Starting phenix.real_space_refine on Sun Sep 13 07:00:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6r7g_4740/09_2026/6r7g_4740.cif Found real_map, /net/cci-nas-00/data/ceres_data/6r7g_4740/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6r7g_4740/09_2026/6r7g_4740.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6r7g_4740/09_2026/6r7g_4740.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6r7g_4740/09_2026/6r7g_4740.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6r7g_4740/09_2026/6r7g_4740.cif" model { file = "/net/cci-nas-00/data/ceres_data/6r7g_4740/09_2026/6r7g_4740.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6r7g_4740/09_2026/6r7g_4740.cif" } 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-2.2.1-6174/lib/python3.11/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: {'RNAv2': 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: 2.78, 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: 1.77 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: 2.48 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: 3.17 Time building geometry restraints manager: 2.43 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: 28283 1.40 - 2.79: 2195 2.79 - 4.19: 443 4.19 - 5.58: 73 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 - 14.46: 11710 14.46 - 28.93: 1237 28.93 - 43.39: 354 43.39 - 57.86: 136 57.86 - 72.32: 50 Dihedral angle restraints: 13487 sinusoidal: 5583 harmonic: 7904 Sorted by residual: dihedral pdb=" C4' U R 29 " pdb=" C3' U R 29 " pdb=" C2' U R 29 " pdb=" C1' U R 29 " ideal model delta sinusoidal sigma weight residual 36.34 -35.97 72.32 1 3.10e+00 1.04e-01 6.96e+02 dihedral pdb=" C4' U R 54 " pdb=" C3' U R 54 " pdb=" C2' U R 54 " pdb=" C1' U R 54 " ideal model delta sinusoidal sigma weight residual 36.34 -35.17 71.51 1 3.10e+00 1.04e-01 6.82e+02 dihedral pdb=" C4' U R 34 " pdb=" C3' U R 34 " pdb=" C2' U R 34 " pdb=" C1' U R 34 " ideal model delta sinusoidal sigma weight residual 36.35 -35.10 71.45 1 3.10e+00 1.04e-01 6.81e+02 ... (remaining 13484 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2635 0.059 - 0.119: 711 0.119 - 0.178: 145 0.178 - 0.237: 75 0.237 - 0.297: 29 Chirality restraints: 3595 Sorted by residual: chirality pdb=" C2' U R 44 " pdb=" C3' U R 44 " pdb=" O2' U R 44 " pdb=" C1' U R 44 " both_signs ideal model delta sigma weight residual False -2.79 -2.49 -0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" C2' U R 49 " pdb=" C3' U R 49 " pdb=" O2' U R 49 " pdb=" C1' U R 49 " both_signs ideal model delta sigma weight residual False -2.79 -2.49 -0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" C2' U R 19 " pdb=" C3' U R 19 " pdb=" O2' U R 19 " pdb=" C1' U R 19 " both_signs ideal model delta sigma weight residual False -2.79 -2.49 -0.30 2.00e-01 2.50e+01 2.19e+00 ... (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: 4.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.140 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 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 : 0.891 6.978 31033 Z= 0.493 Chirality : 0.066 0.297 3595 Planarity : 0.006 0.037 3826 Dihedral : 14.636 72.320 8313 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/Z covalent geometry : bond 0.00641 / 0.29 (22551) covalent geometry : angle 0.89097 / 0.49 (31033) hydrogen bonds : bond 0.24454 / 16.16 ( 923) hydrogen bonds : angle 7.63175 / 5.33 ( 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 : 0.958 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: 0.8343 time to fit residues: 495.5293 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 : 0.823 ------------------------------------------------------------------------------- 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: 4.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 6.9990 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... A 166 ASN B 166 ASN ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 166 ASN C 206 GLN D 149 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: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.145406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.126486 restraints weight = 18882.338| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 0.85 r_work: 0.3231 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 2.09 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 22551 Z= 0.131 Angle : 0.702 10.360 31033 Z= 0.319 Chirality : 0.063 0.689 3595 Planarity : 0.004 0.029 3826 Dihedral : 11.492 119.850 3679 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.22 % Allowed : 6.61 % Favored : 92.17 % 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: 0.01 (0.15), residues: 2691 helix: -0.14 (0.13), residues: 1456 sheet: None (None), residues: 0 loop : 0.44 (0.18), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 45 TYR 0.008 0.001 TYR F 130 PHE 0.016 0.002 PHE I 164 TRP 0.014 0.001 TRP J 135 HIS 0.002 0.001 HIS I 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.13 (22551) covalent geometry : angle 0.70206 / 0.32 (31033) hydrogen bonds : bond 0.04435 / 2.89 ( 923) hydrogen bonds : angle 4.83283 / 3.33 ( 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 486 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 460 time to evaluate : 0.531 Fit side-chains REVERT: A 58 ASP cc_start: 0.7508 (m-30) cc_final: 0.7169 (m-30) REVERT: A 89 ASP cc_start: 0.8474 (m-30) cc_final: 0.8068 (m-30) REVERT: A 156 GLU cc_start: 0.8392 (pm20) cc_final: 0.8183 (pm20) REVERT: B 58 ASP cc_start: 0.7764 (m-30) cc_final: 0.7383 (m-30) REVERT: C 30 SER cc_start: 0.7907 (p) cc_final: 0.7698 (t) REVERT: C 58 ASP cc_start: 0.7836 (m-30) cc_final: 0.7372 (m-30) REVERT: C 89 ASP cc_start: 0.8610 (m-30) cc_final: 0.8371 (m-30) REVERT: E 58 ASP cc_start: 0.7998 (m-30) cc_final: 0.7595 (m-30) REVERT: E 74 ASP cc_start: 0.7192 (p0) cc_final: 0.6925 (p0) REVERT: E 219 ARG cc_start: 0.8839 (mtp85) cc_final: 0.8596 (mtp85) REVERT: F 78 GLN cc_start: 0.8701 (mp10) cc_final: 0.8440 (mp10) REVERT: G 106 ASN cc_start: 0.6814 (t0) cc_final: 0.6579 (t0) REVERT: H 76 MET cc_start: 0.8030 (OUTLIER) cc_final: 0.7682 (ttm) REVERT: H 156 GLU cc_start: 0.8572 (pm20) cc_final: 0.8357 (pm20) REVERT: I 106 ASN cc_start: 0.6371 (t0) cc_final: 0.6123 (t0) REVERT: I 128 MET cc_start: 0.9259 (mmm) cc_final: 0.8969 (mmm) REVERT: J 35 ILE cc_start: 0.8535 (OUTLIER) cc_final: 0.8004 (mp) REVERT: J 45 ARG cc_start: 0.7534 (mmt-90) cc_final: 0.7297 (tpt170) REVERT: J 175 MET cc_start: 0.8602 (tpp) cc_final: 0.8351 (tpp) REVERT: J 177 LYS cc_start: 0.7714 (tttm) cc_final: 0.7506 (tttp) REVERT: K 89 ASP cc_start: 0.8567 (m-30) cc_final: 0.8364 (m-30) REVERT: L 104 TYR cc_start: 0.8215 (m-80) cc_final: 0.7773 (m-80) REVERT: M 119 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7450 (mm-30) outliers start: 26 outliers final: 6 residues processed: 468 average time/residue: 0.9071 time to fit residues: 466.0112 Evaluate side-chains 413 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 405 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 88 optimal weight: 9.9990 chunk 206 optimal weight: 8.9990 chunk 156 optimal weight: 9.9990 chunk 179 optimal weight: 0.0470 chunk 16 optimal weight: 10.0000 chunk 258 optimal weight: 0.5980 chunk 260 optimal weight: 7.9990 chunk 73 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 235 optimal weight: 10.0000 overall best weight: 3.5284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 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 206 GLN ** L 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 141 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.136495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.116365 restraints weight = 18669.079| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 0.92 r_work: 0.3104 rms_B_bonded: 1.21 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 2.01 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.1811 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= 0.201 Angle : 0.758 10.630 31033 Z= 0.366 Chirality : 0.060 0.547 3595 Planarity : 0.005 0.033 3826 Dihedral : 12.216 147.049 3674 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.08 % Allowed : 7.97 % Favored : 90.95 % 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: 0.88 (0.16), residues: 2691 helix: 0.70 (0.14), residues: 1443 sheet: None (None), residues: 0 loop : 0.67 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 45 TYR 0.017 0.002 TYR F 130 PHE 0.028 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/Z covalent geometry : bond 0.00431 / 0.20 (22551) covalent geometry : angle 0.75752 / 0.37 (31033) hydrogen bonds : bond 0.05579 / 3.62 ( 923) hydrogen bonds : angle 4.87994 / 3.35 ( 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 446 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 423 time to evaluate : 0.956 Fit side-chains REVERT: A 58 ASP cc_start: 0.7622 (m-30) cc_final: 0.7263 (m-30) REVERT: A 89 ASP cc_start: 0.8614 (m-30) cc_final: 0.8236 (m-30) REVERT: A 128 MET cc_start: 0.9338 (mmm) cc_final: 0.9042 (mmm) REVERT: A 156 GLU cc_start: 0.8413 (pm20) cc_final: 0.8213 (pm20) REVERT: A 177 LYS cc_start: 0.7999 (tttm) cc_final: 0.7250 (mppt) REVERT: B 58 ASP cc_start: 0.7860 (m-30) cc_final: 0.7495 (m-30) REVERT: C 58 ASP cc_start: 0.7811 (m-30) cc_final: 0.7414 (m-30) REVERT: C 89 ASP cc_start: 0.8676 (m-30) cc_final: 0.8456 (m-30) REVERT: C 175 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.8271 (tpp) REVERT: E 35 ILE cc_start: 0.8645 (OUTLIER) cc_final: 0.8215 (mp) REVERT: E 58 ASP cc_start: 0.7914 (m-30) cc_final: 0.7622 (m-30) REVERT: H 76 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7786 (ttm) REVERT: I 106 ASN cc_start: 0.6383 (t0) cc_final: 0.6145 (t0) REVERT: I 128 MET cc_start: 0.9344 (mmm) cc_final: 0.9004 (mmm) REVERT: J 35 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.8072 (mp) REVERT: J 45 ARG cc_start: 0.7571 (mmt-90) cc_final: 0.7325 (tpt170) REVERT: J 175 MET cc_start: 0.8724 (tpp) cc_final: 0.8466 (tpp) REVERT: J 177 LYS cc_start: 0.7957 (tttm) cc_final: 0.7749 (tttp) REVERT: K 61 LYS cc_start: 0.8710 (mttt) cc_final: 0.8397 (mtpt) REVERT: K 177 LYS cc_start: 0.7882 (tttm) cc_final: 0.7599 (tttp) REVERT: L 89 ASP cc_start: 0.8674 (m-30) cc_final: 0.8427 (m-30) REVERT: M 33 PHE cc_start: 0.8456 (m-80) cc_final: 0.8185 (m-80) REVERT: M 119 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7455 (mm-30) REVERT: M 178 GLU cc_start: 0.7299 (mt-10) cc_final: 0.6925 (mm-30) outliers start: 23 outliers final: 9 residues processed: 435 average time/residue: 0.9835 time to fit residues: 467.2942 Evaluate side-chains 423 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 410 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain C residue 175 MET Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain H residue 76 MET Chi-restraints excluded: chain J residue 35 ILE 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: 9.9990 chunk 246 optimal weight: 8.9990 chunk 75 optimal weight: 0.7980 chunk 221 optimal weight: 7.9990 chunk 207 optimal weight: 7.9990 chunk 224 optimal weight: 10.0000 chunk 208 optimal weight: 7.9990 chunk 233 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 198 optimal weight: 5.9990 chunk 205 optimal weight: 1.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** G 206 GLN ** 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 = 0.3445 r_free = 0.3445 target = 0.134402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.114276 restraints weight = 18883.111| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 0.90 r_work: 0.3073 rms_B_bonded: 1.22 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 2.01 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 22551 Z= 0.253 Angle : 0.870 12.211 31033 Z= 0.418 Chirality : 0.068 0.681 3595 Planarity : 0.005 0.044 3826 Dihedral : 12.538 155.569 3672 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.13 % Allowed : 8.21 % Favored : 90.67 % 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: 1.02 (0.16), residues: 2691 helix: 0.78 (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 M 124 TYR 0.019 0.003 TYR F 130 PHE 0.034 0.004 PHE H 164 TRP 0.015 0.002 TRP M 135 HIS 0.004 0.001 HIS K 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.25 (22551) covalent geometry : angle 0.87011 / 0.42 (31033) hydrogen bonds : bond 0.05916 / 3.84 ( 923) hydrogen bonds : angle 4.93750 / 3.39 ( 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: 24 poor density : 424 time to evaluate : 0.973 Fit side-chains REVERT: A 58 ASP cc_start: 0.7706 (m-30) cc_final: 0.7351 (m-30) REVERT: A 89 ASP cc_start: 0.8631 (m-30) cc_final: 0.8244 (m-30) REVERT: A 128 MET cc_start: 0.9351 (mmm) cc_final: 0.9026 (mmm) REVERT: A 177 LYS cc_start: 0.8052 (tttm) cc_final: 0.7331 (mppt) REVERT: B 199 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8883 (mtpp) REVERT: C 58 ASP cc_start: 0.7860 (m-30) cc_final: 0.7496 (m-30) REVERT: C 175 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.8167 (tpp) REVERT: G 98 MET cc_start: 0.8973 (mmp) cc_final: 0.8727 (mmp) REVERT: H 76 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.7761 (ttm) REVERT: I 128 MET cc_start: 0.9369 (mmm) cc_final: 0.9079 (mmm) REVERT: J 98 MET cc_start: 0.8860 (mmp) cc_final: 0.8506 (mmp) REVERT: J 177 LYS cc_start: 0.8132 (tttm) cc_final: 0.7914 (tttp) REVERT: K 61 LYS cc_start: 0.8702 (mttt) cc_final: 0.8399 (mtpt) REVERT: K 76 MET cc_start: 0.8043 (ttm) cc_final: 0.7675 (ttm) REVERT: K 177 LYS cc_start: 0.7976 (tttm) cc_final: 0.7670 (tttp) REVERT: L 89 ASP cc_start: 0.8782 (m-30) cc_final: 0.8531 (m-30) REVERT: L 177 LYS cc_start: 0.7661 (tttm) cc_final: 0.7460 (tttm) REVERT: M 178 GLU cc_start: 0.7185 (mt-10) cc_final: 0.6983 (mm-30) outliers start: 24 outliers final: 10 residues processed: 436 average time/residue: 0.9824 time to fit residues: 466.9525 Evaluate side-chains 427 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 414 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain C residue 175 MET Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain E residue 225 THR 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: 4.9990 chunk 157 optimal weight: 4.9990 chunk 237 optimal weight: 5.9990 chunk 252 optimal weight: 6.9990 chunk 118 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 215 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 229 optimal weight: 6.9990 chunk 208 optimal weight: 0.1980 chunk 13 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 ** K 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 149 GLN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.142450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.123505 restraints weight = 18690.143| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 0.83 r_work: 0.3194 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 2.08 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 22551 Z= 0.121 Angle : 0.628 8.999 31033 Z= 0.296 Chirality : 0.055 0.486 3595 Planarity : 0.004 0.030 3826 Dihedral : 11.692 135.953 3672 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.75 % Allowed : 9.19 % Favored : 90.06 % 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: 1.45 (0.16), residues: 2691 helix: 1.25 (0.14), residues: 1443 sheet: None (None), residues: 0 loop : 0.82 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 45 TYR 0.009 0.001 TYR F 130 PHE 0.029 0.002 PHE H 164 TRP 0.014 0.001 TRP D 135 HIS 0.001 0.000 HIS K 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 (22551) covalent geometry : angle 0.62826 / 0.30 (31033) hydrogen bonds : bond 0.03958 / 2.58 ( 923) hydrogen bonds : angle 4.57908 / 3.15 ( 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 443 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 427 time to evaluate : 0.786 Fit side-chains REVERT: A 89 ASP cc_start: 0.8494 (m-30) cc_final: 0.8154 (m-30) REVERT: A 128 MET cc_start: 0.9282 (mmm) cc_final: 0.9076 (mmm) REVERT: A 177 LYS cc_start: 0.8026 (tttm) cc_final: 0.7293 (mppt) REVERT: B 69 MET cc_start: 0.7209 (ptm) cc_final: 0.7003 (mtp) REVERT: B 199 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8804 (mtpp) REVERT: C 63 GLU cc_start: 0.7839 (tt0) cc_final: 0.7545 (mm-30) REVERT: E 58 ASP cc_start: 0.8001 (m-30) cc_final: 0.7568 (m-30) REVERT: E 69 MET cc_start: 0.7861 (ptm) cc_final: 0.7525 (mtp) REVERT: E 76 MET cc_start: 0.8150 (OUTLIER) cc_final: 0.7843 (mmt) REVERT: F 78 GLN cc_start: 0.8669 (mp10) cc_final: 0.8404 (mp10) REVERT: G 106 ASN cc_start: 0.6796 (t0) cc_final: 0.6418 (t0) REVERT: H 76 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7697 (ttm) REVERT: I 128 MET cc_start: 0.9329 (mmm) cc_final: 0.9015 (mmm) REVERT: J 45 ARG cc_start: 0.7550 (mmt-90) cc_final: 0.7273 (tpt170) REVERT: J 177 LYS cc_start: 0.8049 (tttm) cc_final: 0.7818 (tttp) REVERT: K 61 LYS cc_start: 0.8709 (mttt) cc_final: 0.8407 (mtpt) REVERT: K 177 LYS cc_start: 0.7925 (tttm) cc_final: 0.7608 (tttp) REVERT: L 89 ASP cc_start: 0.8617 (m-30) cc_final: 0.8362 (m-30) REVERT: M 128 MET cc_start: 0.9281 (mmm) cc_final: 0.8961 (mmm) outliers start: 16 outliers final: 6 residues processed: 433 average time/residue: 0.9918 time to fit residues: 468.8341 Evaluate side-chains 433 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 424 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain E residue 76 MET Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain H residue 76 MET Chi-restraints excluded: chain I residue 225 THR Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain L residue 143 SER Chi-restraints excluded: chain M residue 177 LYS 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: 1.9990 chunk 230 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 143 optimal weight: 0.7980 chunk 220 optimal weight: 20.0000 chunk 167 optimal weight: 0.9990 chunk 209 optimal weight: 20.0000 chunk 201 optimal weight: 5.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** E 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 = 0.3504 r_free = 0.3504 target = 0.139433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.119896 restraints weight = 18825.105| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 0.87 r_work: 0.3143 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 2.08 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22551 Z= 0.147 Angle : 0.661 8.459 31033 Z= 0.316 Chirality : 0.056 0.493 3595 Planarity : 0.004 0.030 3826 Dihedral : 11.847 140.858 3672 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.03 % Allowed : 9.10 % Favored : 89.87 % 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: 1.58 (0.16), residues: 2691 helix: 1.34 (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 0.000 ARG I 45 TYR 0.013 0.002 TYR F 130 PHE 0.028 0.002 PHE H 164 TRP 0.012 0.001 TRP D 135 HIS 0.002 0.000 HIS B 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.15 (22551) covalent geometry : angle 0.66103 / 0.32 (31033) hydrogen bonds : bond 0.04501 / 2.93 ( 923) hydrogen bonds : angle 4.62709 / 3.18 ( 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 460 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 438 time to evaluate : 0.970 Fit side-chains REVERT: A 89 ASP cc_start: 0.8565 (m-30) cc_final: 0.8176 (m-30) REVERT: A 128 MET cc_start: 0.9307 (mmm) cc_final: 0.9029 (mmm) REVERT: A 177 LYS cc_start: 0.8028 (tttm) cc_final: 0.7278 (mppt) REVERT: C 63 GLU cc_start: 0.7863 (tt0) cc_final: 0.7553 (mm-30) REVERT: D 37 ASP cc_start: 0.7539 (p0) cc_final: 0.7298 (p0) REVERT: E 58 ASP cc_start: 0.8035 (m-30) cc_final: 0.7606 (m-30) REVERT: E 69 MET cc_start: 0.7852 (ptm) cc_final: 0.7471 (mtp) REVERT: F 78 GLN cc_start: 0.8690 (mp10) cc_final: 0.8433 (mp10) REVERT: G 106 ASN cc_start: 0.6753 (t0) cc_final: 0.6367 (t0) REVERT: H 76 MET cc_start: 0.8071 (OUTLIER) cc_final: 0.7817 (ttm) REVERT: I 128 MET cc_start: 0.9346 (mmm) cc_final: 0.9103 (mmm) REVERT: J 35 ILE cc_start: 0.8545 (OUTLIER) cc_final: 0.8059 (mp) REVERT: J 177 LYS cc_start: 0.8070 (tttm) cc_final: 0.7841 (tttp) REVERT: K 61 LYS cc_start: 0.8726 (mttt) cc_final: 0.8428 (mtpt) REVERT: K 177 LYS cc_start: 0.7912 (tttm) cc_final: 0.7607 (tttp) REVERT: L 89 ASP cc_start: 0.8651 (m-30) cc_final: 0.8387 (m-30) REVERT: M 112 ARG cc_start: 0.8862 (mtp180) cc_final: 0.8633 (mtp180) REVERT: M 177 LYS cc_start: 0.7731 (OUTLIER) cc_final: 0.7519 (tttt) outliers start: 22 outliers final: 10 residues processed: 450 average time/residue: 0.9722 time to fit residues: 478.1543 Evaluate side-chains 443 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 430 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain E residue 225 THR 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 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 Chi-restraints excluded: chain M residue 177 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 260 optimal weight: 7.9990 chunk 264 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 121 optimal weight: 7.9990 chunk 226 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 167 optimal weight: 4.9990 chunk 145 optimal weight: 5.9990 chunk 202 optimal weight: 0.2980 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** 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 = 0.3486 r_free = 0.3486 target = 0.137814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.118069 restraints weight = 18730.811| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 0.86 r_work: 0.3126 rms_B_bonded: 1.22 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 2.03 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22551 Z= 0.171 Angle : 0.716 9.408 31033 Z= 0.343 Chirality : 0.058 0.532 3595 Planarity : 0.004 0.029 3826 Dihedral : 12.025 144.348 3672 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.03 % Allowed : 9.05 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.30 (0.14), residues: 1443 sheet: None (None), residues: 0 loop : 0.95 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 45 TYR 0.014 0.002 TYR F 130 PHE 0.029 0.003 PHE H 164 TRP 0.012 0.002 TRP D 135 HIS 0.002 0.001 HIS B 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.17 (22551) covalent geometry : angle 0.71564 / 0.34 (31033) hydrogen bonds : bond 0.04871 / 3.17 ( 923) hydrogen bonds : angle 4.71700 / 3.24 ( 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 456 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 434 time to evaluate : 0.815 Fit side-chains REVERT: A 89 ASP cc_start: 0.8597 (m-30) cc_final: 0.8225 (m-30) REVERT: A 128 MET cc_start: 0.9317 (mmm) cc_final: 0.9005 (mmm) REVERT: A 177 LYS cc_start: 0.8044 (tttm) cc_final: 0.7306 (mppt) REVERT: B 69 MET cc_start: 0.7286 (ptm) cc_final: 0.6989 (mtp) REVERT: E 58 ASP cc_start: 0.7997 (m-30) cc_final: 0.7636 (m-30) REVERT: E 69 MET cc_start: 0.7852 (ptm) cc_final: 0.7457 (mtp) REVERT: F 156 GLU cc_start: 0.8604 (pm20) cc_final: 0.8389 (pm20) REVERT: G 106 ASN cc_start: 0.6792 (t0) cc_final: 0.6402 (t0) REVERT: H 76 MET cc_start: 0.8083 (OUTLIER) cc_final: 0.7835 (ttm) REVERT: I 128 MET cc_start: 0.9356 (mmm) cc_final: 0.9084 (mmm) REVERT: J 35 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.8127 (mp) REVERT: J 177 LYS cc_start: 0.8083 (tttm) cc_final: 0.7858 (tttp) REVERT: K 61 LYS cc_start: 0.8716 (mttt) cc_final: 0.8420 (mtpt) REVERT: K 177 LYS cc_start: 0.7935 (tttm) cc_final: 0.7631 (tttp) REVERT: L 89 ASP cc_start: 0.8659 (m-30) cc_final: 0.8411 (m-30) REVERT: M 178 GLU cc_start: 0.7121 (mp0) cc_final: 0.6526 (mp0) outliers start: 22 outliers final: 12 residues processed: 447 average time/residue: 0.9222 time to fit residues: 451.0743 Evaluate side-chains 440 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 426 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain E residue 225 THR 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 Chi-restraints excluded: chain M residue 177 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 27 optimal weight: 3.9990 chunk 261 optimal weight: 7.9990 chunk 6 optimal weight: 0.0770 chunk 255 optimal weight: 7.9990 chunk 163 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 139 optimal weight: 10.0000 chunk 231 optimal weight: 9.9990 chunk 11 optimal weight: 0.5980 chunk 171 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 overall best weight: 1.7142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** 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 95 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 = 0.3512 r_free = 0.3512 target = 0.139995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.120608 restraints weight = 18694.907| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 0.86 r_work: 0.3157 rms_B_bonded: 1.22 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 2.03 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 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 : 0.003 0.032 22551 Z= 0.140 Angle : 0.659 8.228 31033 Z= 0.314 Chirality : 0.056 0.483 3595 Planarity : 0.004 0.029 3826 Dihedral : 11.804 139.939 3672 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.84 % Allowed : 9.43 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.65 (0.16), residues: 2691 helix: 1.40 (0.14), residues: 1443 sheet: None (None), residues: 0 loop : 0.94 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 45 TYR 0.012 0.002 TYR F 130 PHE 0.029 0.002 PHE H 164 TRP 0.012 0.001 TRP D 135 HIS 0.002 0.000 HIS B 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 (22551) covalent geometry : angle 0.65935 / 0.31 (31033) hydrogen bonds : bond 0.04355 / 2.84 ( 923) hydrogen bonds : angle 4.61217 / 3.17 ( 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 447 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 429 time to evaluate : 0.858 Fit side-chains REVERT: A 89 ASP cc_start: 0.8515 (m-30) cc_final: 0.8117 (m-30) REVERT: A 128 MET cc_start: 0.9295 (mmm) cc_final: 0.9032 (mmm) REVERT: A 177 LYS cc_start: 0.8030 (tttm) cc_final: 0.7307 (mppt) REVERT: B 69 MET cc_start: 0.7263 (ptm) cc_final: 0.7023 (mtp) REVERT: C 63 GLU cc_start: 0.7859 (tt0) cc_final: 0.7550 (mm-30) REVERT: E 58 ASP cc_start: 0.7984 (m-30) cc_final: 0.7529 (m-30) REVERT: E 69 MET cc_start: 0.7879 (ptm) cc_final: 0.7508 (mtp) REVERT: E 74 ASP cc_start: 0.7547 (p0) cc_final: 0.7275 (p0) REVERT: G 106 ASN cc_start: 0.6760 (t0) cc_final: 0.6405 (t0) REVERT: H 67 LYS cc_start: 0.7811 (mtpm) cc_final: 0.7593 (ttmm) REVERT: H 76 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7771 (ttm) REVERT: I 128 MET cc_start: 0.9344 (mmm) cc_final: 0.9110 (mmm) REVERT: J 35 ILE cc_start: 0.8550 (OUTLIER) cc_final: 0.8060 (mp) REVERT: J 177 LYS cc_start: 0.8070 (tttm) cc_final: 0.7840 (tttp) REVERT: K 61 LYS cc_start: 0.8722 (mttt) cc_final: 0.8428 (mtpt) REVERT: K 177 LYS cc_start: 0.7899 (tttm) cc_final: 0.7578 (tttp) REVERT: L 89 ASP cc_start: 0.8649 (m-30) cc_final: 0.8396 (m-30) REVERT: M 178 GLU cc_start: 0.7158 (mp0) cc_final: 0.6647 (mp0) outliers start: 18 outliers final: 12 residues processed: 438 average time/residue: 0.9321 time to fit residues: 446.1124 Evaluate side-chains 435 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 421 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain E residue 225 THR 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 Chi-restraints excluded: chain M residue 177 LYS 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: 6.9990 chunk 141 optimal weight: 7.9990 chunk 94 optimal weight: 7.9990 chunk 204 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 202 optimal weight: 0.9990 chunk 250 optimal weight: 9.9990 chunk 239 optimal weight: 10.0000 chunk 262 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3499 r_free = 0.3499 target = 0.138125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.118487 restraints weight = 19187.901| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 0.82 r_work: 0.3148 rms_B_bonded: 1.18 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 1.95 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22551 Z= 0.197 Angle : 0.765 10.407 31033 Z= 0.367 Chirality : 0.061 0.562 3595 Planarity : 0.005 0.031 3826 Dihedral : 12.184 148.020 3672 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.84 % Allowed : 9.33 % 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: 1.55 (0.16), residues: 2691 helix: 1.25 (0.14), residues: 1443 sheet: None (None), residues: 0 loop : 0.98 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 45 TYR 0.015 0.002 TYR F 130 PHE 0.030 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/Z covalent geometry : bond 0.00421 / 0.20 (22551) covalent geometry : angle 0.76451 / 0.37 (31033) hydrogen bonds : bond 0.05213 / 3.39 ( 923) hydrogen bonds : angle 4.77427 / 3.28 ( 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 442 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 424 time to evaluate : 0.829 Fit side-chains REVERT: A 89 ASP cc_start: 0.8613 (m-30) cc_final: 0.8273 (m-30) REVERT: A 128 MET cc_start: 0.9326 (mmm) cc_final: 0.8985 (mmm) REVERT: A 177 LYS cc_start: 0.8059 (tttm) cc_final: 0.7308 (mppt) REVERT: B 69 MET cc_start: 0.7341 (ptm) cc_final: 0.7038 (mtp) REVERT: B 199 LYS cc_start: 0.9105 (OUTLIER) cc_final: 0.8840 (mtpp) REVERT: C 63 GLU cc_start: 0.7889 (tt0) cc_final: 0.7605 (mt-10) REVERT: E 35 ILE cc_start: 0.8663 (OUTLIER) cc_final: 0.8239 (mp) REVERT: E 58 ASP cc_start: 0.8044 (m-30) cc_final: 0.7715 (m-30) REVERT: G 106 ASN cc_start: 0.6816 (t0) cc_final: 0.6430 (t0) REVERT: H 76 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.7737 (ttm) REVERT: I 128 MET cc_start: 0.9333 (mmm) cc_final: 0.9034 (mmm) REVERT: J 35 ILE cc_start: 0.8587 (OUTLIER) cc_final: 0.8143 (mp) REVERT: J 177 LYS cc_start: 0.8087 (tttm) cc_final: 0.7855 (tttp) REVERT: K 61 LYS cc_start: 0.8688 (mttt) cc_final: 0.8405 (mtpt) REVERT: K 177 LYS cc_start: 0.7945 (tttm) cc_final: 0.7630 (tttp) REVERT: L 89 ASP cc_start: 0.8721 (m-30) cc_final: 0.8489 (m-30) REVERT: M 128 MET cc_start: 0.9269 (mmm) cc_final: 0.8971 (mmm) outliers start: 18 outliers final: 11 residues processed: 434 average time/residue: 0.9678 time to fit residues: 458.5496 Evaluate side-chains 435 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 420 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 225 THR 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 Chi-restraints excluded: chain M residue 177 LYS 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: 7.9990 chunk 108 optimal weight: 8.9990 chunk 193 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 196 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 199 optimal weight: 9.9990 chunk 98 optimal weight: 3.9990 chunk 56 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 106 ASN ** 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 = 0.3485 r_free = 0.3485 target = 0.136905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.117118 restraints weight = 19187.498| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 0.84 r_work: 0.3123 rms_B_bonded: 1.17 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 1.94 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 22551 Z= 0.234 Angle : 0.844 12.095 31033 Z= 0.406 Chirality : 0.066 0.615 3595 Planarity : 0.005 0.039 3826 Dihedral : 12.423 152.815 3672 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.84 % Allowed : 9.47 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.11 (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 0.006 0.001 ARG I 45 TYR 0.017 0.003 TYR F 130 PHE 0.031 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/Z covalent geometry : bond 0.00506 / 0.23 (22551) covalent geometry : angle 0.84365 / 0.41 (31033) hydrogen bonds : bond 0.05609 / 3.65 ( 923) hydrogen bonds : angle 4.84754 / 3.33 ( 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 446 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 428 time to evaluate : 0.824 Fit side-chains REVERT: A 89 ASP cc_start: 0.8605 (m-30) cc_final: 0.8266 (m-30) REVERT: A 128 MET cc_start: 0.9336 (mmm) cc_final: 0.8971 (mmm) REVERT: A 177 LYS cc_start: 0.8060 (tttm) cc_final: 0.7319 (mppt) REVERT: B 69 MET cc_start: 0.7356 (ptm) cc_final: 0.7068 (mtp) REVERT: B 199 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8857 (mtpp) REVERT: E 35 ILE cc_start: 0.8665 (OUTLIER) cc_final: 0.8247 (mp) REVERT: E 69 MET cc_start: 0.7858 (ptm) cc_final: 0.7420 (mtp) REVERT: E 74 ASP cc_start: 0.7495 (p0) cc_final: 0.7270 (p0) REVERT: H 76 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.7765 (ttm) REVERT: I 128 MET cc_start: 0.9335 (mmm) cc_final: 0.9032 (mmm) REVERT: J 177 LYS cc_start: 0.8102 (tttm) cc_final: 0.7865 (tttp) REVERT: K 61 LYS cc_start: 0.8687 (mttt) cc_final: 0.8396 (mtpt) REVERT: K 177 LYS cc_start: 0.7942 (tttm) cc_final: 0.7629 (tttp) REVERT: L 89 ASP cc_start: 0.8760 (m-30) cc_final: 0.8531 (m-30) outliers start: 18 outliers final: 12 residues processed: 439 average time/residue: 0.9868 time to fit residues: 472.7226 Evaluate side-chains 438 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 423 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain H residue 76 MET 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 Chi-restraints excluded: chain M residue 100 ASP Chi-restraints excluded: chain M residue 177 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 32 optimal weight: 4.9990 chunk 211 optimal weight: 0.0770 chunk 204 optimal weight: 6.9990 chunk 132 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 253 optimal weight: 2.9990 chunk 221 optimal weight: 5.9990 chunk 233 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 overall best weight: 1.7344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 106 ASN ** 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 = 0.3512 r_free = 0.3512 target = 0.139927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.120875 restraints weight = 18706.317| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 0.84 r_work: 0.3158 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 2.06 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22551 Z= 0.144 Angle : 0.678 8.336 31033 Z= 0.324 Chirality : 0.057 0.504 3595 Planarity : 0.004 0.029 3826 Dihedral : 11.856 140.319 3672 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.94 % Allowed : 9.66 % Favored : 89.40 % 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: 1.63 (0.16), residues: 2691 helix: 1.35 (0.14), residues: 1443 sheet: None (None), residues: 0 loop : 0.96 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 45 TYR 0.012 0.002 TYR F 130 PHE 0.030 0.002 PHE H 164 TRP 0.013 0.001 TRP D 135 HIS 0.002 0.000 HIS B 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (22551) covalent geometry : angle 0.67777 / 0.32 (31033) hydrogen bonds : bond 0.04421 / 2.88 ( 923) hydrogen bonds : angle 4.63785 / 3.18 ( 2496) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11314.98 seconds wall clock time: 192 minutes 34.57 seconds (11554.57 seconds total)