Starting phenix.real_space_refine on Thu Mar 5 10:36:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6r7g_4740/03_2026/6r7g_4740.cif Found real_map, /net/cci-nas-00/data/ceres_data/6r7g_4740/03_2026/6r7g_4740.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6r7g_4740/03_2026/6r7g_4740.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6r7g_4740/03_2026/6r7g_4740.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6r7g_4740/03_2026/6r7g_4740.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6r7g_4740/03_2026/6r7g_4740.map" } resolution = 2.2 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= 0.001 sd= 0.009 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 69 5.49 5 S 130 5.16 5 C 13595 2.51 5 N 3687 2.21 5 O 4531 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 91 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22012 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1580 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 14, 'TRANS': 194} Chain: "R" Number of atoms: 1380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1380 Classifications: {'RNA': 69} Modifications used: {'rna2p_pyr': 13, 'rna3p_pyr': 56} Link IDs: {'rna2p': 13, 'rna3p': 55} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "I" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 70 Classifications: {'water': 70} Link IDs: {None: 69} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M Time building chain proxies: 2.84, per 1000 atoms: 0.13 Number of scatterers: 22012 At special positions: 0 Unit cell: (139.763, 141.417, 109.991, 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 130 16.00 P 69 15.00 O 4531 8.00 N 3687 7.00 C 13595 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: 1.71 Conformation dependent library (CDL) restraints added in 1.0 seconds 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5174 Finding SS restraints... Secondary structure from input PDB file: 169 helices and 0 sheets defined 59.8% alpha, 0.0% beta 0 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 2.53 Creating SS restraints... Processing helix chain 'A' and resid 30 through 34 removed outlier: 3.660A pdb=" N THR A 34 " --> pdb=" O GLY A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 44 Processing helix chain 'A' and resid 55 through 69 Processing helix chain 'A' and resid 72 through 74 No H-bonds generated for 'chain 'A' and resid 72 through 74' Processing helix chain 'A' and resid 75 through 90 removed outlier: 3.618A pdb=" N ASP A 89 " --> pdb=" O ARG A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 118 Processing helix chain 'A' and resid 122 through 130 removed outlier: 3.762A pdb=" N TYR A 130 " --> pdb=" O PHE A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 142 Processing helix chain 'A' and resid 154 through 161 removed outlier: 3.533A pdb=" N LYS A 158 " --> pdb=" O PRO A 155 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N PHE A 159 " --> pdb=" O GLU A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 169 removed outlier: 4.053A pdb=" N THR A 169 " --> pdb=" O ASN A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 206 Processing helix chain 'A' and resid 214 through 219 Processing helix chain 'A' and resid 227 through 231 removed outlier: 3.622A pdb=" N VAL A 231 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 34 removed outlier: 3.660A pdb=" N THR B 34 " --> pdb=" O GLY B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 44 Processing helix chain 'B' and resid 55 through 69 Processing helix chain 'B' and resid 72 through 74 No H-bonds generated for 'chain 'B' and resid 72 through 74' Processing helix chain 'B' and resid 75 through 90 removed outlier: 3.619A pdb=" N ASP B 89 " --> pdb=" O ARG B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 118 Processing helix chain 'B' and resid 122 through 130 removed outlier: 3.762A pdb=" N TYR B 130 " --> pdb=" O PHE B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 142 Processing helix chain 'B' and resid 154 through 161 removed outlier: 3.533A pdb=" N LYS B 158 " --> pdb=" O PRO B 155 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N PHE B 159 " --> pdb=" O GLU B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 169 removed outlier: 4.053A pdb=" N THR B 169 " --> pdb=" O ASN B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 206 Processing helix chain 'B' and resid 214 through 219 Processing helix chain 'B' and resid 227 through 231 removed outlier: 3.623A pdb=" N VAL B 231 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 34 removed outlier: 3.661A pdb=" N THR C 34 " --> pdb=" O GLY C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 44 Processing helix chain 'C' and resid 55 through 69 Processing helix chain 'C' and resid 72 through 74 No H-bonds generated for 'chain 'C' and resid 72 through 74' Processing helix chain 'C' and resid 75 through 90 removed outlier: 3.619A pdb=" N ASP C 89 " --> pdb=" O ARG C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 118 Processing helix chain 'C' and resid 122 through 130 removed outlier: 3.763A pdb=" N TYR C 130 " --> pdb=" O PHE C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 142 Processing helix chain 'C' and resid 154 through 161 removed outlier: 3.532A pdb=" N LYS C 158 " --> pdb=" O PRO C 155 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N PHE C 159 " --> pdb=" O GLU C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 169 removed outlier: 4.054A pdb=" N THR C 169 " --> pdb=" O ASN C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 206 Processing helix chain 'C' and resid 214 through 219 Processing helix chain 'C' and resid 227 through 231 removed outlier: 3.622A pdb=" N VAL C 231 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 34 removed outlier: 3.660A pdb=" N THR D 34 " --> pdb=" O GLY D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 44 Processing helix chain 'D' and resid 55 through 69 Processing helix chain 'D' and resid 72 through 74 No H-bonds generated for 'chain 'D' and resid 72 through 74' Processing helix chain 'D' and resid 75 through 90 removed outlier: 3.618A pdb=" N ASP D 89 " --> pdb=" O ARG D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 118 Processing helix chain 'D' and resid 122 through 130 removed outlier: 3.763A pdb=" N TYR D 130 " --> pdb=" O PHE D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 142 Processing helix chain 'D' and resid 154 through 161 removed outlier: 3.532A pdb=" N LYS D 158 " --> pdb=" O PRO D 155 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N PHE D 159 " --> pdb=" O GLU D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 169 removed outlier: 4.053A pdb=" N THR D 169 " --> pdb=" O ASN D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 206 Processing helix chain 'D' and resid 214 through 219 Processing helix chain 'D' and resid 227 through 231 removed outlier: 3.622A pdb=" N VAL D 231 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 34 removed outlier: 3.659A pdb=" N THR E 34 " --> pdb=" O GLY E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 44 Processing helix chain 'E' and resid 55 through 69 Processing helix chain 'E' and resid 72 through 74 No H-bonds generated for 'chain 'E' and resid 72 through 74' Processing helix chain 'E' and resid 75 through 90 removed outlier: 3.618A pdb=" N ASP E 89 " --> pdb=" O ARG E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 118 Processing helix chain 'E' and resid 122 through 130 removed outlier: 3.763A pdb=" N TYR E 130 " --> pdb=" O PHE E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 142 Processing helix chain 'E' and resid 154 through 161 removed outlier: 3.532A pdb=" N LYS E 158 " --> pdb=" O PRO E 155 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N PHE E 159 " --> pdb=" O GLU E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 169 removed outlier: 4.052A pdb=" N THR E 169 " --> pdb=" O ASN E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 206 Processing helix chain 'E' and resid 214 through 219 Processing helix chain 'E' and resid 227 through 231 removed outlier: 3.622A pdb=" N VAL E 231 " --> pdb=" O ALA E 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 34 removed outlier: 3.660A pdb=" N THR F 34 " --> pdb=" O GLY F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 44 Processing helix chain 'F' and resid 55 through 69 Processing helix chain 'F' and resid 72 through 74 No H-bonds generated for 'chain 'F' and resid 72 through 74' Processing helix chain 'F' and resid 75 through 90 removed outlier: 3.619A pdb=" N ASP F 89 " --> pdb=" O ARG F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 118 Processing helix chain 'F' and resid 122 through 130 removed outlier: 3.763A pdb=" N TYR F 130 " --> pdb=" O PHE F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 142 Processing helix chain 'F' and resid 154 through 161 removed outlier: 3.533A pdb=" N LYS F 158 " --> pdb=" O PRO F 155 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N PHE F 159 " --> pdb=" O GLU F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 169 removed outlier: 4.053A pdb=" N THR F 169 " --> pdb=" O ASN F 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 206 Processing helix chain 'F' and resid 214 through 219 Processing helix chain 'F' and resid 227 through 231 removed outlier: 3.621A pdb=" N VAL F 231 " --> pdb=" O ALA F 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 34 removed outlier: 3.661A pdb=" N THR G 34 " --> pdb=" O GLY G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 44 Processing helix chain 'G' and resid 55 through 69 Processing helix chain 'G' and resid 72 through 74 No H-bonds generated for 'chain 'G' and resid 72 through 74' Processing helix chain 'G' and resid 75 through 90 removed outlier: 3.618A pdb=" N ASP G 89 " --> pdb=" O ARG G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 118 Processing helix chain 'G' and resid 122 through 130 removed outlier: 3.763A pdb=" N TYR G 130 " --> pdb=" O PHE G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 142 Processing helix chain 'G' and resid 154 through 161 removed outlier: 3.533A pdb=" N LYS G 158 " --> pdb=" O PRO G 155 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N PHE G 159 " --> pdb=" O GLU G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 169 removed outlier: 4.052A pdb=" N THR G 169 " --> pdb=" O ASN G 166 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 206 Processing helix chain 'G' and resid 214 through 219 Processing helix chain 'G' and resid 227 through 231 removed outlier: 3.623A pdb=" N VAL G 231 " --> pdb=" O ALA G 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 34 removed outlier: 3.660A pdb=" N THR H 34 " --> pdb=" O GLY H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 44 Processing helix chain 'H' and resid 55 through 69 Processing helix chain 'H' and resid 72 through 74 No H-bonds generated for 'chain 'H' and resid 72 through 74' Processing helix chain 'H' and resid 75 through 90 removed outlier: 3.618A pdb=" N ASP H 89 " --> pdb=" O ARG H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 109 through 118 Processing helix chain 'H' and resid 122 through 130 removed outlier: 3.763A pdb=" N TYR H 130 " --> pdb=" O PHE H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 142 Processing helix chain 'H' and resid 154 through 161 removed outlier: 3.532A pdb=" N LYS H 158 " --> pdb=" O PRO H 155 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N PHE H 159 " --> pdb=" O GLU H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 169 removed outlier: 4.052A pdb=" N THR H 169 " --> pdb=" O ASN H 166 " (cutoff:3.500A) Processing helix chain 'H' and resid 185 through 206 Processing helix chain 'H' and resid 214 through 219 Processing helix chain 'H' and resid 227 through 231 removed outlier: 3.622A pdb=" N VAL H 231 " --> pdb=" O ALA H 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 30 through 34 removed outlier: 3.660A pdb=" N THR I 34 " --> pdb=" O GLY I 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 38 through 44 Processing helix chain 'I' and resid 55 through 69 Processing helix chain 'I' and resid 72 through 74 No H-bonds generated for 'chain 'I' and resid 72 through 74' Processing helix chain 'I' and resid 75 through 90 removed outlier: 3.619A pdb=" N ASP I 89 " --> pdb=" O ARG I 85 " (cutoff:3.500A) Processing helix chain 'I' and resid 109 through 118 Processing helix chain 'I' and resid 122 through 130 removed outlier: 3.763A pdb=" N TYR I 130 " --> pdb=" O PHE I 126 " (cutoff:3.500A) Processing helix chain 'I' and resid 130 through 142 Processing helix chain 'I' and resid 154 through 161 removed outlier: 3.533A pdb=" N LYS I 158 " --> pdb=" O PRO I 155 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N PHE I 159 " --> pdb=" O GLU I 156 " (cutoff:3.500A) Processing helix chain 'I' and resid 164 through 169 removed outlier: 4.053A pdb=" N THR I 169 " --> pdb=" O ASN I 166 " (cutoff:3.500A) Processing helix chain 'I' and resid 185 through 206 Processing helix chain 'I' and resid 214 through 219 Processing helix chain 'I' and resid 227 through 231 removed outlier: 3.622A pdb=" N VAL I 231 " --> pdb=" O ALA I 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 34 removed outlier: 3.660A pdb=" N THR J 34 " --> pdb=" O GLY J 31 " (cutoff:3.500A) Processing helix chain 'J' and resid 38 through 44 Processing helix chain 'J' and resid 55 through 69 Processing helix chain 'J' and resid 72 through 74 No H-bonds generated for 'chain 'J' and resid 72 through 74' Processing helix chain 'J' and resid 75 through 90 removed outlier: 3.618A pdb=" N ASP J 89 " --> pdb=" O ARG J 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 118 Processing helix chain 'J' and resid 122 through 130 removed outlier: 3.763A pdb=" N TYR J 130 " --> pdb=" O PHE J 126 " (cutoff:3.500A) Processing helix chain 'J' and resid 130 through 142 Processing helix chain 'J' and resid 154 through 161 removed outlier: 3.532A pdb=" N LYS J 158 " --> pdb=" O PRO J 155 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N PHE J 159 " --> pdb=" O GLU J 156 " (cutoff:3.500A) Processing helix chain 'J' and resid 164 through 169 removed outlier: 4.053A pdb=" N THR J 169 " --> pdb=" O ASN J 166 " (cutoff:3.500A) Processing helix chain 'J' and resid 185 through 206 Processing helix chain 'J' and resid 214 through 219 Processing helix chain 'J' and resid 227 through 231 removed outlier: 3.622A pdb=" N VAL J 231 " --> pdb=" O ALA J 228 " (cutoff:3.500A) Processing helix chain 'K' and resid 30 through 34 removed outlier: 3.660A pdb=" N THR K 34 " --> pdb=" O GLY K 31 " (cutoff:3.500A) Processing helix chain 'K' and resid 38 through 44 Processing helix chain 'K' and resid 55 through 69 Processing helix chain 'K' and resid 72 through 74 No H-bonds generated for 'chain 'K' and resid 72 through 74' Processing helix chain 'K' and resid 75 through 90 removed outlier: 3.618A pdb=" N ASP K 89 " --> pdb=" O ARG K 85 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 118 Processing helix chain 'K' and resid 122 through 130 removed outlier: 3.763A pdb=" N TYR K 130 " --> pdb=" O PHE K 126 " (cutoff:3.500A) Processing helix chain 'K' and resid 130 through 142 Processing helix chain 'K' and resid 154 through 161 removed outlier: 3.532A pdb=" N LYS K 158 " --> pdb=" O PRO K 155 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N PHE K 159 " --> pdb=" O GLU K 156 " (cutoff:3.500A) Processing helix chain 'K' and resid 164 through 169 removed outlier: 4.052A pdb=" N THR K 169 " --> pdb=" O ASN K 166 " (cutoff:3.500A) Processing helix chain 'K' and resid 185 through 206 Processing helix chain 'K' and resid 214 through 219 Processing helix chain 'K' and resid 227 through 231 removed outlier: 3.622A pdb=" N VAL K 231 " --> pdb=" O ALA K 228 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 34 removed outlier: 3.660A pdb=" N THR L 34 " --> pdb=" O GLY L 31 " (cutoff:3.500A) Processing helix chain 'L' and resid 38 through 44 Processing helix chain 'L' and resid 55 through 69 Processing helix chain 'L' and resid 72 through 74 No H-bonds generated for 'chain 'L' and resid 72 through 74' Processing helix chain 'L' and resid 75 through 90 removed outlier: 3.619A pdb=" N ASP L 89 " --> pdb=" O ARG L 85 " (cutoff:3.500A) Processing helix chain 'L' and resid 109 through 118 Processing helix chain 'L' and resid 122 through 130 removed outlier: 3.763A pdb=" N TYR L 130 " --> pdb=" O PHE L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 142 Processing helix chain 'L' and resid 154 through 161 removed outlier: 3.532A pdb=" N LYS L 158 " --> pdb=" O PRO L 155 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N PHE L 159 " --> pdb=" O GLU L 156 " (cutoff:3.500A) Processing helix chain 'L' and resid 164 through 169 removed outlier: 4.053A pdb=" N THR L 169 " --> pdb=" O ASN L 166 " (cutoff:3.500A) Processing helix chain 'L' and resid 185 through 206 Processing helix chain 'L' and resid 214 through 219 Processing helix chain 'L' and resid 227 through 231 removed outlier: 3.622A pdb=" N VAL L 231 " --> pdb=" O ALA L 228 " (cutoff:3.500A) Processing helix chain 'M' and resid 30 through 34 removed outlier: 3.660A pdb=" N THR M 34 " --> pdb=" O GLY M 31 " (cutoff:3.500A) Processing helix chain 'M' and resid 38 through 44 Processing helix chain 'M' and resid 55 through 69 Processing helix chain 'M' and resid 72 through 74 No H-bonds generated for 'chain 'M' and resid 72 through 74' Processing helix chain 'M' and resid 75 through 90 removed outlier: 3.619A pdb=" N ASP M 89 " --> pdb=" O ARG M 85 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 118 Processing helix chain 'M' and resid 122 through 130 removed outlier: 3.763A pdb=" N TYR M 130 " --> pdb=" O PHE M 126 " (cutoff:3.500A) Processing helix chain 'M' and resid 130 through 142 Processing helix chain 'M' and resid 154 through 161 removed outlier: 3.532A pdb=" N LYS M 158 " --> pdb=" O PRO M 155 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N PHE M 159 " --> pdb=" O GLU M 156 " (cutoff:3.500A) Processing helix chain 'M' and resid 164 through 169 removed outlier: 4.053A pdb=" N THR M 169 " --> pdb=" O ASN M 166 " (cutoff:3.500A) Processing helix chain 'M' and resid 185 through 206 Processing helix chain 'M' and resid 214 through 219 Processing helix chain 'M' and resid 227 through 231 removed outlier: 3.623A pdb=" N VAL M 231 " --> pdb=" O ALA M 228 " (cutoff:3.500A) 923 hydrogen bonds defined for protein. 2496 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 41 stacking parallelities Total time for adding SS restraints: 3.87 Time building geometry restraints manager: 2.38 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: 5279 1.33 - 1.45: 4789 1.45 - 1.57: 12112 1.57 - 1.69: 150 1.69 - 1.81: 221 Bond restraints: 22551 Sorted by residual: bond pdb=" CA PHE F 164 " pdb=" CB PHE F 164 " ideal model delta sigma weight residual 1.532 1.566 -0.034 1.51e-02 4.39e+03 5.07e+00 bond pdb=" CA PHE K 164 " pdb=" CB PHE K 164 " ideal model delta sigma weight residual 1.532 1.566 -0.034 1.51e-02 4.39e+03 5.05e+00 bond pdb=" CA PHE M 164 " pdb=" CB PHE M 164 " ideal model delta sigma weight residual 1.532 1.566 -0.034 1.51e-02 4.39e+03 4.97e+00 bond pdb=" CA PHE C 164 " pdb=" CB PHE C 164 " ideal model delta sigma weight residual 1.532 1.566 -0.034 1.51e-02 4.39e+03 4.94e+00 bond pdb=" CA PHE I 164 " pdb=" CB PHE I 164 " ideal model delta sigma weight residual 1.532 1.565 -0.033 1.51e-02 4.39e+03 4.91e+00 ... (remaining 22546 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 28498 1.40 - 2.79: 2096 2.79 - 4.19: 354 4.19 - 5.58: 46 5.58 - 6.98: 39 Bond angle restraints: 31033 Sorted by residual: angle pdb=" CA PHE B 164 " pdb=" CB PHE B 164 " pdb=" CG PHE B 164 " ideal model delta sigma weight residual 113.80 117.11 -3.31 1.00e+00 1.00e+00 1.10e+01 angle pdb=" CA PHE J 164 " pdb=" CB PHE J 164 " pdb=" CG PHE J 164 " ideal model delta sigma weight residual 113.80 117.11 -3.31 1.00e+00 1.00e+00 1.09e+01 angle pdb=" CA PHE H 164 " pdb=" CB PHE H 164 " pdb=" CG PHE H 164 " ideal model delta sigma weight residual 113.80 117.09 -3.29 1.00e+00 1.00e+00 1.08e+01 angle pdb=" CA PHE I 164 " pdb=" CB PHE I 164 " pdb=" CG PHE I 164 " ideal model delta sigma weight residual 113.80 117.09 -3.29 1.00e+00 1.00e+00 1.08e+01 angle pdb=" CA PHE C 164 " pdb=" CB PHE C 164 " pdb=" CG PHE C 164 " ideal model delta sigma weight residual 113.80 117.08 -3.28 1.00e+00 1.00e+00 1.07e+01 ... (remaining 31028 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.52: 13406 35.52 - 71.04: 356 71.04 - 106.56: 0 106.56 - 142.08: 0 142.08 - 177.61: 1 Dihedral angle restraints: 13763 sinusoidal: 5859 harmonic: 7904 Sorted by residual: dihedral pdb=" O4' U R 29 " pdb=" C1' U R 29 " pdb=" N1 U R 29 " pdb=" C2 U R 29 " ideal model delta sinusoidal sigma weight residual -128.00 49.61 -177.61 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" CA ASP C 209 " pdb=" C ASP C 209 " pdb=" N PHE C 210 " pdb=" CA PHE C 210 " ideal model delta harmonic sigma weight residual 180.00 -156.60 -23.40 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA ASP H 209 " pdb=" C ASP H 209 " pdb=" N PHE H 210 " pdb=" CA PHE H 210 " ideal model delta harmonic sigma weight residual -180.00 -156.64 -23.36 0 5.00e+00 4.00e-02 2.18e+01 ... (remaining 13760 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2094 0.038 - 0.077: 950 0.077 - 0.115: 394 0.115 - 0.154: 117 0.154 - 0.192: 40 Chirality restraints: 3595 Sorted by residual: chirality pdb=" CA PHE D 164 " pdb=" N PHE D 164 " pdb=" C PHE D 164 " pdb=" CB PHE D 164 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.24e-01 chirality pdb=" CA PHE E 164 " pdb=" N PHE E 164 " pdb=" C PHE E 164 " pdb=" CB PHE E 164 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.13e-01 chirality pdb=" CA PHE A 164 " pdb=" N PHE A 164 " pdb=" C PHE A 164 " pdb=" CB PHE A 164 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.04e-01 ... (remaining 3592 not shown) Planarity restraints: 3826 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 162 " 0.013 2.00e-02 2.50e+03 2.04e-02 7.26e+00 pdb=" CG PHE B 162 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE B 162 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE B 162 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 PHE B 162 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 162 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 162 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE L 162 " 0.013 2.00e-02 2.50e+03 2.03e-02 7.24e+00 pdb=" CG PHE L 162 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE L 162 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE L 162 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE L 162 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE L 162 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE L 162 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " 0.013 2.00e-02 2.50e+03 2.03e-02 7.24e+00 pdb=" CG PHE A 162 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " -0.000 2.00e-02 2.50e+03 ... (remaining 3823 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 30 2.48 - 3.09: 14744 3.09 - 3.69: 35603 3.69 - 4.30: 54259 4.30 - 4.90: 81154 Nonbonded interactions: 185790 Sorted by model distance: nonbonded pdb=" O2 U R 65 " pdb=" O HOH R 101 " model vdw 1.880 3.040 nonbonded pdb=" OP2 U R 24 " pdb=" O HOH R 102 " model vdw 1.942 3.040 nonbonded pdb=" O2 U R 55 " pdb=" O HOH R 103 " model vdw 2.054 3.040 nonbonded pdb=" O2 U R 5 " pdb=" O HOH R 104 " model vdw 2.065 3.040 nonbonded pdb=" OP1 U R 23 " pdb=" O HOH R 105 " model vdw 2.094 3.040 ... (remaining 185785 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' } 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: 4.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 20.260 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.720 ------------------------------------------------------------------------------- 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 : 0.006 0.055 22551 Z= 0.289 Angle : 0.850 6.978 31033 Z= 0.490 Chirality : 0.054 0.192 3595 Planarity : 0.006 0.037 3826 Dihedral : 14.935 177.605 8589 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.05 % Allowed : 3.05 % Favored : 93.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.46 (0.13), residues: 2691 helix: -2.64 (0.09), residues: 1430 sheet: None (None), residues: 0 loop : -0.10 (0.16), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 219 TYR 0.013 0.003 TYR E 130 PHE 0.046 0.005 PHE L 162 TRP 0.010 0.002 TRP E 135 HIS 0.003 0.001 HIS B 86 Details of bonding type rmsd covalent geometry : bond 0.00638 (22551) covalent geometry : angle 0.85024 (31033) hydrogen bonds : bond 0.24454 ( 923) hydrogen bonds : angle 7.63175 ( 2496) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 492 time to evaluate : 0.778 Fit side-chains REVERT: A 58 ASP cc_start: 0.7589 (m-30) cc_final: 0.7267 (m-30) REVERT: A 89 ASP cc_start: 0.8312 (m-30) cc_final: 0.8100 (m-30) REVERT: A 128 MET cc_start: 0.9149 (mmm) cc_final: 0.8802 (mmm) REVERT: A 177 LYS cc_start: 0.7827 (tttm) cc_final: 0.7364 (mppt) REVERT: B 69 MET cc_start: 0.7546 (ptm) cc_final: 0.7224 (ptm) REVERT: B 138 MET cc_start: 0.8514 (mtm) cc_final: 0.8288 (mtm) REVERT: C 104 TYR cc_start: 0.8253 (m-80) cc_final: 0.7973 (m-80) REVERT: D 156 GLU cc_start: 0.8239 (pm20) cc_final: 0.8018 (pm20) REVERT: F 63 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7268 (mt-10) REVERT: F 78 GLN cc_start: 0.8572 (mp10) cc_final: 0.8307 (mp10) REVERT: G 156 GLU cc_start: 0.8278 (pm20) cc_final: 0.8070 (pm20) REVERT: I 128 MET cc_start: 0.9205 (mmm) cc_final: 0.8861 (mmm) REVERT: J 175 MET cc_start: 0.8232 (tpp) cc_final: 0.8023 (tpp) REVERT: K 69 MET cc_start: 0.8038 (ptm) cc_final: 0.7826 (ptm) REVERT: L 76 MET cc_start: 0.7855 (tpp) cc_final: 0.7442 (tpp) REVERT: L 104 TYR cc_start: 0.8221 (m-80) cc_final: 0.7829 (m-80) REVERT: M 33 PHE cc_start: 0.8525 (m-80) cc_final: 0.8232 (m-80) REVERT: M 128 MET cc_start: 0.9096 (mmm) cc_final: 0.8718 (mmm) REVERT: M 141 ASN cc_start: 0.8501 (m-40) cc_final: 0.8301 (m110) outliers start: 65 outliers final: 6 residues processed: 536 average time/residue: 0.8409 time to fit residues: 496.6430 Evaluate side-chains 410 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 404 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain J residue 42 SER Chi-restraints excluded: chain J residue 74 ASP Chi-restraints excluded: chain K residue 42 SER Chi-restraints excluded: chain L residue 42 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN B 166 ASN ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 166 ASN C 206 GLN D 166 ASN ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 ASN ** F 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 166 ASN ** G 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 166 ASN G 206 GLN ** H 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 166 ASN ** I 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 166 ASN J 95 GLN ** J 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 166 ASN K 95 GLN ** K 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 166 ASN K 206 GLN L 95 GLN ** L 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 166 ASN M 95 GLN M 166 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.141999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.121974 restraints weight = 18900.445| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 0.91 r_work: 0.3180 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 2.12 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 22551 Z= 0.116 Angle : 0.504 4.978 31033 Z= 0.281 Chirality : 0.041 0.153 3595 Planarity : 0.004 0.029 3826 Dihedral : 12.157 177.715 3955 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.13 % Allowed : 6.61 % Favored : 92.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.03 (0.15), residues: 2691 helix: -0.11 (0.13), residues: 1456 sheet: None (None), residues: 0 loop : 0.43 (0.17), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 45 TYR 0.009 0.001 TYR F 130 PHE 0.019 0.002 PHE I 164 TRP 0.015 0.001 TRP J 135 HIS 0.002 0.000 HIS I 86 Details of bonding type rmsd covalent geometry : bond 0.00221 (22551) covalent geometry : angle 0.50389 (31033) hydrogen bonds : bond 0.04286 ( 923) hydrogen bonds : angle 4.81488 ( 2496) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 457 time to evaluate : 0.836 Fit side-chains REVERT: A 58 ASP cc_start: 0.7522 (m-30) cc_final: 0.7116 (m-30) REVERT: A 61 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7864 (mttm) REVERT: A 89 ASP cc_start: 0.8493 (m-30) cc_final: 0.8160 (m-30) REVERT: A 128 MET cc_start: 0.9223 (mmm) cc_final: 0.9013 (mmm) REVERT: B 58 ASP cc_start: 0.7778 (m-30) cc_final: 0.7400 (m-30) REVERT: B 69 MET cc_start: 0.7352 (ptm) cc_final: 0.7139 (ptm) REVERT: C 30 SER cc_start: 0.7914 (p) cc_final: 0.7695 (t) REVERT: C 58 ASP cc_start: 0.7802 (m-30) cc_final: 0.7380 (m-30) REVERT: C 89 ASP cc_start: 0.8618 (m-30) cc_final: 0.8418 (m-30) REVERT: D 199 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8475 (mttm) REVERT: E 58 ASP cc_start: 0.7940 (m-30) cc_final: 0.7559 (m-30) REVERT: E 74 ASP cc_start: 0.7196 (p0) cc_final: 0.6913 (p0) REVERT: F 78 GLN cc_start: 0.8708 (mp10) cc_final: 0.8458 (mp10) REVERT: G 106 ASN cc_start: 0.6812 (OUTLIER) cc_final: 0.6572 (t0) REVERT: H 76 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.7713 (ttm) REVERT: I 89 ASP cc_start: 0.8699 (m-30) cc_final: 0.8459 (m-30) REVERT: I 106 ASN cc_start: 0.6370 (t0) cc_final: 0.6124 (t0) REVERT: I 128 MET cc_start: 0.9267 (mmm) cc_final: 0.8970 (mmm) REVERT: J 35 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8029 (mp) REVERT: J 45 ARG cc_start: 0.7530 (mmt-90) cc_final: 0.7284 (tpt170) REVERT: J 175 MET cc_start: 0.8615 (tpp) cc_final: 0.8371 (tpp) REVERT: J 177 LYS cc_start: 0.7719 (tttm) cc_final: 0.7510 (tttp) REVERT: K 89 ASP cc_start: 0.8564 (m-30) cc_final: 0.8356 (m-30) REVERT: L 104 TYR cc_start: 0.8226 (m-80) cc_final: 0.7791 (m-80) REVERT: M 119 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7491 (mm-30) REVERT: M 128 MET cc_start: 0.9199 (mmm) cc_final: 0.8978 (mmm) outliers start: 24 outliers final: 6 residues processed: 464 average time/residue: 0.9297 time to fit residues: 470.9877 Evaluate side-chains 416 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 405 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain D residue 199 LYS Chi-restraints excluded: chain G residue 106 ASN Chi-restraints excluded: chain H residue 76 MET Chi-restraints excluded: chain J residue 35 ILE Chi-restraints excluded: chain J residue 74 ASP Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 128 MET Chi-restraints excluded: chain M residue 73 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 103 optimal weight: 8.9990 chunk 88 optimal weight: 5.9990 chunk 206 optimal weight: 6.9990 chunk 156 optimal weight: 9.9990 chunk 179 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 258 optimal weight: 8.9990 chunk 260 optimal weight: 9.9990 chunk 73 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 235 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 GLN ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 95 GLN ** F 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 GLN ** I 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 141 ASN ** K 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 149 GLN K 206 GLN ** L 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.134690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.114478 restraints weight = 19058.309| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 0.90 r_work: 0.3083 rms_B_bonded: 1.20 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 1.98 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 22551 Z= 0.250 Angle : 0.704 5.599 31033 Z= 0.388 Chirality : 0.050 0.176 3595 Planarity : 0.005 0.043 3826 Dihedral : 12.603 177.613 3950 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.22 % Allowed : 7.69 % Favored : 91.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.80 (0.16), residues: 2691 helix: 0.60 (0.13), residues: 1443 sheet: None (None), residues: 0 loop : 0.69 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 124 TYR 0.020 0.003 TYR F 130 PHE 0.032 0.004 PHE H 164 TRP 0.013 0.002 TRP M 135 HIS 0.004 0.001 HIS B 86 Details of bonding type rmsd covalent geometry : bond 0.00541 (22551) covalent geometry : angle 0.70420 (31033) hydrogen bonds : bond 0.06105 ( 923) hydrogen bonds : angle 4.95293 ( 2496) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 423 time to evaluate : 0.804 Fit side-chains REVERT: A 58 ASP cc_start: 0.7707 (m-30) cc_final: 0.7341 (m-30) REVERT: A 89 ASP cc_start: 0.8638 (m-30) cc_final: 0.8248 (m-30) REVERT: A 128 MET cc_start: 0.9328 (mmm) cc_final: 0.8962 (mmm) REVERT: A 177 LYS cc_start: 0.8021 (tttm) cc_final: 0.7246 (mppt) REVERT: B 35 ILE cc_start: 0.8825 (OUTLIER) cc_final: 0.8455 (mt) REVERT: B 199 LYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8756 (mtpp) REVERT: C 58 ASP cc_start: 0.7879 (m-30) cc_final: 0.7537 (m-30) REVERT: C 175 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.8285 (tpp) REVERT: D 199 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8635 (mtpm) REVERT: E 35 ILE cc_start: 0.8653 (OUTLIER) cc_final: 0.8265 (mp) REVERT: H 63 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7676 (mt-10) REVERT: H 76 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.7845 (ttm) REVERT: I 128 MET cc_start: 0.9335 (mmm) cc_final: 0.8980 (mmm) REVERT: J 142 ASN cc_start: 0.8502 (t0) cc_final: 0.8252 (t0) REVERT: J 177 LYS cc_start: 0.8069 (tttm) cc_final: 0.7863 (tttp) REVERT: K 177 LYS cc_start: 0.7953 (tttm) cc_final: 0.7642 (tttp) outliers start: 26 outliers final: 12 residues processed: 437 average time/residue: 1.0280 time to fit residues: 487.8034 Evaluate side-chains 431 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 413 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain C residue 175 MET Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain D residue 199 LYS Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 76 MET Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain H residue 35 ILE Chi-restraints excluded: chain H residue 76 MET Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 128 MET Chi-restraints excluded: chain L residue 143 SER Chi-restraints excluded: chain M residue 73 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 79 optimal weight: 6.9990 chunk 246 optimal weight: 6.9990 chunk 75 optimal weight: 0.6980 chunk 221 optimal weight: 6.9990 chunk 207 optimal weight: 0.0020 chunk 224 optimal weight: 9.9990 chunk 208 optimal weight: 4.9990 chunk 233 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 198 optimal weight: 4.9990 chunk 205 optimal weight: 8.9990 overall best weight: 2.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 GLN ** I 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 206 GLN ** L 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.135151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.115913 restraints weight = 18802.285| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 0.80 r_work: 0.3088 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 2.17 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22551 Z= 0.174 Angle : 0.591 5.187 31033 Z= 0.327 Chirality : 0.045 0.163 3595 Planarity : 0.004 0.030 3826 Dihedral : 12.354 176.691 3948 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.84 % Allowed : 8.77 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.16), residues: 2691 helix: 0.96 (0.14), residues: 1443 sheet: None (None), residues: 0 loop : 0.79 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 45 TYR 0.015 0.002 TYR F 130 PHE 0.032 0.003 PHE H 164 TRP 0.014 0.002 TRP D 135 HIS 0.002 0.001 HIS B 86 Details of bonding type rmsd covalent geometry : bond 0.00369 (22551) covalent geometry : angle 0.59087 (31033) hydrogen bonds : bond 0.05034 ( 923) hydrogen bonds : angle 4.77279 ( 2496) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 430 time to evaluate : 0.835 Fit side-chains REVERT: A 58 ASP cc_start: 0.7705 (m-30) cc_final: 0.7289 (m-30) REVERT: A 89 ASP cc_start: 0.8628 (m-30) cc_final: 0.8231 (m-30) REVERT: A 128 MET cc_start: 0.9325 (mmm) cc_final: 0.9030 (mmm) REVERT: A 156 GLU cc_start: 0.8463 (pm20) cc_final: 0.8247 (pm20) REVERT: A 177 LYS cc_start: 0.8075 (tttm) cc_final: 0.7401 (mppt) REVERT: B 35 ILE cc_start: 0.8851 (OUTLIER) cc_final: 0.8457 (mt) REVERT: B 58 ASP cc_start: 0.7922 (m-30) cc_final: 0.7571 (m-30) REVERT: B 199 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8750 (mttp) REVERT: C 89 ASP cc_start: 0.8663 (m-30) cc_final: 0.8462 (m-30) REVERT: C 175 MET cc_start: 0.8663 (OUTLIER) cc_final: 0.8261 (tpp) REVERT: D 199 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8534 (mttm) REVERT: E 35 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8257 (mp) REVERT: E 58 ASP cc_start: 0.8015 (m-30) cc_final: 0.7735 (m-30) REVERT: H 76 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7846 (ttm) REVERT: I 106 ASN cc_start: 0.6395 (t0) cc_final: 0.6189 (t0) REVERT: I 128 MET cc_start: 0.9351 (mmm) cc_final: 0.9081 (mmm) REVERT: I 219 ARG cc_start: 0.8860 (mtp85) cc_final: 0.8599 (mtp85) REVERT: J 142 ASN cc_start: 0.8648 (t0) cc_final: 0.8323 (t0) REVERT: J 177 LYS cc_start: 0.8136 (tttm) cc_final: 0.7935 (tttp) REVERT: K 177 LYS cc_start: 0.7978 (tttm) cc_final: 0.7685 (tttp) REVERT: M 119 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7557 (mm-30) outliers start: 18 outliers final: 9 residues processed: 437 average time/residue: 1.0072 time to fit residues: 477.8927 Evaluate side-chains 440 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 425 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain C residue 175 MET Chi-restraints excluded: chain D residue 199 LYS Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 76 MET Chi-restraints excluded: chain H residue 76 MET Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 128 MET Chi-restraints excluded: chain L residue 143 SER Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 100 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 115 optimal weight: 10.0000 chunk 157 optimal weight: 5.9990 chunk 237 optimal weight: 3.9990 chunk 252 optimal weight: 6.9990 chunk 118 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 215 optimal weight: 8.9990 chunk 52 optimal weight: 4.9990 chunk 229 optimal weight: 8.9990 chunk 208 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 GLN ** I 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 206 GLN ** L 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.136149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.116268 restraints weight = 18690.276| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 0.84 r_work: 0.3100 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 2.21 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22551 Z= 0.152 Angle : 0.552 4.999 31033 Z= 0.305 Chirality : 0.043 0.156 3595 Planarity : 0.004 0.029 3826 Dihedral : 12.223 176.569 3948 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.03 % Allowed : 9.15 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.16), residues: 2691 helix: 1.18 (0.14), residues: 1443 sheet: None (None), residues: 0 loop : 0.86 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 45 TYR 0.014 0.002 TYR F 130 PHE 0.031 0.003 PHE H 164 TRP 0.013 0.001 TRP D 135 HIS 0.002 0.001 HIS B 86 Details of bonding type rmsd covalent geometry : bond 0.00319 (22551) covalent geometry : angle 0.55205 (31033) hydrogen bonds : bond 0.04710 ( 923) hydrogen bonds : angle 4.69584 ( 2496) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 428 time to evaluate : 0.791 Fit side-chains REVERT: A 58 ASP cc_start: 0.7650 (m-30) cc_final: 0.7256 (m-30) REVERT: A 89 ASP cc_start: 0.8592 (m-30) cc_final: 0.8174 (m-30) REVERT: A 128 MET cc_start: 0.9317 (mmm) cc_final: 0.9043 (mmm) REVERT: A 156 GLU cc_start: 0.8473 (pm20) cc_final: 0.8256 (pm20) REVERT: A 177 LYS cc_start: 0.8069 (tttm) cc_final: 0.7379 (mppt) REVERT: B 35 ILE cc_start: 0.8861 (OUTLIER) cc_final: 0.8476 (mt) REVERT: B 199 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8747 (mttp) REVERT: C 89 ASP cc_start: 0.8679 (m-30) cc_final: 0.8475 (m-30) REVERT: C 175 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8237 (tpp) REVERT: D 67 LYS cc_start: 0.7750 (mtpp) cc_final: 0.7519 (mtpp) REVERT: D 199 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8531 (mttm) REVERT: E 58 ASP cc_start: 0.8104 (m-30) cc_final: 0.7732 (m-30) REVERT: E 69 MET cc_start: 0.7847 (ptm) cc_final: 0.7450 (mtp) REVERT: F 78 GLN cc_start: 0.8719 (mp10) cc_final: 0.8470 (mp10) REVERT: G 199 LYS cc_start: 0.8969 (OUTLIER) cc_final: 0.8677 (mtpm) REVERT: H 76 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7877 (ttm) REVERT: I 128 MET cc_start: 0.9352 (mmm) cc_final: 0.9092 (mmm) REVERT: J 35 ILE cc_start: 0.8598 (OUTLIER) cc_final: 0.8116 (mp) REVERT: J 142 ASN cc_start: 0.8682 (t0) cc_final: 0.8333 (t0) REVERT: J 177 LYS cc_start: 0.8125 (tttm) cc_final: 0.7916 (tttp) REVERT: K 63 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7979 (mt-10) REVERT: K 177 LYS cc_start: 0.7946 (tttm) cc_final: 0.7656 (tttp) REVERT: M 119 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7573 (mm-30) REVERT: M 128 MET cc_start: 0.9297 (mmm) cc_final: 0.8962 (mmm) outliers start: 22 outliers final: 11 residues processed: 439 average time/residue: 1.0266 time to fit residues: 489.6135 Evaluate side-chains 443 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 425 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain C residue 175 MET Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain D residue 199 LYS Chi-restraints excluded: chain E residue 76 MET Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain G residue 199 LYS Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 76 MET Chi-restraints excluded: chain I residue 225 THR Chi-restraints excluded: chain J residue 35 ILE Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 143 SER Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 100 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 11 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 212 optimal weight: 4.9990 chunk 230 optimal weight: 4.9990 chunk 59 optimal weight: 9.9990 chunk 87 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 220 optimal weight: 20.0000 chunk 167 optimal weight: 6.9990 chunk 209 optimal weight: 6.9990 chunk 201 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 GLN ** I 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 206 GLN ** L 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.135157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.116090 restraints weight = 18810.502| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 0.82 r_work: 0.3102 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 2.05 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22551 Z= 0.178 Angle : 0.597 5.267 31033 Z= 0.329 Chirality : 0.045 0.163 3595 Planarity : 0.004 0.029 3826 Dihedral : 12.319 176.883 3948 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.98 % Allowed : 9.47 % Favored : 89.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.16), residues: 2691 helix: 1.15 (0.14), residues: 1443 sheet: None (None), residues: 0 loop : 0.91 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 45 TYR 0.015 0.002 TYR F 130 PHE 0.031 0.003 PHE H 164 TRP 0.013 0.002 TRP M 135 HIS 0.003 0.001 HIS B 86 Details of bonding type rmsd covalent geometry : bond 0.00379 (22551) covalent geometry : angle 0.59667 (31033) hydrogen bonds : bond 0.05088 ( 923) hydrogen bonds : angle 4.77348 ( 2496) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 430 time to evaluate : 0.890 Fit side-chains REVERT: A 58 ASP cc_start: 0.7692 (m-30) cc_final: 0.7270 (m-30) REVERT: A 89 ASP cc_start: 0.8613 (m-30) cc_final: 0.8197 (m-30) REVERT: A 128 MET cc_start: 0.9321 (mmm) cc_final: 0.9018 (mmm) REVERT: A 156 GLU cc_start: 0.8426 (pm20) cc_final: 0.8216 (pm20) REVERT: A 177 LYS cc_start: 0.8138 (tttm) cc_final: 0.7471 (mppt) REVERT: B 35 ILE cc_start: 0.8850 (OUTLIER) cc_final: 0.8472 (mt) REVERT: B 199 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8732 (mttp) REVERT: C 89 ASP cc_start: 0.8664 (m-30) cc_final: 0.8460 (m-30) REVERT: C 175 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8155 (tpp) REVERT: D 199 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8526 (mttm) REVERT: E 58 ASP cc_start: 0.8068 (m-30) cc_final: 0.7751 (m-30) REVERT: E 69 MET cc_start: 0.7831 (ptm) cc_final: 0.7453 (mtp) REVERT: G 199 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8672 (mtpm) REVERT: H 76 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7892 (ttm) REVERT: I 128 MET cc_start: 0.9351 (mmm) cc_final: 0.9063 (mmm) REVERT: J 35 ILE cc_start: 0.8604 (OUTLIER) cc_final: 0.8154 (mp) REVERT: J 177 LYS cc_start: 0.8151 (tttm) cc_final: 0.7948 (tttp) REVERT: K 177 LYS cc_start: 0.7963 (tttm) cc_final: 0.7669 (tttp) REVERT: M 119 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7551 (mm-30) outliers start: 21 outliers final: 12 residues processed: 443 average time/residue: 1.0319 time to fit residues: 496.3312 Evaluate side-chains 445 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 426 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain C residue 175 MET Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain D residue 199 LYS Chi-restraints excluded: chain E residue 76 MET Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain G residue 199 LYS Chi-restraints excluded: chain H residue 76 MET Chi-restraints excluded: chain I residue 225 THR Chi-restraints excluded: chain J residue 35 ILE Chi-restraints excluded: chain J residue 225 THR Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 143 SER Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 100 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 260 optimal weight: 10.0000 chunk 264 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 34 optimal weight: 0.0670 chunk 97 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 226 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 167 optimal weight: 0.9990 chunk 145 optimal weight: 6.9990 chunk 202 optimal weight: 0.1980 overall best weight: 1.6524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 95 GLN ** G 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 GLN ** I 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 206 GLN ** L 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.137984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.118125 restraints weight = 18772.054| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 0.86 r_work: 0.3127 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 2.03 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22551 Z= 0.132 Angle : 0.521 5.543 31033 Z= 0.288 Chirality : 0.042 0.151 3595 Planarity : 0.004 0.029 3826 Dihedral : 12.120 176.529 3948 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.89 % Allowed : 9.62 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.16), residues: 2691 helix: 1.32 (0.14), residues: 1443 sheet: None (None), residues: 0 loop : 0.91 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 45 TYR 0.011 0.002 TYR F 130 PHE 0.030 0.002 PHE H 164 TRP 0.013 0.001 TRP D 135 HIS 0.001 0.000 HIS B 86 Details of bonding type rmsd covalent geometry : bond 0.00273 (22551) covalent geometry : angle 0.52062 (31033) hydrogen bonds : bond 0.04352 ( 923) hydrogen bonds : angle 4.63175 ( 2496) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 439 time to evaluate : 0.786 Fit side-chains REVERT: A 89 ASP cc_start: 0.8519 (m-30) cc_final: 0.8089 (m-30) REVERT: A 128 MET cc_start: 0.9302 (mmm) cc_final: 0.9058 (mmm) REVERT: A 156 GLU cc_start: 0.8401 (pm20) cc_final: 0.8188 (pm20) REVERT: A 177 LYS cc_start: 0.8022 (tttm) cc_final: 0.7289 (mppt) REVERT: B 35 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8425 (mt) REVERT: B 69 MET cc_start: 0.7281 (ptm) cc_final: 0.6985 (mtp) REVERT: B 199 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8716 (mttp) REVERT: C 89 ASP cc_start: 0.8645 (m-30) cc_final: 0.8429 (m-30) REVERT: D 199 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8488 (mttm) REVERT: E 58 ASP cc_start: 0.7970 (m-30) cc_final: 0.7510 (m-30) REVERT: E 69 MET cc_start: 0.7842 (ptm) cc_final: 0.7488 (mtp) REVERT: G 106 ASN cc_start: 0.6747 (t0) cc_final: 0.6334 (t0) REVERT: G 199 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8656 (mtpm) REVERT: H 76 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7815 (ttm) REVERT: I 128 MET cc_start: 0.9344 (mmm) cc_final: 0.9111 (mmm) REVERT: I 219 ARG cc_start: 0.8817 (mtp85) cc_final: 0.8449 (mtp85) REVERT: J 35 ILE cc_start: 0.8546 (OUTLIER) cc_final: 0.8071 (mp) REVERT: J 177 LYS cc_start: 0.8092 (tttm) cc_final: 0.7868 (tttp) REVERT: K 61 LYS cc_start: 0.8722 (mttt) cc_final: 0.8418 (mtpt) REVERT: K 63 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7880 (mt-10) REVERT: K 177 LYS cc_start: 0.7906 (tttm) cc_final: 0.7590 (tttp) REVERT: M 119 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7494 (mm-30) outliers start: 19 outliers final: 10 residues processed: 447 average time/residue: 1.0185 time to fit residues: 494.5882 Evaluate side-chains 444 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 428 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain D residue 199 LYS Chi-restraints excluded: chain E residue 76 MET Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain G residue 199 LYS Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 76 MET Chi-restraints excluded: chain J residue 35 ILE Chi-restraints excluded: chain J residue 225 THR Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 143 SER Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 100 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 27 optimal weight: 0.4980 chunk 261 optimal weight: 10.0000 chunk 6 optimal weight: 0.0270 chunk 255 optimal weight: 0.9980 chunk 163 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 139 optimal weight: 9.9990 chunk 231 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 171 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 149 GLN H 206 GLN I 95 GLN I 136 ASN ** J 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 206 GLN ** L 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.142892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.123513 restraints weight = 18763.448| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 0.86 r_work: 0.3198 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 2.06 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 22551 Z= 0.102 Angle : 0.459 4.870 31033 Z= 0.253 Chirality : 0.040 0.142 3595 Planarity : 0.004 0.031 3826 Dihedral : 11.837 176.159 3948 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.75 % Allowed : 9.66 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.16), residues: 2691 helix: 1.62 (0.14), residues: 1443 sheet: None (None), residues: 0 loop : 0.81 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 45 TYR 0.009 0.001 TYR C 130 PHE 0.027 0.002 PHE H 164 TRP 0.013 0.001 TRP E 135 HIS 0.001 0.000 HIS J 86 Details of bonding type rmsd covalent geometry : bond 0.00202 (22551) covalent geometry : angle 0.45878 (31033) hydrogen bonds : bond 0.03579 ( 923) hydrogen bonds : angle 4.39963 ( 2496) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 436 time to evaluate : 0.852 Fit side-chains REVERT: A 89 ASP cc_start: 0.8423 (m-30) cc_final: 0.8013 (m-30) REVERT: A 177 LYS cc_start: 0.7975 (tttm) cc_final: 0.7248 (mppt) REVERT: B 35 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8342 (mt) REVERT: B 199 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8667 (mttp) REVERT: C 89 ASP cc_start: 0.8632 (m-30) cc_final: 0.8350 (m-30) REVERT: E 69 MET cc_start: 0.7828 (ptm) cc_final: 0.7452 (mtp) REVERT: E 74 ASP cc_start: 0.7524 (p0) cc_final: 0.7217 (p0) REVERT: G 67 LYS cc_start: 0.7640 (mtpp) cc_final: 0.7384 (ttmm) REVERT: G 106 ASN cc_start: 0.6616 (t0) cc_final: 0.6290 (t0) REVERT: G 199 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8651 (mtpm) REVERT: H 69 MET cc_start: 0.8071 (ptp) cc_final: 0.7796 (ptm) REVERT: I 128 MET cc_start: 0.9303 (mmm) cc_final: 0.9057 (mmm) REVERT: I 219 ARG cc_start: 0.8772 (mtp85) cc_final: 0.8435 (mtp85) REVERT: J 35 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.7999 (mp) REVERT: J 177 LYS cc_start: 0.8023 (tttm) cc_final: 0.7807 (tttp) REVERT: K 61 LYS cc_start: 0.8683 (mttt) cc_final: 0.8402 (mtpt) REVERT: K 63 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7869 (mt-10) REVERT: K 177 LYS cc_start: 0.7774 (tttm) cc_final: 0.7502 (tttp) REVERT: M 128 MET cc_start: 0.9297 (mmm) cc_final: 0.9079 (mmm) REVERT: M 177 LYS cc_start: 0.7402 (tttt) cc_final: 0.7195 (ttmm) outliers start: 16 outliers final: 4 residues processed: 443 average time/residue: 0.9987 time to fit residues: 481.1131 Evaluate side-chains 431 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 423 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain G residue 199 LYS Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain I residue 225 THR Chi-restraints excluded: chain J residue 35 ILE Chi-restraints excluded: chain J residue 225 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 125 optimal weight: 5.9990 chunk 256 optimal weight: 9.9990 chunk 141 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 204 optimal weight: 6.9990 chunk 83 optimal weight: 0.9980 chunk 202 optimal weight: 9.9990 chunk 250 optimal weight: 10.0000 chunk 239 optimal weight: 10.0000 chunk 262 optimal weight: 9.9990 chunk 55 optimal weight: 20.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 GLN ** I 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 206 GLN ** L 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.135384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.114758 restraints weight = 19167.726| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 0.91 r_work: 0.3090 rms_B_bonded: 1.21 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 2.00 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 22551 Z= 0.241 Angle : 0.686 5.313 31033 Z= 0.379 Chirality : 0.049 0.172 3595 Planarity : 0.005 0.040 3826 Dihedral : 12.439 177.023 3948 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.75 % Allowed : 10.04 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.48 (0.16), residues: 2691 helix: 1.16 (0.14), residues: 1443 sheet: None (None), residues: 0 loop : 0.99 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 219 TYR 0.017 0.003 TYR F 130 PHE 0.028 0.004 PHE H 164 TRP 0.012 0.002 TRP M 135 HIS 0.003 0.001 HIS I 86 Details of bonding type rmsd covalent geometry : bond 0.00520 (22551) covalent geometry : angle 0.68640 (31033) hydrogen bonds : bond 0.05689 ( 923) hydrogen bonds : angle 4.83435 ( 2496) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 429 time to evaluate : 0.739 Fit side-chains REVERT: A 89 ASP cc_start: 0.8645 (m-30) cc_final: 0.8319 (m-30) REVERT: A 177 LYS cc_start: 0.8001 (tttm) cc_final: 0.7242 (mppt) REVERT: B 35 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8418 (mt) REVERT: B 199 LYS cc_start: 0.9119 (OUTLIER) cc_final: 0.8769 (mtpp) REVERT: C 199 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8753 (mttm) REVERT: E 58 ASP cc_start: 0.8016 (m-30) cc_final: 0.7629 (m-30) REVERT: G 67 LYS cc_start: 0.7745 (mtpp) cc_final: 0.7450 (ttmm) REVERT: I 128 MET cc_start: 0.9342 (mmm) cc_final: 0.9009 (mmm) REVERT: J 142 ASN cc_start: 0.8728 (t0) cc_final: 0.8308 (t0) REVERT: J 177 LYS cc_start: 0.8130 (tttm) cc_final: 0.7874 (tttp) REVERT: K 61 LYS cc_start: 0.8716 (mttt) cc_final: 0.8398 (mtpt) REVERT: K 177 LYS cc_start: 0.7938 (tttm) cc_final: 0.7619 (tttp) outliers start: 16 outliers final: 8 residues processed: 439 average time/residue: 0.9830 time to fit residues: 469.0697 Evaluate side-chains 436 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 425 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain I residue 225 THR Chi-restraints excluded: chain J residue 225 THR Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain M residue 73 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 246 optimal weight: 5.9990 chunk 140 optimal weight: 10.0000 chunk 265 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 196 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 199 optimal weight: 9.9990 chunk 98 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 GLN ** I 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 206 GLN ** L 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.136205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.115245 restraints weight = 19151.368| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 0.92 r_work: 0.3102 rms_B_bonded: 1.21 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 2.00 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 22551 Z= 0.206 Angle : 0.643 5.100 31033 Z= 0.356 Chirality : 0.047 0.166 3595 Planarity : 0.005 0.034 3826 Dihedral : 12.410 176.845 3948 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.61 % Allowed : 10.27 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.16), residues: 2691 helix: 1.12 (0.14), residues: 1443 sheet: None (None), residues: 0 loop : 0.97 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 45 TYR 0.016 0.002 TYR F 130 PHE 0.030 0.003 PHE H 164 TRP 0.012 0.002 TRP M 135 HIS 0.003 0.001 HIS B 86 Details of bonding type rmsd covalent geometry : bond 0.00442 (22551) covalent geometry : angle 0.64288 (31033) hydrogen bonds : bond 0.05321 ( 923) hydrogen bonds : angle 4.79348 ( 2496) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 427 time to evaluate : 0.808 Fit side-chains REVERT: A 89 ASP cc_start: 0.8625 (m-30) cc_final: 0.8315 (m-30) REVERT: A 177 LYS cc_start: 0.8018 (tttm) cc_final: 0.7261 (mppt) REVERT: B 35 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8405 (mt) REVERT: B 199 LYS cc_start: 0.9095 (OUTLIER) cc_final: 0.8771 (mtpp) REVERT: C 89 ASP cc_start: 0.8652 (m-30) cc_final: 0.8424 (m-30) REVERT: C 199 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8749 (mttm) REVERT: E 58 ASP cc_start: 0.8016 (m-30) cc_final: 0.7692 (m-30) REVERT: E 69 MET cc_start: 0.7865 (ptm) cc_final: 0.7458 (mtp) REVERT: E 74 ASP cc_start: 0.7467 (p0) cc_final: 0.7234 (p0) REVERT: G 67 LYS cc_start: 0.7768 (mtpp) cc_final: 0.7476 (ttmm) REVERT: I 128 MET cc_start: 0.9346 (mmm) cc_final: 0.9050 (mmm) REVERT: J 142 ASN cc_start: 0.8724 (t0) cc_final: 0.8313 (t0) REVERT: J 177 LYS cc_start: 0.8147 (tttm) cc_final: 0.7902 (tttp) REVERT: K 61 LYS cc_start: 0.8720 (mttt) cc_final: 0.8410 (mtpt) REVERT: K 177 LYS cc_start: 0.7961 (tttm) cc_final: 0.7640 (tttp) outliers start: 13 outliers final: 9 residues processed: 435 average time/residue: 0.9691 time to fit residues: 457.7181 Evaluate side-chains 439 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 427 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain I residue 225 THR Chi-restraints excluded: chain J residue 225 THR Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 143 SER Chi-restraints excluded: chain M residue 73 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 32 optimal weight: 3.9990 chunk 211 optimal weight: 4.9990 chunk 204 optimal weight: 7.9990 chunk 132 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 253 optimal weight: 1.9990 chunk 221 optimal weight: 6.9990 chunk 233 optimal weight: 0.9990 chunk 109 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 73 optimal weight: 0.8980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 GLN ** I 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 206 GLN ** L 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.140976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.120411 restraints weight = 19252.058| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 0.91 r_work: 0.3177 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 2.06 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 22551 Z= 0.122 Angle : 0.510 5.135 31033 Z= 0.282 Chirality : 0.042 0.149 3595 Planarity : 0.004 0.029 3826 Dihedral : 12.068 176.644 3948 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.38 % Allowed : 10.41 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.67 (0.16), residues: 2691 helix: 1.40 (0.14), residues: 1443 sheet: None (None), residues: 0 loop : 0.97 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 45 TYR 0.011 0.002 TYR A 130 PHE 0.029 0.002 PHE H 164 TRP 0.013 0.001 TRP E 135 HIS 0.001 0.000 HIS B 86 Details of bonding type rmsd covalent geometry : bond 0.00249 (22551) covalent geometry : angle 0.50965 (31033) hydrogen bonds : bond 0.04087 ( 923) hydrogen bonds : angle 4.55482 ( 2496) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11888.69 seconds wall clock time: 202 minutes 5.01 seconds (12125.01 seconds total)