc_start: 0.7837 (mmm160) cc_final: 0.7516 (mmm160) REVERT: K 78 TYR cc_start: 0.8184 (t80) cc_final: 0.7688 (t80) REVERT: M 3 PHE cc_start: 0.8400 (t80) cc_final: 0.8179 (t80) REVERT: M 43 CYS cc_start: 0.8104 (p) cc_final: 0.7589 (p) REVERT: N 22 GLN cc_start: 0.8326 (mt0) cc_final: 0.7941 (mt0) REVERT: N 26 ASP cc_start: 0.7811 (t0) cc_final: 0.7446 (t0) REVERT: O 9 ARG cc_start: 0.6636 (ttt180) cc_final: 0.6389 (ttt180) REVERT: O 17 MET cc_start: 0.8472 (tpp) cc_final: 0.8239 (mmm) REVERT: O 44 GLU cc_start: 0.7047 (mt-10) cc_final: 0.6557 (mt-10) REVERT: O 49 ASP cc_start: 0.7456 (t0) cc_final: 0.6619 (t0) REVERT: P 65 SER cc_start: 0.9281 (p) cc_final: 0.8947 (p) REVERT: P 70 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8593 (mm) outliers start: 31 outliers final: 21 residues processed: 515 average time/residue: 0.2337 time to fit residues: 166.9746 Evaluate side-chains 504 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 481 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain E residue 36 GLU Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain G residue 15 MET Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain H residue 37 GLU Chi-restraints excluded: chain I residue 17 MET Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain J residue 76 TRP Chi-restraints excluded: chain K residue 57 MET Chi-restraints excluded: chain L residue 73 LEU 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 15 MET Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 40 ILE Chi-restraints excluded: chain P residue 70 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 104 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 GLN E 85 ASN ** G 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 85 ASN ** J 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 13 GLN O 85 ASN ** P 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.125383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.117022 restraints weight = 16414.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.119914 restraints weight = 8195.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.121757 restraints weight = 4607.750| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 1.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11296 Z= 0.238 Angle : 0.676 9.198 15168 Z= 0.359 Chirality : 0.044 0.169 1712 Planarity : 0.004 0.040 1920 Dihedral : 4.765 21.197 1424 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.61 % Allowed : 26.58 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.23), residues: 1328 helix: 0.10 (0.16), residues: 1136 sheet: None (None), residues: 0 loop : -1.65 (0.37), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 76 HIS 0.002 0.001 HIS N 56 PHE 0.037 0.002 PHE O 81 TYR 0.018 0.001 TYR H 78 ARG 0.011 0.001 ARG A 52 =============================================================================== Job complete usr+sys time: 3030.12 seconds wall clock time: 54 minutes 24.06 seconds (3264.06 seconds total)