Starting phenix.real_space_refine on Mon Oct 26 13:23:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/35sy_77176/10_2026/35sy_77176.cif Found real_map, /net/cci-nas-00/data/ceres_data/35sy_77176/10_2026/35sy_77176.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/35sy_77176/10_2026/35sy_77176.map" default_real_map = "/net/cci-nas-00/data/ceres_data/35sy_77176/10_2026/35sy_77176.map" model { file = "/net/cci-nas-00/data/ceres_data/35sy_77176/10_2026/35sy_77176.cif" } default_model = "/net/cci-nas-00/data/ceres_data/35sy_77176/10_2026/35sy_77176.cif" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 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: 5 Type Number sf(0) Gaussians P 178 5.49 5 S 143 5.16 5 C 12534 2.51 5 N 3542 2.21 5 O 4341 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20738 Number of models: 1 Model: "" Number of chains: 14 Chain: "D" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1544 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 186} Chain: "E" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1544 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 186} Chain: "F" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1544 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 186} Chain: "G" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1544 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 186} Chain: "H" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1544 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 186} Chain: "I" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1544 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 186} Chain: "J" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1544 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 186} Chain: "K" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1544 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 186} Chain: "L" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1544 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 186} Chain: "M" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1544 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 186} Chain: "N" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1544 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 186} Chain: "B" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 937 Classifications: {'DNA': 45} Link IDs: {'rna3p': 44} Chain: "A" Number of atoms: 1901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1901 Classifications: {'RNA': 88} Modifications used: {'rna2p_pur': 23, 'rna2p_pyr': 16, 'rna3p_pur': 30, 'rna3p_pyr': 19} Link IDs: {'rna2p': 38, 'rna3p': 49} Chain: "C" Number of atoms: 916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 916 Classifications: {'DNA': 45} Link IDs: {'rna3p': 44} Time building chain proxies: 4.47, per 1000 atoms: 0.22 Number of scatterers: 20738 At special positions: 0 Unit cell: (102.6, 111.72, 221.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 143 16.00 P 178 15.00 O 4341 8.00 N 3542 7.00 C 12534 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.67 Conformation dependent library (CDL) restraints added in 593.5 milliseconds 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4026 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 33 sheets defined 42.3% alpha, 36.9% beta 42 base pairs and 78 stacking pairs defined. Time for finding SS restraints: 2.21 Creating SS restraints... Processing helix chain 'D' and resid 19 through 23 Processing helix chain 'D' and resid 26 through 37 Processing helix chain 'D' and resid 42 through 58 removed outlier: 3.854A pdb=" N CYS D 58 " --> pdb=" O LEU D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 82 Processing helix chain 'D' and resid 83 through 85 No H-bonds generated for 'chain 'D' and resid 83 through 85' Processing helix chain 'D' and resid 86 through 93 removed outlier: 3.823A pdb=" N ASP D 91 " --> pdb=" O GLY D 87 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ARG D 92 " --> pdb=" O LYS D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 116 Processing helix chain 'D' and resid 117 through 120 removed outlier: 6.846A pdb=" N ASP D 120 " --> pdb=" O LYS D 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 117 through 120' Processing helix chain 'D' and resid 158 through 173 Processing helix chain 'E' and resid 19 through 23 Processing helix chain 'E' and resid 26 through 37 Processing helix chain 'E' and resid 42 through 56 removed outlier: 3.522A pdb=" N THR E 56 " --> pdb=" O SER E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 82 Processing helix chain 'E' and resid 83 through 85 No H-bonds generated for 'chain 'E' and resid 83 through 85' Processing helix chain 'E' and resid 86 through 93 removed outlier: 3.832A pdb=" N ASP E 91 " --> pdb=" O GLY E 87 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG E 92 " --> pdb=" O LYS E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 116 Processing helix chain 'E' and resid 117 through 120 removed outlier: 6.527A pdb=" N ASP E 120 " --> pdb=" O LYS E 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 117 through 120' Processing helix chain 'E' and resid 158 through 173 Processing helix chain 'F' and resid 19 through 23 removed outlier: 3.741A pdb=" N ASP F 23 " --> pdb=" O THR F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 37 Processing helix chain 'F' and resid 42 through 56 Processing helix chain 'F' and resid 70 through 82 Processing helix chain 'F' and resid 83 through 85 No H-bonds generated for 'chain 'F' and resid 83 through 85' Processing helix chain 'F' and resid 86 through 93 removed outlier: 3.864A pdb=" N ASP F 91 " --> pdb=" O GLY F 87 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ARG F 92 " --> pdb=" O LYS F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 116 Processing helix chain 'F' and resid 117 through 120 removed outlier: 6.429A pdb=" N ASP F 120 " --> pdb=" O LYS F 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 117 through 120' Processing helix chain 'F' and resid 158 through 173 Processing helix chain 'G' and resid 18 through 23 removed outlier: 4.677A pdb=" N LEU G 21 " --> pdb=" O ALA G 18 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP G 23 " --> pdb=" O THR G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 42 through 56 Processing helix chain 'G' and resid 70 through 82 Processing helix chain 'G' and resid 83 through 85 No H-bonds generated for 'chain 'G' and resid 83 through 85' Processing helix chain 'G' and resid 86 through 93 removed outlier: 3.641A pdb=" N ASP G 91 " --> pdb=" O GLY G 87 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG G 92 " --> pdb=" O LYS G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 116 Processing helix chain 'G' and resid 117 through 120 removed outlier: 6.621A pdb=" N ASP G 120 " --> pdb=" O LYS G 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 117 through 120' Processing helix chain 'G' and resid 158 through 173 Processing helix chain 'H' and resid 19 through 23 removed outlier: 3.575A pdb=" N ASP H 23 " --> pdb=" O THR H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 37 Processing helix chain 'H' and resid 42 through 57 Processing helix chain 'H' and resid 70 through 82 Processing helix chain 'H' and resid 83 through 85 No H-bonds generated for 'chain 'H' and resid 83 through 85' Processing helix chain 'H' and resid 86 through 93 removed outlier: 3.507A pdb=" N ASP H 91 " --> pdb=" O GLY H 87 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG H 92 " --> pdb=" O LYS H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 116 Processing helix chain 'H' and resid 117 through 120 removed outlier: 6.437A pdb=" N ASP H 120 " --> pdb=" O LYS H 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 117 through 120' Processing helix chain 'H' and resid 158 through 173 Processing helix chain 'I' and resid 19 through 23 removed outlier: 3.513A pdb=" N SER I 22 " --> pdb=" O ASP I 19 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASP I 23 " --> pdb=" O THR I 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 19 through 23' Processing helix chain 'I' and resid 26 through 37 removed outlier: 3.551A pdb=" N LEU I 35 " --> pdb=" O TYR I 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 57 Processing helix chain 'I' and resid 70 through 82 Processing helix chain 'I' and resid 83 through 85 No H-bonds generated for 'chain 'I' and resid 83 through 85' Processing helix chain 'I' and resid 86 through 93 removed outlier: 3.519A pdb=" N ASP I 91 " --> pdb=" O GLY I 87 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG I 92 " --> pdb=" O LYS I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 116 Processing helix chain 'I' and resid 117 through 120 removed outlier: 6.442A pdb=" N ASP I 120 " --> pdb=" O LYS I 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 117 through 120' Processing helix chain 'I' and resid 158 through 173 Processing helix chain 'J' and resid 19 through 23 removed outlier: 3.509A pdb=" N ASP J 23 " --> pdb=" O THR J 20 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 37 Processing helix chain 'J' and resid 42 through 57 Processing helix chain 'J' and resid 70 through 82 Processing helix chain 'J' and resid 83 through 85 No H-bonds generated for 'chain 'J' and resid 83 through 85' Processing helix chain 'J' and resid 86 through 93 removed outlier: 3.504A pdb=" N ARG J 92 " --> pdb=" O LYS J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 116 Processing helix chain 'J' and resid 117 through 120 removed outlier: 6.272A pdb=" N ASP J 120 " --> pdb=" O LYS J 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 117 through 120' Processing helix chain 'J' and resid 158 through 173 Processing helix chain 'K' and resid 19 through 23 removed outlier: 3.771A pdb=" N ASP K 23 " --> pdb=" O THR K 20 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 37 Processing helix chain 'K' and resid 42 through 57 removed outlier: 3.664A pdb=" N THR K 56 " --> pdb=" O SER K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 82 Processing helix chain 'K' and resid 83 through 85 No H-bonds generated for 'chain 'K' and resid 83 through 85' Processing helix chain 'K' and resid 86 through 93 removed outlier: 3.729A pdb=" N ARG K 92 " --> pdb=" O LYS K 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 116 Processing helix chain 'K' and resid 117 through 120 removed outlier: 6.575A pdb=" N ASP K 120 " --> pdb=" O LYS K 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 117 through 120' Processing helix chain 'K' and resid 158 through 173 Processing helix chain 'L' and resid 19 through 23 Processing helix chain 'L' and resid 26 through 37 Processing helix chain 'L' and resid 42 through 57 Processing helix chain 'L' and resid 70 through 82 Processing helix chain 'L' and resid 83 through 85 No H-bonds generated for 'chain 'L' and resid 83 through 85' Processing helix chain 'L' and resid 86 through 93 removed outlier: 3.810A pdb=" N ARG L 92 " --> pdb=" O LYS L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 116 Processing helix chain 'L' and resid 117 through 120 removed outlier: 6.447A pdb=" N ASP L 120 " --> pdb=" O LYS L 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 117 through 120' Processing helix chain 'L' and resid 158 through 173 Processing helix chain 'M' and resid 19 through 23 removed outlier: 3.609A pdb=" N ASP M 23 " --> pdb=" O THR M 20 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 37 Processing helix chain 'M' and resid 42 through 57 removed outlier: 3.529A pdb=" N THR M 56 " --> pdb=" O SER M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 70 through 82 Processing helix chain 'M' and resid 83 through 85 No H-bonds generated for 'chain 'M' and resid 83 through 85' Processing helix chain 'M' and resid 86 through 93 removed outlier: 3.883A pdb=" N ARG M 92 " --> pdb=" O LYS M 88 " (cutoff:3.500A) Processing helix chain 'M' and resid 111 through 116 Processing helix chain 'M' and resid 117 through 120 removed outlier: 6.511A pdb=" N ASP M 120 " --> pdb=" O LYS M 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 117 through 120' Processing helix chain 'M' and resid 158 through 173 Processing helix chain 'N' and resid 26 through 37 Processing helix chain 'N' and resid 42 through 58 removed outlier: 3.527A pdb=" N SER N 57 " --> pdb=" O GLN N 53 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N CYS N 58 " --> pdb=" O LEU N 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 70 through 82 removed outlier: 3.657A pdb=" N LYS N 82 " --> pdb=" O LYS N 78 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 85 No H-bonds generated for 'chain 'N' and resid 83 through 85' Processing helix chain 'N' and resid 86 through 93 removed outlier: 3.538A pdb=" N ILE N 90 " --> pdb=" O LEU N 86 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG N 92 " --> pdb=" O LYS N 88 " (cutoff:3.500A) Processing helix chain 'N' and resid 111 through 116 Processing helix chain 'N' and resid 118 through 120 No H-bonds generated for 'chain 'N' and resid 118 through 120' Processing helix chain 'N' and resid 158 through 173 Processing sheet with id=AA1, first strand: chain 'D' and resid 60 through 61 removed outlier: 5.345A pdb=" N PHE D 66 " --> pdb=" O MET D 103 " (cutoff:3.500A) removed outlier: 9.616A pdb=" N VAL D 100 " --> pdb=" O GLY D 149 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N GLY D 149 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLU D 147 " --> pdb=" O PRO D 102 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 60 through 61 removed outlier: 5.345A pdb=" N PHE D 66 " --> pdb=" O MET D 103 " (cutoff:3.500A) removed outlier: 9.616A pdb=" N VAL D 100 " --> pdb=" O GLY D 149 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N GLY D 149 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLU D 147 " --> pdb=" O PRO D 102 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N TRP D 144 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N LEU D 3 " --> pdb=" O GLU D 192 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N GLU D 192 " --> pdb=" O LEU D 3 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ASN D 5 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 14 through 15 Processing sheet with id=AA4, first strand: chain 'E' and resid 60 through 61 removed outlier: 5.412A pdb=" N PHE E 66 " --> pdb=" O MET E 103 " (cutoff:3.500A) removed outlier: 9.597A pdb=" N VAL E 100 " --> pdb=" O GLY E 149 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N GLY E 149 " --> pdb=" O VAL E 100 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLU E 147 " --> pdb=" O PRO E 102 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 60 through 61 removed outlier: 5.412A pdb=" N PHE E 66 " --> pdb=" O MET E 103 " (cutoff:3.500A) removed outlier: 9.597A pdb=" N VAL E 100 " --> pdb=" O GLY E 149 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N GLY E 149 " --> pdb=" O VAL E 100 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLU E 147 " --> pdb=" O PRO E 102 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N TRP E 144 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU E 3 " --> pdb=" O GLU E 192 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLU E 192 " --> pdb=" O LEU E 3 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ASN E 5 " --> pdb=" O MET E 190 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 14 through 15 Processing sheet with id=AA7, first strand: chain 'F' and resid 60 through 61 removed outlier: 5.400A pdb=" N PHE F 66 " --> pdb=" O MET F 103 " (cutoff:3.500A) removed outlier: 9.664A pdb=" N VAL F 100 " --> pdb=" O GLY F 149 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N GLY F 149 " --> pdb=" O VAL F 100 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLU F 147 " --> pdb=" O PRO F 102 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 60 through 61 removed outlier: 5.400A pdb=" N PHE F 66 " --> pdb=" O MET F 103 " (cutoff:3.500A) removed outlier: 9.664A pdb=" N VAL F 100 " --> pdb=" O GLY F 149 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N GLY F 149 " --> pdb=" O VAL F 100 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLU F 147 " --> pdb=" O PRO F 102 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N TRP F 144 " --> pdb=" O GLY F 10 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU F 3 " --> pdb=" O GLU F 192 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N GLU F 192 " --> pdb=" O LEU F 3 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ASN F 5 " --> pdb=" O MET F 190 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 14 through 15 Processing sheet with id=AB1, first strand: chain 'G' and resid 60 through 61 removed outlier: 5.258A pdb=" N PHE G 66 " --> pdb=" O MET G 103 " (cutoff:3.500A) removed outlier: 9.407A pdb=" N VAL G 100 " --> pdb=" O GLY G 149 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N GLY G 149 " --> pdb=" O VAL G 100 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLU G 147 " --> pdb=" O PRO G 102 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 60 through 61 removed outlier: 5.258A pdb=" N PHE G 66 " --> pdb=" O MET G 103 " (cutoff:3.500A) removed outlier: 9.407A pdb=" N VAL G 100 " --> pdb=" O GLY G 149 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N GLY G 149 " --> pdb=" O VAL G 100 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLU G 147 " --> pdb=" O PRO G 102 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N TRP G 144 " --> pdb=" O GLY G 10 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU G 3 " --> pdb=" O GLU G 192 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLU G 192 " --> pdb=" O LEU G 3 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ASN G 5 " --> pdb=" O MET G 190 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 14 through 15 Processing sheet with id=AB4, first strand: chain 'H' and resid 60 through 61 removed outlier: 5.333A pdb=" N PHE H 66 " --> pdb=" O MET H 103 " (cutoff:3.500A) removed outlier: 9.679A pdb=" N VAL H 100 " --> pdb=" O GLY H 149 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N GLY H 149 " --> pdb=" O VAL H 100 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLU H 147 " --> pdb=" O PRO H 102 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 60 through 61 removed outlier: 5.333A pdb=" N PHE H 66 " --> pdb=" O MET H 103 " (cutoff:3.500A) removed outlier: 9.679A pdb=" N VAL H 100 " --> pdb=" O GLY H 149 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N GLY H 149 " --> pdb=" O VAL H 100 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLU H 147 " --> pdb=" O PRO H 102 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N TRP H 144 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER H 191 " --> pdb=" O ASN H 5 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LYS H 7 " --> pdb=" O ILE H 189 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ILE H 189 " --> pdb=" O LYS H 7 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N THR H 9 " --> pdb=" O VAL H 187 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N VAL H 187 " --> pdb=" O THR H 9 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 14 through 15 Processing sheet with id=AB7, first strand: chain 'I' and resid 60 through 61 removed outlier: 5.129A pdb=" N PHE I 66 " --> pdb=" O MET I 103 " (cutoff:3.500A) removed outlier: 9.583A pdb=" N VAL I 100 " --> pdb=" O GLY I 149 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N GLY I 149 " --> pdb=" O VAL I 100 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLU I 147 " --> pdb=" O PRO I 102 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 60 through 61 removed outlier: 5.129A pdb=" N PHE I 66 " --> pdb=" O MET I 103 " (cutoff:3.500A) removed outlier: 9.583A pdb=" N VAL I 100 " --> pdb=" O GLY I 149 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N GLY I 149 " --> pdb=" O VAL I 100 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLU I 147 " --> pdb=" O PRO I 102 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N TRP I 144 " --> pdb=" O GLY I 10 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU I 3 " --> pdb=" O GLU I 192 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N GLU I 192 " --> pdb=" O LEU I 3 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN I 5 " --> pdb=" O MET I 190 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 14 through 15 Processing sheet with id=AC1, first strand: chain 'J' and resid 60 through 61 removed outlier: 5.288A pdb=" N PHE J 66 " --> pdb=" O MET J 103 " (cutoff:3.500A) removed outlier: 9.694A pdb=" N VAL J 100 " --> pdb=" O GLY J 149 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N GLY J 149 " --> pdb=" O VAL J 100 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N GLU J 147 " --> pdb=" O PRO J 102 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 60 through 61 removed outlier: 5.288A pdb=" N PHE J 66 " --> pdb=" O MET J 103 " (cutoff:3.500A) removed outlier: 9.694A pdb=" N VAL J 100 " --> pdb=" O GLY J 149 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N GLY J 149 " --> pdb=" O VAL J 100 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N GLU J 147 " --> pdb=" O PRO J 102 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N TRP J 144 " --> pdb=" O GLY J 10 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU J 3 " --> pdb=" O GLU J 192 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLU J 192 " --> pdb=" O LEU J 3 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ASN J 5 " --> pdb=" O MET J 190 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 14 through 15 Processing sheet with id=AC4, first strand: chain 'K' and resid 60 through 61 removed outlier: 5.434A pdb=" N PHE K 66 " --> pdb=" O MET K 103 " (cutoff:3.500A) removed outlier: 9.530A pdb=" N VAL K 100 " --> pdb=" O GLY K 149 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N GLY K 149 " --> pdb=" O VAL K 100 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU K 147 " --> pdb=" O PRO K 102 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 60 through 61 removed outlier: 5.434A pdb=" N PHE K 66 " --> pdb=" O MET K 103 " (cutoff:3.500A) removed outlier: 9.530A pdb=" N VAL K 100 " --> pdb=" O GLY K 149 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N GLY K 149 " --> pdb=" O VAL K 100 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU K 147 " --> pdb=" O PRO K 102 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N TRP K 144 " --> pdb=" O GLY K 10 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU K 3 " --> pdb=" O GLU K 192 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLU K 192 " --> pdb=" O LEU K 3 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ASN K 5 " --> pdb=" O MET K 190 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 14 through 15 Processing sheet with id=AC7, first strand: chain 'L' and resid 60 through 61 removed outlier: 5.299A pdb=" N PHE L 66 " --> pdb=" O MET L 103 " (cutoff:3.500A) removed outlier: 9.800A pdb=" N VAL L 100 " --> pdb=" O GLY L 149 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N GLY L 149 " --> pdb=" O VAL L 100 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU L 147 " --> pdb=" O PRO L 102 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 60 through 61 removed outlier: 5.299A pdb=" N PHE L 66 " --> pdb=" O MET L 103 " (cutoff:3.500A) removed outlier: 9.800A pdb=" N VAL L 100 " --> pdb=" O GLY L 149 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N GLY L 149 " --> pdb=" O VAL L 100 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU L 147 " --> pdb=" O PRO L 102 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N TRP L 144 " --> pdb=" O GLY L 10 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU L 3 " --> pdb=" O GLU L 192 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLU L 192 " --> pdb=" O LEU L 3 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASN L 5 " --> pdb=" O MET L 190 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 14 through 15 Processing sheet with id=AD1, first strand: chain 'M' and resid 60 through 61 removed outlier: 5.334A pdb=" N PHE M 66 " --> pdb=" O MET M 103 " (cutoff:3.500A) removed outlier: 9.504A pdb=" N VAL M 100 " --> pdb=" O GLY M 149 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N GLY M 149 " --> pdb=" O VAL M 100 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLU M 147 " --> pdb=" O PRO M 102 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 60 through 61 removed outlier: 5.334A pdb=" N PHE M 66 " --> pdb=" O MET M 103 " (cutoff:3.500A) removed outlier: 9.504A pdb=" N VAL M 100 " --> pdb=" O GLY M 149 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N GLY M 149 " --> pdb=" O VAL M 100 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLU M 147 " --> pdb=" O PRO M 102 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N TRP M 144 " --> pdb=" O GLY M 10 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU M 3 " --> pdb=" O GLU M 192 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLU M 192 " --> pdb=" O LEU M 3 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ASN M 5 " --> pdb=" O MET M 190 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 14 through 15 Processing sheet with id=AD4, first strand: chain 'N' and resid 60 through 61 removed outlier: 5.388A pdb=" N PHE N 66 " --> pdb=" O MET N 103 " (cutoff:3.500A) removed outlier: 9.517A pdb=" N VAL N 100 " --> pdb=" O GLY N 149 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N GLY N 149 " --> pdb=" O VAL N 100 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLU N 147 " --> pdb=" O PRO N 102 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 60 through 61 removed outlier: 5.388A pdb=" N PHE N 66 " --> pdb=" O MET N 103 " (cutoff:3.500A) removed outlier: 9.517A pdb=" N VAL N 100 " --> pdb=" O GLY N 149 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N GLY N 149 " --> pdb=" O VAL N 100 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLU N 147 " --> pdb=" O PRO N 102 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N TRP N 144 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU N 3 " --> pdb=" O GLU N 192 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N GLU N 192 " --> pdb=" O LEU N 3 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ASN N 5 " --> pdb=" O MET N 190 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 14 through 15 940 hydrogen bonds defined for protein. 2619 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 102 hydrogen bonds 194 hydrogen bond angles 0 basepair planarities 42 basepair parallelities 78 stacking parallelities Total time for adding SS restraints: 3.36 Time building geometry restraints manager: 2.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4969 1.33 - 1.45: 4745 1.45 - 1.57: 11191 1.57 - 1.69: 353 1.69 - 1.81: 242 Bond restraints: 21500 Sorted by residual: bond pdb=" C3' DA B 12 " pdb=" C2' DA B 12 " ideal model delta sigma weight residual 1.516 1.549 -0.033 8.00e-03 1.56e+04 1.75e+01 bond pdb=" C3' DG B 15 " pdb=" C2' DG B 15 " ideal model delta sigma weight residual 1.516 1.547 -0.031 8.00e-03 1.56e+04 1.51e+01 bond pdb=" C1' DC C 40 " pdb=" N1 DC C 40 " ideal model delta sigma weight residual 1.468 1.522 -0.054 1.40e-02 5.10e+03 1.50e+01 bond pdb=" C3' DT C 15 " pdb=" C2' DT C 15 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.42e+01 bond pdb=" C3' DA C 54 " pdb=" C2' DA C 54 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.39e+01 ... (remaining 21495 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 29429 2.42 - 4.84: 378 4.84 - 7.26: 7 7.26 - 9.68: 0 9.68 - 12.10: 2 Bond angle restraints: 29816 Sorted by residual: angle pdb=" O4' DT C 17 " pdb=" C1' DT C 17 " pdb=" N1 DT C 17 " ideal model delta sigma weight residual 108.00 111.76 -3.76 7.00e-01 2.04e+00 2.88e+01 angle pdb=" N1 C A 27 " pdb=" C2 C A 27 " pdb=" O2 C A 27 " ideal model delta sigma weight residual 118.90 122.09 -3.19 6.00e-01 2.78e+00 2.83e+01 angle pdb=" O4' DC C 13 " pdb=" C1' DC C 13 " pdb=" N1 DC C 13 " ideal model delta sigma weight residual 108.00 111.69 -3.69 7.00e-01 2.04e+00 2.77e+01 angle pdb=" O4' DC C 40 " pdb=" C1' DC C 40 " pdb=" N1 DC C 40 " ideal model delta sigma weight residual 108.00 111.50 -3.50 7.00e-01 2.04e+00 2.50e+01 angle pdb=" C4' DC C 13 " pdb=" O4' DC C 13 " pdb=" C1' DC C 13 " ideal model delta sigma weight residual 110.10 105.11 4.99 1.00e+00 1.00e+00 2.49e+01 ... (remaining 29811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.27: 12342 34.27 - 68.54: 617 68.54 - 102.81: 32 102.81 - 137.08: 2 137.08 - 171.35: 6 Dihedral angle restraints: 12999 sinusoidal: 6773 harmonic: 6226 Sorted by residual: dihedral pdb=" O4' U A 30 " pdb=" C1' U A 30 " pdb=" N1 U A 30 " pdb=" C2 U A 30 " ideal model delta sinusoidal sigma weight residual 232.00 67.33 164.67 1 1.70e+01 3.46e-03 6.53e+01 dihedral pdb=" O4' U A 80 " pdb=" C1' U A 80 " pdb=" N1 U A 80 " pdb=" C2 U A 80 " ideal model delta sinusoidal sigma weight residual -160.00 -95.26 -64.74 1 1.50e+01 4.44e-03 2.45e+01 dihedral pdb=" C4' DC C 19 " pdb=" C3' DC C 19 " pdb=" O3' DC C 19 " pdb=" P DA C 20 " ideal model delta sinusoidal sigma weight residual -140.00 31.35 -171.35 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 12996 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 3185 0.096 - 0.193: 220 0.193 - 0.289: 1 0.289 - 0.385: 0 0.385 - 0.481: 1 Chirality restraints: 3407 Sorted by residual: chirality pdb=" P DC C 49 " pdb=" OP1 DC C 49 " pdb=" OP2 DC C 49 " pdb=" O5' DC C 49 " both_signs ideal model delta sigma weight residual True 2.34 -2.82 -0.48 2.00e-01 2.50e+01 5.80e+00 chirality pdb=" C3' G A 78 " pdb=" C4' G A 78 " pdb=" O3' G A 78 " pdb=" C2' G A 78 " both_signs ideal model delta sigma weight residual False -2.74 -2.55 -0.20 2.00e-01 2.50e+01 9.51e-01 chirality pdb=" C1' G A 32 " pdb=" O4' G A 32 " pdb=" C2' G A 32 " pdb=" N9 G A 32 " both_signs ideal model delta sigma weight residual False 2.47 2.28 0.19 2.00e-01 2.50e+01 8.78e-01 ... (remaining 3404 not shown) Planarity restraints: 3148 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C A 27 " 0.026 2.00e-02 2.50e+03 1.41e-02 4.48e+00 pdb=" N1 C A 27 " -0.032 2.00e-02 2.50e+03 pdb=" C2 C A 27 " -0.006 2.00e-02 2.50e+03 pdb=" O2 C A 27 " 0.001 2.00e-02 2.50e+03 pdb=" N3 C A 27 " 0.002 2.00e-02 2.50e+03 pdb=" C4 C A 27 " 0.006 2.00e-02 2.50e+03 pdb=" N4 C A 27 " 0.006 2.00e-02 2.50e+03 pdb=" C5 C A 27 " -0.001 2.00e-02 2.50e+03 pdb=" C6 C A 27 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U A 12 " -0.023 2.00e-02 2.50e+03 1.36e-02 4.17e+00 pdb=" N1 U A 12 " 0.032 2.00e-02 2.50e+03 pdb=" C2 U A 12 " -0.002 2.00e-02 2.50e+03 pdb=" O2 U A 12 " 0.003 2.00e-02 2.50e+03 pdb=" N3 U A 12 " -0.002 2.00e-02 2.50e+03 pdb=" C4 U A 12 " -0.007 2.00e-02 2.50e+03 pdb=" O4 U A 12 " -0.003 2.00e-02 2.50e+03 pdb=" C5 U A 12 " 0.001 2.00e-02 2.50e+03 pdb=" C6 U A 12 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 32 " 0.027 2.00e-02 2.50e+03 1.16e-02 4.00e+00 pdb=" N9 G A 32 " -0.027 2.00e-02 2.50e+03 pdb=" C8 G A 32 " -0.003 2.00e-02 2.50e+03 pdb=" N7 G A 32 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G A 32 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G A 32 " 0.001 2.00e-02 2.50e+03 pdb=" O6 G A 32 " 0.008 2.00e-02 2.50e+03 pdb=" N1 G A 32 " 0.004 2.00e-02 2.50e+03 pdb=" C2 G A 32 " -0.005 2.00e-02 2.50e+03 pdb=" N2 G A 32 " 0.000 2.00e-02 2.50e+03 pdb=" N3 G A 32 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G A 32 " -0.004 2.00e-02 2.50e+03 ... (remaining 3145 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.97: 8747 2.97 - 3.45: 18281 3.45 - 3.93: 33401 3.93 - 4.42: 38285 4.42 - 4.90: 63073 Nonbonded interactions: 161787 Sorted by model distance: nonbonded pdb=" O4' DC C 40 " pdb=" O2 DC C 40 " model vdw 2.483 3.040 nonbonded pdb=" O5' DC B 50 " pdb=" O4' DC B 50 " model vdw 2.504 2.432 nonbonded pdb=" O5' DA B 19 " pdb=" O4' DA B 19 " model vdw 2.510 2.432 nonbonded pdb=" O4' DC B 50 " pdb=" O2 DC B 50 " model vdw 2.532 3.040 nonbonded pdb=" O4' C A 27 " pdb=" C6 C A 27 " model vdw 2.551 2.672 ... (remaining 161782 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 '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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.270 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: 0.340 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 19.390 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 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 : 0.003 0.054 21500 Z= 0.278 Angle : 0.599 12.100 29816 Z= 0.488 Chirality : 0.049 0.481 3407 Planarity : 0.004 0.036 3148 Dihedral : 17.600 171.349 8973 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.18), residues: 2123 helix: 1.54 (0.19), residues: 748 sheet: 1.31 (0.23), residues: 506 loop : 0.03 (0.19), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 39 TYR 0.010 0.001 TYR G 59 PHE 0.009 0.001 PHE H 14 TRP 0.004 0.001 TRP L 178 HIS 0.002 0.001 HIS K 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.28 (21500) covalent geometry : angle 0.59913 / 0.49 (29816) hydrogen bonds : bond 0.16231 / 11.01 ( 965) hydrogen bonds : angle 7.10574 / 4.93 ( 2813) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 343 time to evaluate : 0.688 Fit side-chains REVERT: F 40 LYS cc_start: 0.7873 (mtmm) cc_final: 0.7669 (mtpp) REVERT: F 64 LEU cc_start: 0.8546 (mp) cc_final: 0.8303 (mp) REVERT: G 63 GLN cc_start: 0.8094 (pm20) cc_final: 0.7829 (pm20) REVERT: G 64 LEU cc_start: 0.8972 (mp) cc_final: 0.8768 (mp) REVERT: G 71 GLU cc_start: 0.7394 (tt0) cc_final: 0.7146 (tt0) REVERT: G 135 MET cc_start: 0.8188 (tpt) cc_final: 0.7871 (tpt) REVERT: H 95 MET cc_start: 0.8967 (ptm) cc_final: 0.8655 (ptt) REVERT: H 135 MET cc_start: 0.8724 (tpt) cc_final: 0.8333 (tpt) REVERT: I 63 GLN cc_start: 0.8106 (mm-40) cc_final: 0.7872 (mm-40) REVERT: I 72 MET cc_start: 0.8718 (ttp) cc_final: 0.8312 (ttm) REVERT: I 103 MET cc_start: 0.8996 (ttt) cc_final: 0.8748 (ttt) REVERT: J 51 GLU cc_start: 0.8523 (tt0) cc_final: 0.8182 (mp0) REVERT: J 72 MET cc_start: 0.8628 (ttm) cc_final: 0.8369 (ttm) REVERT: K 2 LYS cc_start: 0.8030 (mmtt) cc_final: 0.7637 (mtpt) REVERT: L 68 MET cc_start: 0.9108 (ttm) cc_final: 0.8866 (ttp) REVERT: L 103 MET cc_start: 0.9114 (ttp) cc_final: 0.8912 (ttm) REVERT: L 155 GLU cc_start: 0.8460 (mt-10) cc_final: 0.7955 (tm-30) REVERT: M 59 TYR cc_start: 0.8512 (m-80) cc_final: 0.8226 (m-80) REVERT: M 72 MET cc_start: 0.8136 (ttm) cc_final: 0.7871 (ttp) REVERT: M 85 LYS cc_start: 0.7918 (mttt) cc_final: 0.7523 (mmmt) REVERT: M 88 LYS cc_start: 0.8089 (mttt) cc_final: 0.7618 (tttt) REVERT: N 163 LEU cc_start: 0.7090 (tt) cc_final: 0.6738 (mp) outliers start: 0 outliers final: 0 residues processed: 343 average time/residue: 0.1538 time to fit residues: 80.7683 Evaluate side-chains 272 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: [216, 98, 194, 107, 10, 66, 130, 124, 103, 200, 212] chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 0.8980 chunk 212 optimal weight: 9.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 119 GLN E 107 ASN H 119 GLN J 63 GLN M 119 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.154175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.112004 restraints weight = 24792.842| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.59 r_work: 0.3237 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 21500 Z= 0.229 Angle : 0.626 8.796 29816 Z= 0.356 Chirality : 0.050 0.365 3407 Planarity : 0.005 0.041 3148 Dihedral : 21.875 173.084 4672 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 1.00 % Allowed : 5.29 % Favored : 93.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.18), residues: 2123 helix: 1.22 (0.19), residues: 825 sheet: 0.86 (0.23), residues: 528 loop : -0.33 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 179 TYR 0.017 0.002 TYR G 59 PHE 0.017 0.002 PHE H 14 TRP 0.018 0.002 TRP E 178 HIS 0.007 0.002 HIS K 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.23 (21500) covalent geometry : angle 0.62622 / 0.36 (29816) hydrogen bonds : bond 0.05395 / 3.65 ( 965) hydrogen bonds : angle 5.43557 / 3.77 ( 2813) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 282 time to evaluate : 0.823 Fit side-chains REVERT: D 63 GLN cc_start: 0.8353 (mt0) cc_final: 0.7981 (mp10) REVERT: F 40 LYS cc_start: 0.7954 (mtmm) cc_final: 0.7711 (mtpp) REVERT: F 64 LEU cc_start: 0.8618 (mp) cc_final: 0.8386 (mp) REVERT: G 63 GLN cc_start: 0.8172 (pm20) cc_final: 0.7832 (pm20) REVERT: G 64 LEU cc_start: 0.8889 (mp) cc_final: 0.8642 (mp) REVERT: G 99 VAL cc_start: 0.8976 (t) cc_final: 0.8743 (m) REVERT: H 135 MET cc_start: 0.8905 (tpt) cc_final: 0.8527 (tpt) REVERT: H 194 ASN cc_start: 0.6911 (m110) cc_final: 0.6703 (m-40) REVERT: I 4 LEU cc_start: 0.8063 (mt) cc_final: 0.7853 (mp) REVERT: I 63 GLN cc_start: 0.8214 (mm-40) cc_final: 0.7928 (mm-40) REVERT: I 72 MET cc_start: 0.8671 (ttp) cc_final: 0.8083 (ttm) REVERT: J 51 GLU cc_start: 0.8451 (tt0) cc_final: 0.7847 (mm-30) REVERT: J 151 MET cc_start: 0.8810 (mtp) cc_final: 0.8577 (mtp) REVERT: K 104 THR cc_start: 0.8206 (m) cc_final: 0.7998 (m) REVERT: L 155 GLU cc_start: 0.8500 (mt-10) cc_final: 0.7894 (tm-30) REVERT: M 45 ASP cc_start: 0.8238 (m-30) cc_final: 0.7994 (m-30) REVERT: M 85 LYS cc_start: 0.8063 (mttt) cc_final: 0.7689 (mmmt) REVERT: M 88 LYS cc_start: 0.8083 (mttt) cc_final: 0.7448 (tttp) REVERT: N 1 MET cc_start: 0.4997 (mmp) cc_final: 0.4553 (mmp) REVERT: N 94 ILE cc_start: 0.6389 (mm) cc_final: 0.5991 (mt) REVERT: N 151 MET cc_start: 0.7686 (mtp) cc_final: 0.7025 (tpt) REVERT: N 163 LEU cc_start: 0.7034 (tt) cc_final: 0.6654 (mp) outliers start: 19 outliers final: 15 residues processed: 288 average time/residue: 0.1317 time to fit residues: 61.7600 Evaluate side-chains 279 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 264 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain H residue 119 GLN Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain I residue 91 ASP Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain J residue 126 SER Chi-restraints excluded: chain J residue 177 ASP Chi-restraints excluded: chain K residue 68 MET Chi-restraints excluded: chain K residue 145 SER Chi-restraints excluded: chain M residue 89 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: [136, 77, 29, 150, 218, 60, 177, 149, 44, 100, 17] chunk 136 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 29 optimal weight: 0.0010 chunk 150 optimal weight: 0.4980 chunk 218 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 chunk 177 optimal weight: 5.9990 chunk 149 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.2790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 119 GLN E 107 ASN J 63 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.157481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.115811 restraints weight = 24561.398| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.57 r_work: 0.3259 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21500 Z= 0.156 Angle : 0.543 7.061 29816 Z= 0.317 Chirality : 0.046 0.361 3407 Planarity : 0.004 0.041 3148 Dihedral : 21.863 172.934 4672 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.27 % Allowed : 6.45 % Favored : 92.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.18), residues: 2123 helix: 1.50 (0.19), residues: 814 sheet: 0.83 (0.23), residues: 528 loop : -0.39 (0.19), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 181 TYR 0.018 0.001 TYR K 31 PHE 0.010 0.001 PHE H 14 TRP 0.009 0.001 TRP E 178 HIS 0.004 0.001 HIS I 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 (21500) covalent geometry : angle 0.54255 / 0.32 (29816) hydrogen bonds : bond 0.04498 / 3.06 ( 965) hydrogen bonds : angle 5.08091 / 3.52 ( 2813) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 282 time to evaluate : 0.773 Fit side-chains REVERT: D 19 ASP cc_start: 0.8521 (p0) cc_final: 0.8320 (p0) REVERT: F 40 LYS cc_start: 0.7974 (mtmm) cc_final: 0.7766 (mtpp) REVERT: F 64 LEU cc_start: 0.8626 (mp) cc_final: 0.8385 (mp) REVERT: F 114 GLU cc_start: 0.8285 (tp30) cc_final: 0.7710 (mm-30) REVERT: G 63 GLN cc_start: 0.8177 (pm20) cc_final: 0.7787 (pm20) REVERT: G 64 LEU cc_start: 0.8878 (mp) cc_final: 0.8614 (mp) REVERT: G 99 VAL cc_start: 0.8996 (t) cc_final: 0.8774 (m) REVERT: H 114 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7905 (mt-10) REVERT: H 135 MET cc_start: 0.8870 (tpt) cc_final: 0.8522 (tpt) REVERT: I 63 GLN cc_start: 0.8186 (mm-40) cc_final: 0.7948 (mm-40) REVERT: I 72 MET cc_start: 0.8529 (ttp) cc_final: 0.7870 (ttm) REVERT: J 51 GLU cc_start: 0.8505 (tt0) cc_final: 0.7863 (mm-30) REVERT: J 151 MET cc_start: 0.8771 (mtp) cc_final: 0.8557 (mtp) REVERT: K 31 TYR cc_start: 0.8640 (t80) cc_final: 0.8364 (t80) REVERT: K 104 THR cc_start: 0.8159 (m) cc_final: 0.7951 (m) REVERT: L 155 GLU cc_start: 0.8502 (mt-10) cc_final: 0.7870 (tm-30) REVERT: M 45 ASP cc_start: 0.8171 (m-30) cc_final: 0.7957 (m-30) REVERT: M 85 LYS cc_start: 0.8081 (mttt) cc_final: 0.7725 (mmmt) REVERT: M 88 LYS cc_start: 0.8154 (mttt) cc_final: 0.7378 (tttp) REVERT: N 78 LYS cc_start: 0.7895 (tptt) cc_final: 0.7599 (tptt) REVERT: N 163 LEU cc_start: 0.7122 (tt) cc_final: 0.6748 (mp) outliers start: 24 outliers final: 17 residues processed: 290 average time/residue: 0.1316 time to fit residues: 61.4781 Evaluate side-chains 288 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 271 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain I residue 91 ASP Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 177 ASP Chi-restraints excluded: chain K residue 68 MET Chi-restraints excluded: chain K residue 145 SER Chi-restraints excluded: chain L residue 98 ASP Chi-restraints excluded: chain L residue 131 THR Chi-restraints excluded: chain L residue 158 THR Chi-restraints excluded: chain N residue 145 SER Chi-restraints excluded: chain N residue 171 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: [122, 36, 54, 28, 21, 198, 73, 69, 204, 192, 6] chunk 122 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 198 optimal weight: 5.9990 chunk 73 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 204 optimal weight: 2.9990 chunk 192 optimal weight: 8.9990 chunk 6 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 119 GLN E 107 ASN H 119 GLN J 63 GLN M 32 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.154711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.112794 restraints weight = 24730.220| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.62 r_work: 0.3208 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 21500 Z= 0.238 Angle : 0.618 7.265 29816 Z= 0.349 Chirality : 0.050 0.352 3407 Planarity : 0.005 0.043 3148 Dihedral : 21.963 173.977 4672 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 1.90 % Allowed : 7.61 % Favored : 90.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.18), residues: 2123 helix: 1.23 (0.19), residues: 825 sheet: 0.52 (0.23), residues: 528 loop : -0.64 (0.19), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 179 TYR 0.019 0.002 TYR G 59 PHE 0.017 0.002 PHE H 14 TRP 0.007 0.001 TRP L 144 HIS 0.005 0.002 HIS K 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.24 (21500) covalent geometry : angle 0.61788 / 0.35 (29816) hydrogen bonds : bond 0.05228 / 3.56 ( 965) hydrogen bonds : angle 5.04859 / 3.50 ( 2813) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 277 time to evaluate : 0.704 Fit side-chains revert: symmetry clash REVERT: D 19 ASP cc_start: 0.8708 (p0) cc_final: 0.8463 (p0) REVERT: F 40 LYS cc_start: 0.8026 (mtmm) cc_final: 0.7787 (mtpp) REVERT: F 64 LEU cc_start: 0.8683 (mp) cc_final: 0.8407 (mp) REVERT: F 114 GLU cc_start: 0.8396 (tp30) cc_final: 0.7784 (mm-30) REVERT: G 63 GLN cc_start: 0.8141 (pm20) cc_final: 0.7742 (pm20) REVERT: G 64 LEU cc_start: 0.8882 (mp) cc_final: 0.8584 (mp) REVERT: H 135 MET cc_start: 0.8823 (tpt) cc_final: 0.8576 (tpt) REVERT: I 72 MET cc_start: 0.8618 (ttp) cc_final: 0.7905 (ttm) REVERT: J 151 MET cc_start: 0.8795 (mtp) cc_final: 0.8571 (mtp) REVERT: K 31 TYR cc_start: 0.8690 (t80) cc_final: 0.8417 (t80) REVERT: L 155 GLU cc_start: 0.8534 (mt-10) cc_final: 0.7904 (tm-30) REVERT: M 45 ASP cc_start: 0.8231 (m-30) cc_final: 0.8025 (m-30) REVERT: M 85 LYS cc_start: 0.8183 (mttt) cc_final: 0.7785 (mmmt) REVERT: M 88 LYS cc_start: 0.8089 (mttt) cc_final: 0.7381 (tttp) REVERT: N 94 ILE cc_start: 0.6630 (mt) cc_final: 0.6323 (mt) REVERT: N 163 LEU cc_start: 0.7104 (tt) cc_final: 0.6742 (mp) outliers start: 36 outliers final: 27 residues processed: 295 average time/residue: 0.1233 time to fit residues: 59.4344 Evaluate side-chains 289 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 262 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 145 SER Chi-restraints excluded: chain F residue 177 ASP Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 164 MET Chi-restraints excluded: chain I residue 91 ASP Chi-restraints excluded: chain J residue 42 THR Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain J residue 126 SER Chi-restraints excluded: chain J residue 145 SER Chi-restraints excluded: chain J residue 175 VAL Chi-restraints excluded: chain J residue 177 ASP Chi-restraints excluded: chain K residue 68 MET Chi-restraints excluded: chain K residue 143 ASP Chi-restraints excluded: chain K residue 145 SER Chi-restraints excluded: chain L residue 131 THR Chi-restraints excluded: chain L residue 158 THR Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 145 SER Chi-restraints excluded: chain M residue 157 ILE Chi-restraints excluded: chain N residue 171 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: [120, 147, 170, 17, 46, 137, 74, 127, 208, 43, 123] chunk 120 optimal weight: 1.9990 chunk 147 optimal weight: 0.8980 chunk 170 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 127 optimal weight: 0.8980 chunk 208 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 123 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 107 ASN F 171 ASN G 156 GLN K 119 GLN M 111 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.157076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.115466 restraints weight = 24485.978| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.60 r_work: 0.3252 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 21500 Z= 0.134 Angle : 0.518 6.856 29816 Z= 0.304 Chirality : 0.045 0.307 3407 Planarity : 0.004 0.041 3148 Dihedral : 21.847 174.031 4672 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 1.64 % Allowed : 9.20 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.18), residues: 2123 helix: 1.60 (0.19), residues: 814 sheet: 0.59 (0.23), residues: 528 loop : -0.52 (0.19), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 181 TYR 0.014 0.001 TYR K 31 PHE 0.010 0.001 PHE I 148 TRP 0.004 0.001 TRP L 144 HIS 0.003 0.001 HIS I 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (21500) covalent geometry : angle 0.51811 / 0.30 (29816) hydrogen bonds : bond 0.04065 / 2.77 ( 965) hydrogen bonds : angle 4.81964 / 3.34 ( 2813) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 266 time to evaluate : 0.520 Fit side-chains REVERT: D 19 ASP cc_start: 0.8703 (p0) cc_final: 0.8463 (p0) REVERT: F 40 LYS cc_start: 0.8019 (mtmm) cc_final: 0.7780 (mtpp) REVERT: F 64 LEU cc_start: 0.8678 (mp) cc_final: 0.8393 (mp) REVERT: F 114 GLU cc_start: 0.8355 (tp30) cc_final: 0.7749 (mm-30) REVERT: G 63 GLN cc_start: 0.8141 (pm20) cc_final: 0.7739 (pm20) REVERT: G 64 LEU cc_start: 0.8872 (mp) cc_final: 0.8543 (mp) REVERT: H 91 ASP cc_start: 0.8425 (m-30) cc_final: 0.8166 (m-30) REVERT: H 135 MET cc_start: 0.8799 (tpt) cc_final: 0.8544 (tpt) REVERT: I 72 MET cc_start: 0.8550 (ttp) cc_final: 0.7816 (ttm) REVERT: J 51 GLU cc_start: 0.8519 (tt0) cc_final: 0.7922 (mp0) REVERT: J 151 MET cc_start: 0.8739 (mtp) cc_final: 0.8530 (mtp) REVERT: K 31 TYR cc_start: 0.8615 (t80) cc_final: 0.8313 (t80) REVERT: L 155 GLU cc_start: 0.8565 (mt-10) cc_final: 0.7890 (tm-30) REVERT: M 85 LYS cc_start: 0.8187 (mttt) cc_final: 0.7785 (mmmt) REVERT: M 88 LYS cc_start: 0.8078 (mttt) cc_final: 0.7368 (tttp) REVERT: M 106 LYS cc_start: 0.7851 (ttmm) cc_final: 0.7544 (ttpp) REVERT: M 111 ASN cc_start: 0.8697 (OUTLIER) cc_final: 0.8450 (p0) REVERT: N 78 LYS cc_start: 0.7860 (tptt) cc_final: 0.7651 (tptt) REVERT: N 94 ILE cc_start: 0.6695 (mt) cc_final: 0.6315 (mt) REVERT: N 163 LEU cc_start: 0.7152 (tt) cc_final: 0.6772 (mp) outliers start: 31 outliers final: 24 residues processed: 281 average time/residue: 0.1282 time to fit residues: 58.1111 Evaluate side-chains 287 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 262 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 119 GLN Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain I residue 91 ASP Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain J residue 126 SER Chi-restraints excluded: chain J residue 175 VAL Chi-restraints excluded: chain J residue 177 ASP Chi-restraints excluded: chain K residue 68 MET Chi-restraints excluded: chain K residue 91 ASP Chi-restraints excluded: chain K residue 145 SER Chi-restraints excluded: chain L residue 98 ASP Chi-restraints excluded: chain L residue 131 THR Chi-restraints excluded: chain L residue 158 THR Chi-restraints excluded: chain M residue 72 MET Chi-restraints excluded: chain M residue 111 ASN Chi-restraints excluded: chain N residue 145 SER Chi-restraints excluded: chain N residue 171 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: [112, 156, 132, 4, 61, 76, 218, 77, 53, 69, 28] chunk 112 optimal weight: 0.9990 chunk 156 optimal weight: 0.6980 chunk 132 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 218 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 107 ASN G 156 GLN M 111 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.157893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.117049 restraints weight = 24509.596| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.51 r_work: 0.3256 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 21500 Z= 0.124 Angle : 0.501 6.621 29816 Z= 0.295 Chirality : 0.044 0.276 3407 Planarity : 0.004 0.040 3148 Dihedral : 21.795 174.255 4672 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.59 % Allowed : 9.73 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.18), residues: 2123 helix: 1.73 (0.19), residues: 814 sheet: 0.59 (0.23), residues: 528 loop : -0.48 (0.19), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 181 TYR 0.015 0.001 TYR D 31 PHE 0.010 0.001 PHE I 148 TRP 0.003 0.001 TRP G 144 HIS 0.002 0.001 HIS K 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 (21500) covalent geometry : angle 0.50148 / 0.30 (29816) hydrogen bonds : bond 0.03830 / 2.61 ( 965) hydrogen bonds : angle 4.71577 / 3.27 ( 2813) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 267 time to evaluate : 0.673 Fit side-chains REVERT: D 19 ASP cc_start: 0.8711 (p0) cc_final: 0.8426 (p0) REVERT: D 63 GLN cc_start: 0.8231 (mp10) cc_final: 0.7781 (mp10) REVERT: E 68 MET cc_start: 0.8459 (ttm) cc_final: 0.8144 (ttp) REVERT: F 40 LYS cc_start: 0.7991 (mtmm) cc_final: 0.7770 (mtpp) REVERT: F 64 LEU cc_start: 0.8639 (mp) cc_final: 0.8344 (mp) REVERT: F 114 GLU cc_start: 0.8353 (tp30) cc_final: 0.7784 (mm-30) REVERT: G 63 GLN cc_start: 0.8159 (pm20) cc_final: 0.7758 (pm20) REVERT: G 64 LEU cc_start: 0.8842 (mp) cc_final: 0.8482 (mp) REVERT: H 91 ASP cc_start: 0.8437 (m-30) cc_final: 0.8184 (m-30) REVERT: H 135 MET cc_start: 0.8780 (tpt) cc_final: 0.8525 (tpt) REVERT: I 72 MET cc_start: 0.8534 (ttp) cc_final: 0.7802 (ttm) REVERT: J 51 GLU cc_start: 0.8501 (tt0) cc_final: 0.7909 (mp0) REVERT: K 31 TYR cc_start: 0.8586 (t80) cc_final: 0.8298 (t80) REVERT: L 155 GLU cc_start: 0.8540 (mt-10) cc_final: 0.7898 (tm-30) REVERT: M 85 LYS cc_start: 0.8164 (mttt) cc_final: 0.7789 (mmmt) REVERT: M 88 LYS cc_start: 0.8078 (mttt) cc_final: 0.7294 (tttp) REVERT: M 111 ASN cc_start: 0.8846 (OUTLIER) cc_final: 0.8396 (p0) REVERT: N 94 ILE cc_start: 0.6753 (mt) cc_final: 0.6382 (mt) REVERT: N 163 LEU cc_start: 0.7122 (tt) cc_final: 0.6755 (mp) outliers start: 30 outliers final: 27 residues processed: 282 average time/residue: 0.1241 time to fit residues: 56.5591 Evaluate side-chains 286 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 258 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 119 GLN Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain I residue 91 ASP Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 126 SER Chi-restraints excluded: chain J residue 175 VAL Chi-restraints excluded: chain J residue 177 ASP Chi-restraints excluded: chain K residue 68 MET Chi-restraints excluded: chain K residue 91 ASP Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 145 SER Chi-restraints excluded: chain L residue 98 ASP Chi-restraints excluded: chain L residue 131 THR Chi-restraints excluded: chain L residue 158 THR Chi-restraints excluded: chain M residue 72 MET Chi-restraints excluded: chain M residue 111 ASN Chi-restraints excluded: chain N residue 171 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: [136, 163, 133, 86, 212, 80, 72, 75, 71, 125, 209] chunk 136 optimal weight: 0.4980 chunk 163 optimal weight: 4.9990 chunk 133 optimal weight: 6.9990 chunk 86 optimal weight: 0.6980 chunk 212 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 72 optimal weight: 0.3980 chunk 75 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 209 optimal weight: 50.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 156 GLN M 111 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.157438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.116111 restraints weight = 24525.683| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.57 r_work: 0.3256 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 21500 Z= 0.140 Angle : 0.508 6.412 29816 Z= 0.297 Chirality : 0.044 0.257 3407 Planarity : 0.004 0.040 3148 Dihedral : 21.788 174.519 4672 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 1.96 % Allowed : 9.78 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.18), residues: 2123 helix: 1.72 (0.19), residues: 814 sheet: 0.54 (0.23), residues: 528 loop : -0.49 (0.19), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 133 TYR 0.013 0.001 TYR G 59 PHE 0.012 0.001 PHE I 148 TRP 0.004 0.001 TRP F 144 HIS 0.002 0.001 HIS K 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (21500) covalent geometry : angle 0.50812 / 0.30 (29816) hydrogen bonds : bond 0.03913 / 2.66 ( 965) hydrogen bonds : angle 4.67367 / 3.24 ( 2813) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 259 time to evaluate : 0.710 Fit side-chains revert: symmetry clash REVERT: D 19 ASP cc_start: 0.8713 (p0) cc_final: 0.8440 (p0) REVERT: D 63 GLN cc_start: 0.8154 (mp10) cc_final: 0.7710 (mp10) REVERT: F 40 LYS cc_start: 0.7994 (mtmm) cc_final: 0.7778 (mtpp) REVERT: F 64 LEU cc_start: 0.8639 (mp) cc_final: 0.8341 (mp) REVERT: F 114 GLU cc_start: 0.8349 (tp30) cc_final: 0.7785 (mm-30) REVERT: G 63 GLN cc_start: 0.8175 (pm20) cc_final: 0.7775 (pm20) REVERT: G 64 LEU cc_start: 0.8831 (mp) cc_final: 0.8469 (mp) REVERT: H 91 ASP cc_start: 0.8422 (m-30) cc_final: 0.8171 (m-30) REVERT: H 135 MET cc_start: 0.8748 (tpt) cc_final: 0.8528 (tpt) REVERT: I 72 MET cc_start: 0.8519 (ttp) cc_final: 0.7780 (ttm) REVERT: J 51 GLU cc_start: 0.8496 (tt0) cc_final: 0.7904 (mp0) REVERT: J 63 GLN cc_start: 0.8244 (mp-120) cc_final: 0.8011 (mp-120) REVERT: K 31 TYR cc_start: 0.8537 (t80) cc_final: 0.8224 (t80) REVERT: L 155 GLU cc_start: 0.8537 (mt-10) cc_final: 0.7897 (tm-30) REVERT: M 85 LYS cc_start: 0.8176 (mttt) cc_final: 0.7792 (mmmt) REVERT: M 88 LYS cc_start: 0.8085 (mttt) cc_final: 0.7293 (tttp) REVERT: N 94 ILE cc_start: 0.6725 (mt) cc_final: 0.6335 (mt) REVERT: N 163 LEU cc_start: 0.7138 (tt) cc_final: 0.6776 (mp) outliers start: 37 outliers final: 31 residues processed: 280 average time/residue: 0.1230 time to fit residues: 55.9272 Evaluate side-chains 289 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 258 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 119 GLN Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain I residue 91 ASP Chi-restraints excluded: chain I residue 151 MET Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 126 SER Chi-restraints excluded: chain J residue 145 SER Chi-restraints excluded: chain J residue 175 VAL Chi-restraints excluded: chain J residue 177 ASP Chi-restraints excluded: chain K residue 68 MET Chi-restraints excluded: chain K residue 91 ASP Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 145 SER Chi-restraints excluded: chain L residue 98 ASP Chi-restraints excluded: chain L residue 131 THR Chi-restraints excluded: chain L residue 158 THR Chi-restraints excluded: chain M residue 72 MET Chi-restraints excluded: chain N residue 145 SER Chi-restraints excluded: chain N residue 171 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: [72, 214, 99, 196, 34, 103, 16, 89, 216, 44, 77] chunk 72 optimal weight: 0.7980 chunk 214 optimal weight: 9.9990 chunk 99 optimal weight: 0.8980 chunk 196 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 216 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 156 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.156172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.114653 restraints weight = 24482.983| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.58 r_work: 0.3237 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21500 Z= 0.173 Angle : 0.542 6.150 29816 Z= 0.312 Chirality : 0.046 0.278 3407 Planarity : 0.004 0.040 3148 Dihedral : 21.813 174.990 4672 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 2.01 % Allowed : 9.83 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.18), residues: 2123 helix: 1.64 (0.19), residues: 814 sheet: 0.46 (0.23), residues: 528 loop : -0.58 (0.19), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 133 TYR 0.016 0.001 TYR G 59 PHE 0.013 0.002 PHE K 185 TRP 0.006 0.001 TRP K 144 HIS 0.003 0.001 HIS K 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (21500) covalent geometry : angle 0.54226 / 0.31 (29816) hydrogen bonds : bond 0.04325 / 2.94 ( 965) hydrogen bonds : angle 4.70816 / 3.26 ( 2813) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 262 time to evaluate : 0.666 Fit side-chains revert: symmetry clash REVERT: D 19 ASP cc_start: 0.8736 (p0) cc_final: 0.8474 (p0) REVERT: D 63 GLN cc_start: 0.8151 (mp10) cc_final: 0.7712 (mp10) REVERT: F 64 LEU cc_start: 0.8667 (mp) cc_final: 0.8352 (mp) REVERT: F 114 GLU cc_start: 0.8351 (tp30) cc_final: 0.7812 (mm-30) REVERT: F 177 ASP cc_start: 0.8941 (OUTLIER) cc_final: 0.8647 (t0) REVERT: G 63 GLN cc_start: 0.8206 (pm20) cc_final: 0.7798 (pm20) REVERT: G 64 LEU cc_start: 0.8818 (mp) cc_final: 0.8454 (mp) REVERT: H 151 MET cc_start: 0.8742 (mtm) cc_final: 0.8528 (mtp) REVERT: J 51 GLU cc_start: 0.8508 (tt0) cc_final: 0.7924 (mp0) REVERT: K 31 TYR cc_start: 0.8562 (t80) cc_final: 0.8301 (t80) REVERT: L 155 GLU cc_start: 0.8527 (mt-10) cc_final: 0.7887 (tm-30) REVERT: M 12 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.7882 (mtm180) REVERT: M 85 LYS cc_start: 0.8195 (mttt) cc_final: 0.7811 (mmmt) REVERT: M 88 LYS cc_start: 0.8062 (mttt) cc_final: 0.7308 (tttt) REVERT: N 94 ILE cc_start: 0.6699 (mt) cc_final: 0.6302 (mt) REVERT: N 163 LEU cc_start: 0.7163 (tt) cc_final: 0.6811 (mp) outliers start: 38 outliers final: 30 residues processed: 284 average time/residue: 0.1255 time to fit residues: 57.3900 Evaluate side-chains 292 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 260 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 177 ASP Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 119 GLN Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain I residue 91 ASP Chi-restraints excluded: chain J residue 126 SER Chi-restraints excluded: chain J residue 145 SER Chi-restraints excluded: chain J residue 175 VAL Chi-restraints excluded: chain J residue 177 ASP Chi-restraints excluded: chain K residue 68 MET Chi-restraints excluded: chain K residue 91 ASP Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 145 SER Chi-restraints excluded: chain L residue 98 ASP Chi-restraints excluded: chain L residue 131 THR Chi-restraints excluded: chain L residue 158 THR Chi-restraints excluded: chain M residue 12 ARG Chi-restraints excluded: chain M residue 72 MET Chi-restraints excluded: chain M residue 157 ILE Chi-restraints excluded: chain N residue 171 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: [16, 5, 62, 18, 98, 3, 28, 125, 75, 175, 210] chunk 16 optimal weight: 0.5980 chunk 5 optimal weight: 4.9990 chunk 62 optimal weight: 0.0070 chunk 18 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 125 optimal weight: 0.5980 chunk 75 optimal weight: 0.7980 chunk 175 optimal weight: 4.9990 chunk 210 optimal weight: 10.0000 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.158493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.117213 restraints weight = 24459.246| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.58 r_work: 0.3273 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 21500 Z= 0.118 Angle : 0.490 7.753 29816 Z= 0.288 Chirality : 0.043 0.249 3407 Planarity : 0.004 0.040 3148 Dihedral : 21.743 174.902 4672 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.59 % Allowed : 10.47 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.18), residues: 2123 helix: 1.80 (0.19), residues: 814 sheet: 0.53 (0.23), residues: 528 loop : -0.45 (0.19), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG M 181 TYR 0.011 0.001 TYR K 31 PHE 0.010 0.001 PHE E 182 TRP 0.004 0.001 TRP G 144 HIS 0.002 0.001 HIS I 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.12 (21500) covalent geometry : angle 0.49022 / 0.29 (29816) hydrogen bonds : bond 0.03608 / 2.45 ( 965) hydrogen bonds : angle 4.56850 / 3.17 ( 2813) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 265 time to evaluate : 0.705 Fit side-chains revert: symmetry clash REVERT: D 19 ASP cc_start: 0.8701 (p0) cc_final: 0.8447 (p0) REVERT: D 63 GLN cc_start: 0.8197 (mp10) cc_final: 0.7774 (mp10) REVERT: F 64 LEU cc_start: 0.8649 (mp) cc_final: 0.8347 (mp) REVERT: F 114 GLU cc_start: 0.8366 (tp30) cc_final: 0.7843 (mm-30) REVERT: F 177 ASP cc_start: 0.8900 (OUTLIER) cc_final: 0.8637 (t0) REVERT: G 63 GLN cc_start: 0.8203 (pm20) cc_final: 0.7795 (pm20) REVERT: G 64 LEU cc_start: 0.8829 (mp) cc_final: 0.8446 (mp) REVERT: J 51 GLU cc_start: 0.8459 (tt0) cc_final: 0.7895 (mp0) REVERT: J 63 GLN cc_start: 0.8314 (mp-120) cc_final: 0.8064 (mp-120) REVERT: K 31 TYR cc_start: 0.8506 (t80) cc_final: 0.8198 (t80) REVERT: L 155 GLU cc_start: 0.8478 (mt-10) cc_final: 0.7849 (tm-30) REVERT: M 12 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.7801 (mtm180) REVERT: M 85 LYS cc_start: 0.8151 (mttt) cc_final: 0.7792 (mmmt) REVERT: M 88 LYS cc_start: 0.7958 (mttt) cc_final: 0.7201 (tttt) REVERT: M 111 ASN cc_start: 0.8691 (p0) cc_final: 0.8359 (p0) REVERT: N 94 ILE cc_start: 0.6631 (mt) cc_final: 0.6243 (mt) REVERT: N 122 ILE cc_start: 0.5981 (mm) cc_final: 0.5439 (mm) REVERT: N 163 LEU cc_start: 0.7131 (tt) cc_final: 0.6796 (mt) outliers start: 30 outliers final: 24 residues processed: 284 average time/residue: 0.1266 time to fit residues: 58.2701 Evaluate side-chains 283 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 257 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 177 ASP Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 119 GLN Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain I residue 91 ASP Chi-restraints excluded: chain J residue 126 SER Chi-restraints excluded: chain J residue 145 SER Chi-restraints excluded: chain J residue 175 VAL Chi-restraints excluded: chain J residue 177 ASP Chi-restraints excluded: chain K residue 68 MET Chi-restraints excluded: chain K residue 91 ASP Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 145 SER Chi-restraints excluded: chain L residue 131 THR Chi-restraints excluded: chain L residue 158 THR Chi-restraints excluded: chain M residue 12 ARG Chi-restraints excluded: chain M residue 157 ILE Chi-restraints excluded: chain N residue 171 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: [137, 201, 54, 129, 186, 80, 125, 207, 108, 95, 180] chunk 137 optimal weight: 2.9990 chunk 201 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 186 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 125 optimal weight: 0.9990 chunk 207 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 180 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 156 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.158451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.117350 restraints weight = 24509.972| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.57 r_work: 0.3268 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21500 Z= 0.123 Angle : 0.493 9.057 29816 Z= 0.288 Chirality : 0.043 0.249 3407 Planarity : 0.004 0.039 3148 Dihedral : 21.729 175.092 4672 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 1.53 % Allowed : 10.89 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.18), residues: 2123 helix: 1.84 (0.19), residues: 814 sheet: 0.50 (0.23), residues: 528 loop : -0.43 (0.19), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG M 181 TYR 0.014 0.001 TYR D 31 PHE 0.010 0.001 PHE I 148 TRP 0.004 0.001 TRP G 144 HIS 0.002 0.001 HIS K 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (21500) covalent geometry : angle 0.49334 / 0.29 (29816) hydrogen bonds : bond 0.03624 / 2.45 ( 965) hydrogen bonds : angle 4.52161 / 3.13 ( 2813) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 264 time to evaluate : 0.681 Fit side-chains revert: symmetry clash REVERT: D 19 ASP cc_start: 0.8756 (p0) cc_final: 0.8509 (p0) REVERT: D 63 GLN cc_start: 0.8190 (mp10) cc_final: 0.7760 (mp10) REVERT: F 64 LEU cc_start: 0.8646 (mp) cc_final: 0.8345 (mp) REVERT: F 114 GLU cc_start: 0.8364 (tp30) cc_final: 0.7847 (mm-30) REVERT: F 177 ASP cc_start: 0.8893 (OUTLIER) cc_final: 0.8632 (t0) REVERT: G 63 GLN cc_start: 0.8228 (pm20) cc_final: 0.7822 (pm20) REVERT: G 64 LEU cc_start: 0.8819 (mp) cc_final: 0.8436 (mp) REVERT: I 19 ASP cc_start: 0.8414 (p0) cc_final: 0.8200 (p0) REVERT: J 51 GLU cc_start: 0.8474 (tt0) cc_final: 0.7896 (mp0) REVERT: K 31 TYR cc_start: 0.8528 (t80) cc_final: 0.8230 (t80) REVERT: L 155 GLU cc_start: 0.8497 (mt-10) cc_final: 0.7874 (tm-30) REVERT: M 12 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.7836 (mtm180) REVERT: M 85 LYS cc_start: 0.8112 (mttt) cc_final: 0.7800 (mmmt) REVERT: M 88 LYS cc_start: 0.7951 (mttt) cc_final: 0.7220 (tttt) REVERT: M 111 ASN cc_start: 0.8668 (p0) cc_final: 0.8355 (p0) REVERT: N 94 ILE cc_start: 0.6583 (mt) cc_final: 0.6188 (mt) REVERT: N 122 ILE cc_start: 0.6066 (mm) cc_final: 0.5546 (mm) REVERT: N 163 LEU cc_start: 0.7119 (tt) cc_final: 0.6796 (mt) outliers start: 29 outliers final: 27 residues processed: 283 average time/residue: 0.1267 time to fit residues: 57.8637 Evaluate side-chains 291 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 262 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 177 ASP Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 119 GLN Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain I residue 91 ASP Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 126 SER Chi-restraints excluded: chain J residue 145 SER Chi-restraints excluded: chain J residue 175 VAL Chi-restraints excluded: chain J residue 177 ASP Chi-restraints excluded: chain K residue 68 MET Chi-restraints excluded: chain K residue 91 ASP Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 145 SER Chi-restraints excluded: chain L residue 98 ASP Chi-restraints excluded: chain L residue 131 THR Chi-restraints excluded: chain L residue 158 THR Chi-restraints excluded: chain M residue 12 ARG Chi-restraints excluded: chain M residue 157 ILE Chi-restraints excluded: chain N residue 171 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: [93, 63, 80, 73, 180, 200, 191, 39, 223, 137, 18] chunk 93 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 180 optimal weight: 0.7980 chunk 200 optimal weight: 5.9990 chunk 191 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 223 optimal weight: 10.0000 chunk 137 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.155770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.114719 restraints weight = 24634.474| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.53 r_work: 0.3224 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 21500 Z= 0.203 Angle : 0.567 9.671 29816 Z= 0.321 Chirality : 0.047 0.295 3407 Planarity : 0.005 0.039 3148 Dihedral : 21.807 175.715 4672 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.59 % Allowed : 10.89 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.18), residues: 2123 helix: 1.52 (0.19), residues: 825 sheet: 0.36 (0.23), residues: 528 loop : -0.66 (0.19), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 133 TYR 0.017 0.002 TYR G 59 PHE 0.015 0.002 PHE H 14 TRP 0.008 0.001 TRP K 144 HIS 0.005 0.001 HIS K 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.20 (21500) covalent geometry : angle 0.56681 / 0.32 (29816) hydrogen bonds : bond 0.04512 / 3.07 ( 965) hydrogen bonds : angle 4.67376 / 3.24 ( 2813) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5201.60 seconds wall clock time: 89 minutes 33.73 seconds (5373.73 seconds total)