Starting phenix.real_space_refine on Sat Sep 12 18:01:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6xbd_22116/09_2026/6xbd_22116.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xbd_22116/09_2026/6xbd_22116.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6xbd_22116/09_2026/6xbd_22116.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xbd_22116/09_2026/6xbd_22116.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6xbd_22116/09_2026/6xbd_22116.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6xbd_22116/09_2026/6xbd_22116.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6xbd_22116/09_2026/6xbd_22116.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xbd_22116/09_2026/6xbd_22116.map" } resolution = 3.05 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= 0.071 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 2 5.49 5 S 68 5.16 5 C 11140 2.51 5 N 2963 2.21 5 O 3260 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 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: 17433 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1108 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 1 Chain: "B" Number of atoms: 1063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1063 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 6, 'TRANS': 131} Chain breaks: 1 Chain: "C" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1033 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1, 'TRP:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "D" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1096 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain breaks: 2 Chain: "E" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1112 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 6, 'TRANS': 138} Chain breaks: 1 Chain: "F" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1028 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain breaks: 1 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1, 'TRP:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "G" Number of atoms: 1926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1926 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 7, 'TRANS': 248} Chain: "H" Number of atoms: 1918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1918 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 7, 'TRANS': 247} Chain: "I" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 1996 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 18, 'TRANS': 244} Chain: "J" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 1996 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 18, 'TRANS': 244} Chain: "K" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 734 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "L" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 734 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "M" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 821 Classifications: {'peptide': 164} Incomplete info: {'truncation_to_alanine': 163} Link IDs: {'TRANS': 163} Unresolved non-hydrogen bonds: 327 Unresolved non-hydrogen angles: 490 Unresolved non-hydrogen dihedrals: 164 Planarities with less than four sites: {'UNK:plan-1': 163} Unresolved non-hydrogen planarities: 163 Chain: "N" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 780 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 156} Link IDs: {'TRANS': 155} Unresolved non-hydrogen bonds: 312 Unresolved non-hydrogen angles: 468 Unresolved non-hydrogen dihedrals: 156 Planarities with less than four sites: {'UNK:plan-1': 156} Unresolved non-hydrogen planarities: 156 Chain: "G" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'PEF': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Time building chain proxies: 4.23, per 1000 atoms: 0.24 Number of scatterers: 17433 At special positions: 0 Unit cell: (128.96, 104.832, 139.776, 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 68 16.00 P 2 15.00 O 3260 8.00 N 2963 7.00 C 11140 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: 1.50 Conformation dependent library (CDL) restraints added in 778.6 milliseconds 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4448 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 22 sheets defined 63.1% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 2 through 27 Processing helix chain 'A' and resid 142 through 151 Processing helix chain 'B' and resid 5 through 24 Processing helix chain 'B' and resid 142 through 152 Processing helix chain 'C' and resid 5 through 27 Processing helix chain 'C' and resid 142 through 152 Processing helix chain 'D' and resid 3 through 27 Processing helix chain 'D' and resid 142 through 152 removed outlier: 3.507A pdb=" N LEU D 146 " --> pdb=" O VAL D 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 31 removed outlier: 4.165A pdb=" N VAL E 31 " --> pdb=" O LYS E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 152 Processing helix chain 'F' and resid 5 through 29 Processing helix chain 'F' and resid 142 through 151 Processing helix chain 'G' and resid 5 through 31 Processing helix chain 'G' and resid 40 through 52 Processing helix chain 'G' and resid 53 through 55 No H-bonds generated for 'chain 'G' and resid 53 through 55' Processing helix chain 'G' and resid 56 through 79 removed outlier: 3.804A pdb=" N VAL G 77 " --> pdb=" O GLN G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 85 No H-bonds generated for 'chain 'G' and resid 83 through 85' Processing helix chain 'G' and resid 86 through 98 Processing helix chain 'G' and resid 98 through 126 removed outlier: 3.878A pdb=" N SER G 114 " --> pdb=" O GLY G 110 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA G 115 " --> pdb=" O ARG G 111 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR G 117 " --> pdb=" O GLY G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 134 Processing helix chain 'G' and resid 138 through 143 Processing helix chain 'G' and resid 143 through 175 removed outlier: 3.969A pdb=" N ARG G 147 " --> pdb=" O VAL G 143 " (cutoff:3.500A) Proline residue: G 156 - end of helix removed outlier: 3.823A pdb=" N TRP G 168 " --> pdb=" O ALA G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 193 removed outlier: 3.695A pdb=" N VAL G 193 " --> pdb=" O MET G 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 223 removed outlier: 3.559A pdb=" N LEU G 199 " --> pdb=" O TRP G 195 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 258 removed outlier: 3.754A pdb=" N SER G 232 " --> pdb=" O SER G 228 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG G 233 " --> pdb=" O ALA G 229 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR G 236 " --> pdb=" O SER G 232 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG G 237 " --> pdb=" O ARG G 233 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 32 removed outlier: 3.528A pdb=" N GLY H 10 " --> pdb=" O LEU H 6 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N HIS H 11 " --> pdb=" O ALA H 7 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 52 removed outlier: 3.821A pdb=" N ARG H 46 " --> pdb=" O PRO H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 55 No H-bonds generated for 'chain 'H' and resid 53 through 55' Processing helix chain 'H' and resid 56 through 79 removed outlier: 3.511A pdb=" N PHE H 65 " --> pdb=" O VAL H 61 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL H 77 " --> pdb=" O GLN H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 85 No H-bonds generated for 'chain 'H' and resid 83 through 85' Processing helix chain 'H' and resid 86 through 98 removed outlier: 3.618A pdb=" N GLU H 98 " --> pdb=" O SER H 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 98 through 126 removed outlier: 3.955A pdb=" N SER H 114 " --> pdb=" O GLY H 110 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA H 115 " --> pdb=" O ARG H 111 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N THR H 117 " --> pdb=" O GLY H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 135 removed outlier: 3.648A pdb=" N MET H 135 " --> pdb=" O SER H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 138 through 143 Processing helix chain 'H' and resid 143 through 175 removed outlier: 4.177A pdb=" N ARG H 147 " --> pdb=" O VAL H 143 " (cutoff:3.500A) Proline residue: H 156 - end of helix removed outlier: 3.566A pdb=" N VAL H 160 " --> pdb=" O PRO H 156 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TRP H 168 " --> pdb=" O ALA H 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 193 removed outlier: 3.536A pdb=" N ALA H 192 " --> pdb=" O ALA H 188 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL H 193 " --> pdb=" O MET H 189 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 223 removed outlier: 3.588A pdb=" N LEU H 199 " --> pdb=" O TRP H 195 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 258 removed outlier: 4.137A pdb=" N SER H 232 " --> pdb=" O SER H 228 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG H 237 " --> pdb=" O ARG H 233 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 55 removed outlier: 3.532A pdb=" N ARG I 52 " --> pdb=" O THR I 48 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE I 54 " --> pdb=" O LEU I 50 " (cutoff:3.500A) Processing helix chain 'I' and resid 76 through 84 Processing helix chain 'I' and resid 101 through 114 Proline residue: I 109 - end of helix Processing helix chain 'I' and resid 117 through 133 Processing helix chain 'I' and resid 134 through 138 Processing helix chain 'I' and resid 141 through 145 Processing helix chain 'I' and resid 146 through 159 removed outlier: 3.861A pdb=" N ARG I 151 " --> pdb=" O GLY I 147 " (cutoff:3.500A) Processing helix chain 'I' and resid 176 through 194 Processing helix chain 'I' and resid 204 through 209 Processing helix chain 'I' and resid 228 through 233 Processing helix chain 'I' and resid 237 through 246 Processing helix chain 'I' and resid 261 through 266 Processing helix chain 'J' and resid 48 through 55 removed outlier: 3.532A pdb=" N ARG J 52 " --> pdb=" O THR J 48 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE J 54 " --> pdb=" O LEU J 50 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 84 Processing helix chain 'J' and resid 101 through 114 Proline residue: J 109 - end of helix Processing helix chain 'J' and resid 117 through 133 Processing helix chain 'J' and resid 134 through 138 Processing helix chain 'J' and resid 141 through 145 Processing helix chain 'J' and resid 146 through 159 removed outlier: 3.861A pdb=" N ARG J 151 " --> pdb=" O GLY J 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 176 through 194 Processing helix chain 'J' and resid 204 through 209 Processing helix chain 'J' and resid 228 through 233 Processing helix chain 'J' and resid 237 through 246 Processing helix chain 'J' and resid 261 through 266 Processing helix chain 'K' and resid 25 through 30 Processing helix chain 'K' and resid 31 through 37 Processing helix chain 'K' and resid 51 through 67 Processing helix chain 'K' and resid 78 through 88 removed outlier: 3.722A pdb=" N TYR K 88 " --> pdb=" O LEU K 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 25 through 30 Processing helix chain 'L' and resid 31 through 37 Processing helix chain 'L' and resid 51 through 67 Processing helix chain 'L' and resid 78 through 88 removed outlier: 3.723A pdb=" N TYR L 88 " --> pdb=" O LEU L 84 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 164 removed outlier: 3.791A pdb=" N UNK M 22 " --> pdb=" O UNK M 18 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N UNK M 33 " --> pdb=" O UNK M 29 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N UNK M 36 " --> pdb=" O UNK M 32 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N UNK M 37 " --> pdb=" O UNK M 33 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N UNK M 41 " --> pdb=" O UNK M 37 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N UNK M 51 " --> pdb=" O UNK M 47 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N UNK M 75 " --> pdb=" O UNK M 71 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N UNK M 80 " --> pdb=" O UNK M 76 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N UNK M 90 " --> pdb=" O UNK M 86 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N UNK M 143 " --> pdb=" O UNK M 139 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N UNK M 150 " --> pdb=" O UNK M 146 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 39 removed outlier: 3.686A pdb=" N UNK N 10 " --> pdb=" O UNK N 6 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N UNK N 28 " --> pdb=" O UNK N 24 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N UNK N 31 " --> pdb=" O UNK N 27 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N UNK N 32 " --> pdb=" O UNK N 28 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N UNK N 35 " --> pdb=" O UNK N 31 " (cutoff:3.500A) Processing helix chain 'N' and resid 39 through 155 removed outlier: 4.170A pdb=" N UNK N 53 " --> pdb=" O UNK N 49 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N UNK N 54 " --> pdb=" O UNK N 50 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N UNK N 58 " --> pdb=" O UNK N 54 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N UNK N 86 " --> pdb=" O UNK N 82 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N UNK N 97 " --> pdb=" O UNK N 93 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N UNK N 136 " --> pdb=" O UNK N 132 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N UNK N 142 " --> pdb=" O UNK N 138 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N UNK N 155 " --> pdb=" O UNK N 151 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 45 removed outlier: 6.241A pdb=" N ARG A 81 " --> pdb=" O ILE A 71 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ILE A 71 " --> pdb=" O ARG A 81 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N THR A 83 " --> pdb=" O ALA A 69 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 63 through 64 Processing sheet with id=AA3, first strand: chain 'B' and resid 133 through 134 removed outlier: 8.372A pdb=" N ILE B 134 " --> pdb=" O THR B 41 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N TYR B 43 " --> pdb=" O ILE B 134 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ARG B 81 " --> pdb=" O ILE B 71 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ILE B 71 " --> pdb=" O ARG B 81 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N THR B 83 " --> pdb=" O ALA B 69 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N VAL B 64 " --> pdb=" O ILE B 60 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ILE B 60 " --> pdb=" O VAL B 64 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLY B 66 " --> pdb=" O VAL B 58 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE B 101 " --> pdb=" O LYS B 138 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 39 through 45 removed outlier: 3.591A pdb=" N ASP C 70 " --> pdb=" O THR C 83 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N GLU C 85 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N VAL C 68 " --> pdb=" O GLU C 85 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLU C 87 " --> pdb=" O GLY C 66 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N GLY C 66 " --> pdb=" O GLU C 87 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 39 through 45 removed outlier: 6.075A pdb=" N GLU D 85 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N VAL D 68 " --> pdb=" O GLU D 85 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 63 through 66 removed outlier: 5.667A pdb=" N VAL D 64 " --> pdb=" O ILE D 60 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE D 60 " --> pdb=" O VAL D 64 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY D 66 " --> pdb=" O VAL D 58 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N SER D 59 " --> pdb=" O LEU D 114 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASN D 115 " --> pdb=" O SER D 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 40 through 45 removed outlier: 6.785A pdb=" N ARG E 81 " --> pdb=" O ILE E 71 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N ILE E 71 " --> pdb=" O ARG E 81 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N THR E 83 " --> pdb=" O ALA E 69 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N VAL E 64 " --> pdb=" O ILE E 60 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ILE E 60 " --> pdb=" O VAL E 64 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY E 66 " --> pdb=" O VAL E 58 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N SER E 59 " --> pdb=" O LEU E 114 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 40 through 41 Processing sheet with id=AA9, first strand: chain 'F' and resid 40 through 41 removed outlier: 3.539A pdb=" N ASP F 70 " --> pdb=" O THR F 83 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N GLU F 85 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N VAL F 68 " --> pdb=" O GLU F 85 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 58 through 59 removed outlier: 3.644A pdb=" N SER F 100 " --> pdb=" O ALA F 113 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE F 101 " --> pdb=" O LYS F 138 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 21 through 27 removed outlier: 5.357A pdb=" N CYS I 22 " --> pdb=" O ARG I 18 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ARG I 18 " --> pdb=" O CYS I 22 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN I 26 " --> pdb=" O VAL I 14 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N VAL I 14 " --> pdb=" O ASN I 26 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL I 9 " --> pdb=" O VAL I 31 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 21 through 27 removed outlier: 5.357A pdb=" N CYS I 22 " --> pdb=" O ARG I 18 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ARG I 18 " --> pdb=" O CYS I 22 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN I 26 " --> pdb=" O VAL I 14 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N VAL I 14 " --> pdb=" O ASN I 26 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N VAL I 14 " --> pdb=" O HIS I 62 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N HIS I 62 " --> pdb=" O VAL I 14 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 87 through 90 removed outlier: 6.617A pdb=" N SER I 88 " --> pdb=" O MET I 167 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ASP I 169 " --> pdb=" O SER I 88 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU I 90 " --> pdb=" O ASP I 169 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE I 166 " --> pdb=" O VAL I 199 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N VAL I 201 " --> pdb=" O ILE I 166 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N PHE I 168 " --> pdb=" O VAL I 201 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'I' and resid 215 through 219 removed outlier: 3.659A pdb=" N ALA I 225 " --> pdb=" O ILE I 217 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ALA I 219 " --> pdb=" O ILE I 223 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ILE I 223 " --> pdb=" O ALA I 219 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 21 through 27 removed outlier: 5.356A pdb=" N CYS J 22 " --> pdb=" O ARG J 18 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ARG J 18 " --> pdb=" O CYS J 22 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN J 26 " --> pdb=" O VAL J 14 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N VAL J 14 " --> pdb=" O ASN J 26 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL J 9 " --> pdb=" O VAL J 31 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 21 through 27 removed outlier: 5.356A pdb=" N CYS J 22 " --> pdb=" O ARG J 18 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ARG J 18 " --> pdb=" O CYS J 22 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN J 26 " --> pdb=" O VAL J 14 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N VAL J 14 " --> pdb=" O ASN J 26 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N VAL J 14 " --> pdb=" O HIS J 62 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N HIS J 62 " --> pdb=" O VAL J 14 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 87 through 90 removed outlier: 6.617A pdb=" N SER J 88 " --> pdb=" O MET J 167 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ASP J 169 " --> pdb=" O SER J 88 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU J 90 " --> pdb=" O ASP J 169 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE J 166 " --> pdb=" O VAL J 199 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL J 201 " --> pdb=" O ILE J 166 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N PHE J 168 " --> pdb=" O VAL J 201 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'J' and resid 215 through 219 removed outlier: 3.659A pdb=" N ALA J 225 " --> pdb=" O ILE J 217 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ALA J 219 " --> pdb=" O ILE J 223 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ILE J 223 " --> pdb=" O ALA J 219 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 18 through 20 removed outlier: 6.606A pdb=" N GLY K 18 " --> pdb=" O VAL K 47 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ARG K 49 " --> pdb=" O GLY K 18 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 41 through 43 removed outlier: 6.288A pdb=" N ILE K 42 " --> pdb=" O GLN K 75 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'L' and resid 18 through 20 removed outlier: 6.605A pdb=" N GLY L 18 " --> pdb=" O VAL L 47 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ARG L 49 " --> pdb=" O GLY L 18 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 41 through 43 removed outlier: 6.288A pdb=" N ILE L 42 " --> pdb=" O GLN L 75 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 1080 hydrogen bonds defined for protein. 3168 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.88 Time building geometry restraints manager: 1.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2931 1.31 - 1.43: 4166 1.43 - 1.56: 10475 1.56 - 1.68: 6 1.68 - 1.81: 124 Bond restraints: 17702 Sorted by residual: bond pdb=" O4P PEF G 301 " pdb=" P PEF G 301 " ideal model delta sigma weight residual 1.639 1.509 0.130 2.00e-02 2.50e+03 4.20e+01 bond pdb=" O4P PEF G 302 " pdb=" P PEF G 302 " ideal model delta sigma weight residual 1.639 1.510 0.129 2.00e-02 2.50e+03 4.14e+01 bond pdb=" C10 PEF G 302 " pdb=" O2 PEF G 302 " ideal model delta sigma weight residual 1.330 1.442 -0.112 2.00e-02 2.50e+03 3.16e+01 bond pdb=" C10 PEF G 301 " pdb=" O2 PEF G 301 " ideal model delta sigma weight residual 1.330 1.441 -0.111 2.00e-02 2.50e+03 3.06e+01 bond pdb=" C30 PEF G 302 " pdb=" O3 PEF G 302 " ideal model delta sigma weight residual 1.333 1.407 -0.074 2.00e-02 2.50e+03 1.37e+01 ... (remaining 17697 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.11: 23977 3.11 - 6.22: 111 6.22 - 9.33: 13 9.33 - 12.44: 4 12.44 - 15.55: 3 Bond angle restraints: 24108 Sorted by residual: angle pdb=" N ALA G 192 " pdb=" CA ALA G 192 " pdb=" C ALA G 192 " ideal model delta sigma weight residual 111.14 122.24 -11.10 1.08e+00 8.57e-01 1.06e+02 angle pdb=" N VAL G 193 " pdb=" CA VAL G 193 " pdb=" C VAL G 193 " ideal model delta sigma weight residual 109.34 124.43 -15.09 2.08e+00 2.31e-01 5.26e+01 angle pdb=" N ALA H 192 " pdb=" CA ALA H 192 " pdb=" C ALA H 192 " ideal model delta sigma weight residual 111.36 118.91 -7.55 1.09e+00 8.42e-01 4.80e+01 angle pdb=" N GLN H 190 " pdb=" CA GLN H 190 " pdb=" C GLN H 190 " ideal model delta sigma weight residual 111.14 118.52 -7.38 1.08e+00 8.57e-01 4.67e+01 angle pdb=" N SER A 56 " pdb=" CA SER A 56 " pdb=" C SER A 56 " ideal model delta sigma weight residual 109.72 101.47 8.25 1.25e+00 6.40e-01 4.35e+01 ... (remaining 24103 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 9880 17.05 - 34.11: 591 34.11 - 51.16: 91 51.16 - 68.22: 23 68.22 - 85.27: 5 Dihedral angle restraints: 10590 sinusoidal: 3703 harmonic: 6887 Sorted by residual: dihedral pdb=" CA GLU E 37 " pdb=" C GLU E 37 " pdb=" N PRO E 38 " pdb=" CA PRO E 38 " ideal model delta harmonic sigma weight residual 180.00 160.50 19.50 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA PRO B 57 " pdb=" C PRO B 57 " pdb=" N VAL B 58 " pdb=" CA VAL B 58 " ideal model delta harmonic sigma weight residual 180.00 162.90 17.10 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA PRO E 38 " pdb=" C PRO E 38 " pdb=" N THR E 39 " pdb=" CA THR E 39 " ideal model delta harmonic sigma weight residual 180.00 163.22 16.78 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 10587 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 2761 0.081 - 0.163: 180 0.163 - 0.244: 6 0.244 - 0.326: 5 0.326 - 0.407: 4 Chirality restraints: 2956 Sorted by residual: chirality pdb=" CA ALA G 192 " pdb=" N ALA G 192 " pdb=" C ALA G 192 " pdb=" CB ALA G 192 " both_signs ideal model delta sigma weight residual False 2.48 2.08 0.41 2.00e-01 2.50e+01 4.15e+00 chirality pdb=" CA GLN H 190 " pdb=" N GLN H 190 " pdb=" C GLN H 190 " pdb=" CB GLN H 190 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" CA VAL G 193 " pdb=" N VAL G 193 " pdb=" C VAL G 193 " pdb=" CB VAL G 193 " both_signs ideal model delta sigma weight residual False 2.44 2.07 0.37 2.00e-01 2.50e+01 3.49e+00 ... (remaining 2953 not shown) Planarity restraints: 3075 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE G 185 " -0.009 2.00e-02 2.50e+03 1.81e-02 3.29e+00 pdb=" C PHE G 185 " 0.031 2.00e-02 2.50e+03 pdb=" O PHE G 185 " -0.012 2.00e-02 2.50e+03 pdb=" N TRP G 186 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL H 163 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.56e+00 pdb=" C VAL H 163 " 0.028 2.00e-02 2.50e+03 pdb=" O VAL H 163 " -0.010 2.00e-02 2.50e+03 pdb=" N ALA H 164 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL G 163 " -0.008 2.00e-02 2.50e+03 1.52e-02 2.32e+00 pdb=" C VAL G 163 " 0.026 2.00e-02 2.50e+03 pdb=" O VAL G 163 " -0.010 2.00e-02 2.50e+03 pdb=" N ALA G 164 " -0.009 2.00e-02 2.50e+03 ... (remaining 3072 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 217 2.66 - 3.22: 17283 3.22 - 3.78: 26177 3.78 - 4.34: 35683 4.34 - 4.90: 58618 Nonbonded interactions: 137978 Sorted by model distance: nonbonded pdb=" O GLY G 183 " pdb=" OG SER G 187 " model vdw 2.104 3.040 nonbonded pdb=" OG SER K 6 " pdb=" OG SER K 17 " model vdw 2.224 3.040 nonbonded pdb=" OG SER L 6 " pdb=" OG SER L 17 " model vdw 2.224 3.040 nonbonded pdb=" O SER G 55 " pdb=" OG SER G 55 " model vdw 2.286 3.040 nonbonded pdb=" OH TYR L 82 " pdb=" O ARG L 97 " model vdw 2.294 3.040 ... (remaining 137973 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' and ((resid 4 through 10 and (name N or name CA or name C or name O o \ r name CB )) or resid 11 or (resid 12 through 25 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 121 or resid 124 through 152)) selection = (chain 'B' and ((resid 4 through 10 and (name N or name CA or name C or name O o \ r name CB )) or resid 11 or (resid 12 through 25 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 121 or resid 124 through 152)) selection = (chain 'C' and (resid 4 through 25 or resid 37 through 121 or resid 124 through \ 152)) selection = (chain 'D' and ((resid 4 through 10 and (name N or name CA or name C or name O o \ r name CB )) or resid 11 or (resid 12 through 25 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 152)) selection = (chain 'E' and ((resid 4 through 10 and (name N or name CA or name C or name O o \ r name CB )) or resid 11 or (resid 12 through 25 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 121 or resid 124 through 152)) selection = (chain 'F' and (resid 4 through 25 or resid 37 through 121 or resid 124 through \ 152)) } ncs_group { reference = (chain 'G' and resid 5 through 259) selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' } ncs_group { reference = (chain 'M' and (resid 9 through 164 and (name N or name CA or name C or name O o \ r name CB ))) selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 2.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.670 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 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 : 0.004 0.130 17702 Z= 0.191 Angle : 0.661 15.551 24108 Z= 0.353 Chirality : 0.045 0.407 2956 Planarity : 0.003 0.036 3075 Dihedral : 11.688 85.270 6142 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.06 % Allowed : 2.62 % Favored : 97.32 % 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: -2.47 (0.17), residues: 2046 helix: -0.41 (0.16), residues: 876 sheet: -3.38 (0.25), residues: 283 loop : -2.24 (0.20), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 81 TYR 0.010 0.001 TYR F 40 PHE 0.017 0.001 PHE G 185 TRP 0.013 0.001 TRP G 195 HIS 0.002 0.001 HIS I 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.19 (17702) covalent geometry : angle 0.66062 / 0.35 (24108) hydrogen bonds : bond 0.20720 / 13.42 ( 1074) hydrogen bonds : angle 7.65370 / 5.26 ( 3168) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 414 time to evaluate : 0.583 Fit side-chains REVERT: A 92 HIS cc_start: 0.8066 (t-90) cc_final: 0.7804 (t-90) REVERT: A 149 GLN cc_start: 0.8658 (tm-30) cc_final: 0.8413 (tm-30) REVERT: B 118 PHE cc_start: 0.6631 (p90) cc_final: 0.6394 (t80) REVERT: B 132 ASP cc_start: 0.8209 (t0) cc_final: 0.7909 (t0) REVERT: C 37 GLU cc_start: 0.8048 (tp30) cc_final: 0.7807 (mm-30) REVERT: C 88 GLN cc_start: 0.8822 (tp40) cc_final: 0.8324 (tp-100) REVERT: C 91 ASN cc_start: 0.8171 (m-40) cc_final: 0.7655 (m-40) REVERT: C 138 LYS cc_start: 0.8857 (mttp) cc_final: 0.8542 (mtpp) REVERT: D 5 LYS cc_start: 0.7876 (tttm) cc_final: 0.7647 (mmtt) REVERT: D 7 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7877 (mm-30) REVERT: D 37 GLU cc_start: 0.6997 (tm-30) cc_final: 0.6386 (tm-30) REVERT: D 74 ASP cc_start: 0.8385 (t0) cc_final: 0.8036 (t70) REVERT: D 129 LYS cc_start: 0.8759 (pttm) cc_final: 0.8411 (mptt) REVERT: E 138 LYS cc_start: 0.8850 (ttmm) cc_final: 0.8409 (tmtt) REVERT: F 85 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7890 (mt-10) REVERT: F 115 ASN cc_start: 0.8323 (t0) cc_final: 0.8025 (t0) REVERT: G 98 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7497 (mm-30) REVERT: G 127 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7745 (mm-30) REVERT: G 250 ASP cc_start: 0.8728 (t70) cc_final: 0.8091 (t0) REVERT: H 18 ARG cc_start: 0.8408 (ttm170) cc_final: 0.8092 (mtp85) REVERT: H 127 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7375 (mm-30) REVERT: H 191 ASN cc_start: 0.8431 (p0) cc_final: 0.8178 (p0) REVERT: H 223 ASP cc_start: 0.8140 (t0) cc_final: 0.7813 (t0) REVERT: I 10 ASP cc_start: 0.7822 (t0) cc_final: 0.7460 (t0) REVERT: I 130 GLU cc_start: 0.8249 (tp30) cc_final: 0.7990 (tp30) REVERT: I 207 GLU cc_start: 0.7684 (mp0) cc_final: 0.7249 (mp0) REVERT: J 221 LYS cc_start: 0.8895 (mtpt) cc_final: 0.8278 (mtmt) REVERT: K 31 MET cc_start: 0.8119 (ptm) cc_final: 0.7772 (ppp) REVERT: L 22 GLN cc_start: 0.7846 (mp10) cc_final: 0.7601 (mp10) REVERT: L 31 MET cc_start: 0.7374 (ptm) cc_final: 0.7014 (ptp) outliers start: 1 outliers final: 0 residues processed: 414 average time/residue: 0.1763 time to fit residues: 102.2834 Evaluate side-chains 336 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 336 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 20.0000 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 30.0000 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.5980 chunk 200 optimal weight: 0.1980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 2 GLN C 110 GLN D 2 GLN G 40 HIS ** H 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 175 GLN I 226 HIS I 230 GLN J 57 GLN J 175 GLN J 191 ASN J 226 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.118881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.082957 restraints weight = 30227.911| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.81 r_work: 0.2985 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17702 Z= 0.158 Angle : 0.593 6.888 24108 Z= 0.294 Chirality : 0.040 0.158 2956 Planarity : 0.004 0.036 3075 Dihedral : 5.940 58.757 2597 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.01 % Allowed : 9.82 % Favored : 89.17 % 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: -1.17 (0.19), residues: 2046 helix: 0.81 (0.17), residues: 907 sheet: -2.89 (0.25), residues: 303 loop : -1.67 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 77 TYR 0.015 0.001 TYR G 222 PHE 0.015 0.001 PHE G 185 TRP 0.011 0.001 TRP G 195 HIS 0.002 0.001 HIS L 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 (17702) covalent geometry : angle 0.59274 / 0.29 (24108) hydrogen bonds : bond 0.05089 / 3.34 ( 1074) hydrogen bonds : angle 5.56035 / 3.87 ( 3168) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 351 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 GLU cc_start: 0.8450 (pm20) cc_final: 0.8217 (pm20) REVERT: A 132 ASP cc_start: 0.8547 (m-30) cc_final: 0.8134 (m-30) REVERT: B 89 ARG cc_start: 0.8366 (mtp-110) cc_final: 0.8164 (mtp-110) REVERT: B 115 ASN cc_start: 0.7713 (m-40) cc_final: 0.7497 (t0) REVERT: B 118 PHE cc_start: 0.6732 (p90) cc_final: 0.6309 (t80) REVERT: B 132 ASP cc_start: 0.8534 (t0) cc_final: 0.8202 (t0) REVERT: B 138 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.8040 (mptt) REVERT: C 37 GLU cc_start: 0.8142 (tp30) cc_final: 0.7910 (mm-30) REVERT: C 88 GLN cc_start: 0.9027 (tp40) cc_final: 0.8453 (tp-100) REVERT: C 91 ASN cc_start: 0.8433 (m-40) cc_final: 0.7826 (m-40) REVERT: C 132 ASP cc_start: 0.8380 (m-30) cc_final: 0.8034 (m-30) REVERT: C 138 LYS cc_start: 0.8767 (mttp) cc_final: 0.8349 (mtpp) REVERT: D 7 GLU cc_start: 0.8465 (mm-30) cc_final: 0.8129 (mm-30) REVERT: D 74 ASP cc_start: 0.8444 (t0) cc_final: 0.7995 (t70) REVERT: D 129 LYS cc_start: 0.8582 (pttm) cc_final: 0.8114 (mptt) REVERT: E 67 ARG cc_start: 0.7943 (mmt90) cc_final: 0.7674 (mmt90) REVERT: E 138 LYS cc_start: 0.8818 (ttmm) cc_final: 0.8051 (tmtt) REVERT: F 37 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8297 (mt-10) REVERT: F 53 LYS cc_start: 0.8749 (mttp) cc_final: 0.8452 (mttp) REVERT: F 85 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8594 (mt-10) REVERT: F 115 ASN cc_start: 0.8423 (t0) cc_final: 0.8006 (t0) REVERT: G 98 GLU cc_start: 0.8328 (mm-30) cc_final: 0.8121 (mm-30) REVERT: G 127 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8027 (mm-30) REVERT: G 250 ASP cc_start: 0.8989 (t70) cc_final: 0.8507 (t0) REVERT: H 18 ARG cc_start: 0.8360 (ttm170) cc_final: 0.7903 (mtp85) REVERT: H 40 HIS cc_start: 0.7710 (m170) cc_final: 0.7431 (m170) REVERT: H 127 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7981 (mm-30) REVERT: H 223 ASP cc_start: 0.8733 (t0) cc_final: 0.8408 (t0) REVERT: I 10 ASP cc_start: 0.8210 (t0) cc_final: 0.7705 (t0) REVERT: I 130 GLU cc_start: 0.8924 (tp30) cc_final: 0.8699 (tp30) REVERT: I 220 ASP cc_start: 0.8214 (t0) cc_final: 0.7586 (t0) REVERT: J 64 GLU cc_start: 0.8112 (pm20) cc_final: 0.7393 (pm20) REVERT: J 130 GLU cc_start: 0.8898 (tp30) cc_final: 0.8374 (tp30) REVERT: J 207 GLU cc_start: 0.8313 (mp0) cc_final: 0.8029 (mp0) REVERT: J 220 ASP cc_start: 0.8386 (t0) cc_final: 0.8182 (t0) REVERT: J 221 LYS cc_start: 0.8707 (mtpt) cc_final: 0.8114 (mtmt) REVERT: K 31 MET cc_start: 0.8527 (ptm) cc_final: 0.7524 (ppp) REVERT: K 80 LYS cc_start: 0.8885 (ttmm) cc_final: 0.8401 (mtmm) REVERT: L 22 GLN cc_start: 0.7972 (mp10) cc_final: 0.7660 (mp10) REVERT: L 31 MET cc_start: 0.7311 (ptm) cc_final: 0.7030 (ptp) outliers start: 17 outliers final: 7 residues processed: 360 average time/residue: 0.1713 time to fit residues: 87.1435 Evaluate side-chains 342 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 334 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain B residue 138 LYS Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 203 LEU Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain K residue 73 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 181 optimal weight: 0.0040 chunk 47 optimal weight: 8.9990 chunk 74 optimal weight: 0.7980 chunk 184 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 226 optimal weight: 9.9990 chunk 222 optimal weight: 40.0000 chunk 59 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 123 optimal weight: 0.0980 chunk 86 optimal weight: 4.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 92 HIS C 110 GLN D 2 GLN ** I 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 230 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.120325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.085085 restraints weight = 30261.136| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.80 r_work: 0.3017 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17702 Z= 0.130 Angle : 0.543 6.843 24108 Z= 0.266 Chirality : 0.039 0.151 2956 Planarity : 0.003 0.034 3075 Dihedral : 5.525 59.482 2597 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.79 % Allowed : 11.25 % Favored : 86.96 % 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: -0.41 (0.19), residues: 2046 helix: 1.50 (0.18), residues: 908 sheet: -2.65 (0.25), residues: 304 loop : -1.29 (0.23), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 55 TYR 0.015 0.001 TYR G 222 PHE 0.014 0.001 PHE G 185 TRP 0.011 0.001 TRP G 195 HIS 0.010 0.001 HIS I 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (17702) covalent geometry : angle 0.54325 / 0.27 (24108) hydrogen bonds : bond 0.04576 / 3.02 ( 1074) hydrogen bonds : angle 5.09590 / 3.55 ( 3168) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 352 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 HIS cc_start: 0.8226 (t-90) cc_final: 0.8013 (t70) REVERT: A 132 ASP cc_start: 0.8578 (m-30) cc_final: 0.8120 (m-30) REVERT: B 81 ARG cc_start: 0.8693 (ttm-80) cc_final: 0.8419 (ttt90) REVERT: B 115 ASN cc_start: 0.7753 (m-40) cc_final: 0.7516 (t0) REVERT: B 118 PHE cc_start: 0.6701 (p90) cc_final: 0.6372 (t80) REVERT: B 132 ASP cc_start: 0.8498 (t0) cc_final: 0.8178 (t0) REVERT: C 37 GLU cc_start: 0.8123 (tp30) cc_final: 0.7923 (mm-30) REVERT: C 85 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8163 (pt0) REVERT: C 88 GLN cc_start: 0.8979 (tp40) cc_final: 0.8687 (tp-100) REVERT: C 132 ASP cc_start: 0.8343 (m-30) cc_final: 0.7954 (m-30) REVERT: C 138 LYS cc_start: 0.8711 (mttp) cc_final: 0.8301 (mtpp) REVERT: D 7 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8080 (mm-30) REVERT: D 87 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7395 (mm-30) REVERT: D 129 LYS cc_start: 0.8471 (pttm) cc_final: 0.7982 (mptt) REVERT: E 55 ARG cc_start: 0.8337 (mmm160) cc_final: 0.7912 (mmp80) REVERT: E 138 LYS cc_start: 0.8774 (ttmm) cc_final: 0.7974 (tmtt) REVERT: F 115 ASN cc_start: 0.8461 (t0) cc_final: 0.8045 (t0) REVERT: G 98 GLU cc_start: 0.8209 (mm-30) cc_final: 0.8006 (mm-30) REVERT: G 127 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7890 (mm-30) REVERT: G 250 ASP cc_start: 0.8969 (t70) cc_final: 0.8409 (t0) REVERT: H 18 ARG cc_start: 0.8327 (ttm170) cc_final: 0.7846 (mtp85) REVERT: H 40 HIS cc_start: 0.7649 (m170) cc_final: 0.7438 (m170) REVERT: H 127 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7868 (mm-30) REVERT: H 223 ASP cc_start: 0.8740 (t0) cc_final: 0.8442 (t0) REVERT: I 10 ASP cc_start: 0.8187 (t0) cc_final: 0.7530 (t0) REVERT: I 130 GLU cc_start: 0.8882 (tp30) cc_final: 0.8189 (tp30) REVERT: I 220 ASP cc_start: 0.8168 (t0) cc_final: 0.7537 (t70) REVERT: J 26 ASN cc_start: 0.9306 (t0) cc_final: 0.8935 (t0) REVERT: J 130 GLU cc_start: 0.8953 (tp30) cc_final: 0.8389 (tp30) REVERT: J 220 ASP cc_start: 0.8395 (t0) cc_final: 0.8127 (t0) REVERT: J 221 LYS cc_start: 0.8719 (mtpt) cc_final: 0.8141 (mtmt) REVERT: K 31 MET cc_start: 0.8550 (ptm) cc_final: 0.7512 (ppp) REVERT: K 49 ARG cc_start: 0.8174 (ttp80) cc_final: 0.7745 (ptm-80) REVERT: K 80 LYS cc_start: 0.8869 (ttmm) cc_final: 0.8403 (mtmm) REVERT: K 86 LYS cc_start: 0.8982 (ttpp) cc_final: 0.8745 (tppt) REVERT: L 22 GLN cc_start: 0.7802 (mp10) cc_final: 0.7436 (mp10) REVERT: L 31 MET cc_start: 0.7080 (ptm) cc_final: 0.6876 (ptm) REVERT: L 34 GLU cc_start: 0.7978 (pm20) cc_final: 0.7562 (pm20) outliers start: 30 outliers final: 14 residues processed: 365 average time/residue: 0.1705 time to fit residues: 87.7238 Evaluate side-chains 342 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 327 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain C residue 85 GLU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain I residue 115 GLN Chi-restraints excluded: chain I residue 189 GLU Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain K residue 36 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 1 optimal weight: 0.7980 chunk 226 optimal weight: 10.0000 chunk 113 optimal weight: 5.9990 chunk 177 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 197 optimal weight: 7.9990 chunk 147 optimal weight: 0.6980 chunk 61 optimal weight: 6.9990 chunk 158 optimal weight: 8.9990 chunk 206 optimal weight: 30.0000 chunk 196 optimal weight: 0.6980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 HIS C 110 GLN D 2 GLN G 40 HIS I 230 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.118777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.083566 restraints weight = 30275.683| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.77 r_work: 0.2985 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17702 Z= 0.161 Angle : 0.559 6.106 24108 Z= 0.274 Chirality : 0.040 0.237 2956 Planarity : 0.003 0.036 3075 Dihedral : 5.392 59.861 2597 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.02 % Allowed : 13.81 % Favored : 84.17 % 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: -0.12 (0.19), residues: 2046 helix: 1.74 (0.18), residues: 898 sheet: -2.43 (0.26), residues: 304 loop : -1.14 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 124 TYR 0.015 0.001 TYR G 222 PHE 0.014 0.001 PHE G 185 TRP 0.009 0.001 TRP G 195 HIS 0.005 0.001 HIS I 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (17702) covalent geometry : angle 0.55906 / 0.27 (24108) hydrogen bonds : bond 0.04537 / 3.00 ( 1074) hydrogen bonds : angle 5.01246 / 3.50 ( 3168) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 338 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 ASP cc_start: 0.8555 (m-30) cc_final: 0.8000 (m-30) REVERT: B 115 ASN cc_start: 0.7771 (m-40) cc_final: 0.7473 (t0) REVERT: B 118 PHE cc_start: 0.6742 (p90) cc_final: 0.6406 (t80) REVERT: B 132 ASP cc_start: 0.8490 (t0) cc_final: 0.8149 (t0) REVERT: C 85 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8194 (pt0) REVERT: C 88 GLN cc_start: 0.8986 (tp40) cc_final: 0.8564 (tp-100) REVERT: C 132 ASP cc_start: 0.8387 (m-30) cc_final: 0.7981 (m-30) REVERT: C 138 LYS cc_start: 0.8717 (mttp) cc_final: 0.8328 (mtpp) REVERT: D 7 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8054 (mm-30) REVERT: D 87 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7410 (mm-30) REVERT: D 129 LYS cc_start: 0.8527 (pttm) cc_final: 0.8062 (mptt) REVERT: E 55 ARG cc_start: 0.8385 (mmm160) cc_final: 0.8119 (mmp80) REVERT: E 138 LYS cc_start: 0.8788 (ttmm) cc_final: 0.8090 (tmtt) REVERT: F 70 ASP cc_start: 0.8304 (t0) cc_final: 0.7977 (t0) REVERT: F 115 ASN cc_start: 0.8428 (t0) cc_final: 0.8034 (t0) REVERT: F 138 LYS cc_start: 0.8474 (ttmm) cc_final: 0.7822 (ttpt) REVERT: G 127 GLU cc_start: 0.8412 (mm-30) cc_final: 0.8046 (mm-30) REVERT: G 191 ASN cc_start: 0.8125 (m-40) cc_final: 0.7857 (m-40) REVERT: G 250 ASP cc_start: 0.9004 (t70) cc_final: 0.8512 (t0) REVERT: H 18 ARG cc_start: 0.8342 (ttm170) cc_final: 0.7952 (mtp85) REVERT: H 40 HIS cc_start: 0.7686 (m170) cc_final: 0.7473 (m170) REVERT: H 223 ASP cc_start: 0.8719 (t0) cc_final: 0.8428 (t0) REVERT: I 10 ASP cc_start: 0.8174 (t0) cc_final: 0.7505 (t0) REVERT: I 130 GLU cc_start: 0.8902 (tp30) cc_final: 0.8225 (tp30) REVERT: I 144 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8139 (tm-30) REVERT: I 220 ASP cc_start: 0.8075 (t0) cc_final: 0.7518 (t70) REVERT: I 221 LYS cc_start: 0.8753 (mtmm) cc_final: 0.8532 (mtpp) REVERT: J 26 ASN cc_start: 0.9321 (t0) cc_final: 0.8967 (t0) REVERT: J 64 GLU cc_start: 0.8235 (pm20) cc_final: 0.7664 (pm20) REVERT: J 130 GLU cc_start: 0.8975 (tp30) cc_final: 0.8426 (tp30) REVERT: J 220 ASP cc_start: 0.8398 (t0) cc_final: 0.8110 (t0) REVERT: J 221 LYS cc_start: 0.8693 (mtpt) cc_final: 0.8119 (mtmt) REVERT: K 30 GLU cc_start: 0.9014 (mt-10) cc_final: 0.8588 (mt-10) REVERT: K 31 MET cc_start: 0.8537 (ptm) cc_final: 0.7519 (ppp) REVERT: K 49 ARG cc_start: 0.8156 (ttp80) cc_final: 0.7588 (ptm-80) REVERT: K 80 LYS cc_start: 0.8786 (ttmm) cc_final: 0.8462 (tmtt) REVERT: K 86 LYS cc_start: 0.9052 (ttpp) cc_final: 0.8803 (tppt) REVERT: L 22 GLN cc_start: 0.7846 (mp10) cc_final: 0.7450 (mp10) REVERT: L 34 GLU cc_start: 0.8016 (pm20) cc_final: 0.7666 (pm20) outliers start: 34 outliers final: 21 residues processed: 356 average time/residue: 0.1671 time to fit residues: 84.4758 Evaluate side-chains 350 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 328 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 85 GLU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 66 ILE Chi-restraints excluded: chain H residue 203 LEU Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain I residue 115 GLN Chi-restraints excluded: chain I residue 189 GLU Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain J residue 170 GLU Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 73 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 6 optimal weight: 0.2980 chunk 2 optimal weight: 3.9990 chunk 82 optimal weight: 8.9990 chunk 40 optimal weight: 8.9990 chunk 175 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 190 optimal weight: 0.9980 chunk 35 optimal weight: 8.9990 chunk 66 optimal weight: 20.0000 chunk 108 optimal weight: 9.9990 chunk 58 optimal weight: 8.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 110 GLN I 230 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.118761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.082515 restraints weight = 30767.148| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.83 r_work: 0.2947 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 17702 Z= 0.202 Angle : 0.579 6.094 24108 Z= 0.285 Chirality : 0.041 0.180 2956 Planarity : 0.004 0.039 3075 Dihedral : 5.397 58.540 2597 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.02 % Allowed : 15.60 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.19), residues: 2046 helix: 1.79 (0.18), residues: 896 sheet: -2.24 (0.27), residues: 305 loop : -1.04 (0.22), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 89 TYR 0.018 0.001 TYR G 222 PHE 0.023 0.001 PHE A 118 TRP 0.009 0.001 TRP G 195 HIS 0.004 0.001 HIS I 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.20 (17702) covalent geometry : angle 0.57881 / 0.29 (24108) hydrogen bonds : bond 0.04592 / 3.04 ( 1074) hydrogen bonds : angle 4.97896 / 3.48 ( 3168) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 337 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.8683 (mtp85) cc_final: 0.7922 (mtm-85) REVERT: A 132 ASP cc_start: 0.8553 (m-30) cc_final: 0.7966 (m-30) REVERT: B 115 ASN cc_start: 0.7880 (m-40) cc_final: 0.7503 (t0) REVERT: B 118 PHE cc_start: 0.6734 (p90) cc_final: 0.6440 (t80) REVERT: B 132 ASP cc_start: 0.8460 (t0) cc_final: 0.8120 (t0) REVERT: B 138 LYS cc_start: 0.8313 (mppt) cc_final: 0.7976 (mptt) REVERT: C 76 LYS cc_start: 0.9180 (ttpp) cc_final: 0.8938 (mptt) REVERT: C 88 GLN cc_start: 0.8974 (tp40) cc_final: 0.8551 (tp-100) REVERT: C 132 ASP cc_start: 0.8405 (m-30) cc_final: 0.7939 (m-30) REVERT: C 138 LYS cc_start: 0.8759 (mttp) cc_final: 0.8362 (mtpp) REVERT: D 5 LYS cc_start: 0.7799 (tttm) cc_final: 0.7304 (mmtt) REVERT: D 7 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8073 (mm-30) REVERT: D 129 LYS cc_start: 0.8536 (pttm) cc_final: 0.8060 (mptt) REVERT: E 55 ARG cc_start: 0.8410 (mmm160) cc_final: 0.8124 (mmp80) REVERT: F 53 LYS cc_start: 0.8682 (mttp) cc_final: 0.8312 (ttmm) REVERT: F 115 ASN cc_start: 0.8454 (t0) cc_final: 0.8058 (t0) REVERT: F 149 GLN cc_start: 0.9053 (tm-30) cc_final: 0.8614 (tm-30) REVERT: G 127 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8195 (mm-30) REVERT: G 191 ASN cc_start: 0.8003 (m-40) cc_final: 0.7792 (m-40) REVERT: H 18 ARG cc_start: 0.8383 (ttm170) cc_final: 0.7921 (mtp85) REVERT: H 40 HIS cc_start: 0.7703 (m170) cc_final: 0.7455 (m170) REVERT: H 223 ASP cc_start: 0.8756 (t0) cc_final: 0.8459 (t0) REVERT: I 10 ASP cc_start: 0.8171 (t0) cc_final: 0.7910 (m-30) REVERT: I 130 GLU cc_start: 0.8964 (tp30) cc_final: 0.8333 (tp30) REVERT: I 144 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8100 (tm-30) REVERT: I 220 ASP cc_start: 0.8150 (t0) cc_final: 0.7587 (t70) REVERT: I 221 LYS cc_start: 0.8760 (mtmm) cc_final: 0.8532 (mtpp) REVERT: J 26 ASN cc_start: 0.9349 (t0) cc_final: 0.9007 (t0) REVERT: J 64 GLU cc_start: 0.8264 (pm20) cc_final: 0.7679 (pm20) REVERT: J 130 GLU cc_start: 0.9010 (tp30) cc_final: 0.8537 (tp30) REVERT: J 220 ASP cc_start: 0.8426 (t0) cc_final: 0.8128 (t0) REVERT: K 30 GLU cc_start: 0.9047 (mt-10) cc_final: 0.8606 (mt-10) REVERT: K 86 LYS cc_start: 0.9101 (ttpp) cc_final: 0.8820 (tppt) REVERT: L 22 GLN cc_start: 0.7994 (mp10) cc_final: 0.7561 (mp10) REVERT: L 31 MET cc_start: 0.6966 (ptp) cc_final: 0.6734 (ptm) REVERT: L 34 GLU cc_start: 0.8007 (pm20) cc_final: 0.7541 (pm20) outliers start: 34 outliers final: 26 residues processed: 356 average time/residue: 0.1588 time to fit residues: 79.9631 Evaluate side-chains 350 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 324 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain B residue 141 MET Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 66 ILE Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 203 LEU Chi-restraints excluded: chain I residue 17 THR Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain I residue 115 GLN Chi-restraints excluded: chain I residue 189 GLU Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain J residue 170 GLU Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 73 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 155 optimal weight: 1.9990 chunk 209 optimal weight: 30.0000 chunk 32 optimal weight: 0.0980 chunk 149 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 147 optimal weight: 0.9990 chunk 218 optimal weight: 40.0000 chunk 82 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 215 optimal weight: 30.0000 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 110 GLN J 20 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.118110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.082460 restraints weight = 29970.305| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.77 r_work: 0.2978 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17702 Z= 0.166 Angle : 0.559 6.019 24108 Z= 0.275 Chirality : 0.040 0.155 2956 Planarity : 0.004 0.036 3075 Dihedral : 5.334 58.792 2597 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.68 % Allowed : 15.54 % Favored : 81.79 % 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: 0.17 (0.19), residues: 2046 helix: 1.93 (0.18), residues: 897 sheet: -2.11 (0.27), residues: 308 loop : -0.98 (0.22), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 89 TYR 0.018 0.001 TYR G 222 PHE 0.024 0.001 PHE A 118 TRP 0.011 0.001 TRP G 195 HIS 0.002 0.001 HIS L 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (17702) covalent geometry : angle 0.55874 / 0.28 (24108) hydrogen bonds : bond 0.04417 / 2.93 ( 1074) hydrogen bonds : angle 4.86429 / 3.40 ( 3168) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 329 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 ASP cc_start: 0.8578 (m-30) cc_final: 0.8001 (m-30) REVERT: B 115 ASN cc_start: 0.7908 (m-40) cc_final: 0.7469 (t0) REVERT: B 118 PHE cc_start: 0.6705 (p90) cc_final: 0.6444 (t80) REVERT: B 132 ASP cc_start: 0.8426 (t0) cc_final: 0.8069 (t0) REVERT: B 138 LYS cc_start: 0.8325 (mppt) cc_final: 0.8088 (mptt) REVERT: C 76 LYS cc_start: 0.9164 (ttpp) cc_final: 0.8954 (mptt) REVERT: C 88 GLN cc_start: 0.9017 (tp40) cc_final: 0.8552 (tp-100) REVERT: C 132 ASP cc_start: 0.8427 (m-30) cc_final: 0.7969 (m-30) REVERT: C 138 LYS cc_start: 0.8745 (mttp) cc_final: 0.8352 (mtpp) REVERT: D 5 LYS cc_start: 0.7725 (tttm) cc_final: 0.7273 (tptt) REVERT: D 7 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8065 (mm-30) REVERT: D 87 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7568 (mm-30) REVERT: D 129 LYS cc_start: 0.8541 (pttm) cc_final: 0.8085 (mmmt) REVERT: E 55 ARG cc_start: 0.8397 (mmm160) cc_final: 0.8096 (mmp80) REVERT: F 53 LYS cc_start: 0.8675 (mttp) cc_final: 0.8161 (ttmm) REVERT: F 115 ASN cc_start: 0.8450 (t0) cc_final: 0.8061 (t0) REVERT: F 149 GLN cc_start: 0.9076 (tm-30) cc_final: 0.8680 (tm-30) REVERT: G 127 GLU cc_start: 0.8462 (mm-30) cc_final: 0.8133 (mm-30) REVERT: G 191 ASN cc_start: 0.7948 (m-40) cc_final: 0.7678 (m-40) REVERT: H 18 ARG cc_start: 0.8374 (ttm170) cc_final: 0.7919 (mtp85) REVERT: H 40 HIS cc_start: 0.7670 (m170) cc_final: 0.7459 (m170) REVERT: H 223 ASP cc_start: 0.8756 (t0) cc_final: 0.8452 (t0) REVERT: I 10 ASP cc_start: 0.8145 (t0) cc_final: 0.7911 (m-30) REVERT: I 130 GLU cc_start: 0.8948 (tp30) cc_final: 0.8322 (tp30) REVERT: I 144 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8084 (tm-30) REVERT: I 220 ASP cc_start: 0.8188 (t0) cc_final: 0.7612 (t70) REVERT: J 26 ASN cc_start: 0.9365 (t0) cc_final: 0.9027 (t0) REVERT: J 64 GLU cc_start: 0.8260 (pm20) cc_final: 0.7690 (pm20) REVERT: J 130 GLU cc_start: 0.8995 (tp30) cc_final: 0.8549 (tp30) REVERT: J 220 ASP cc_start: 0.8407 (t0) cc_final: 0.8121 (t0) REVERT: J 221 LYS cc_start: 0.8797 (mtmt) cc_final: 0.8228 (mtmt) REVERT: K 30 GLU cc_start: 0.9080 (mt-10) cc_final: 0.8649 (mt-10) REVERT: K 31 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.7633 (ppp) REVERT: K 49 ARG cc_start: 0.8268 (ttp80) cc_final: 0.7720 (ptm-80) REVERT: K 80 LYS cc_start: 0.8698 (ttmm) cc_final: 0.8417 (tmtt) REVERT: K 86 LYS cc_start: 0.9096 (ttpp) cc_final: 0.8836 (tppt) REVERT: L 22 GLN cc_start: 0.8003 (mp10) cc_final: 0.7540 (mp10) REVERT: L 31 MET cc_start: 0.7047 (ptp) cc_final: 0.6772 (ptm) REVERT: L 33 GLU cc_start: 0.7318 (pm20) cc_final: 0.7045 (pm20) REVERT: L 34 GLU cc_start: 0.7999 (pm20) cc_final: 0.7561 (pm20) outliers start: 45 outliers final: 32 residues processed: 358 average time/residue: 0.1649 time to fit residues: 83.9924 Evaluate side-chains 354 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 321 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain B residue 141 MET Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 66 ILE Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 203 LEU Chi-restraints excluded: chain I residue 17 THR Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain I residue 115 GLN Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 189 GLU Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 170 GLU Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain K residue 31 MET Chi-restraints excluded: chain K residue 36 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 96 optimal weight: 0.9990 chunk 221 optimal weight: 30.0000 chunk 105 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 229 optimal weight: 40.0000 chunk 32 optimal weight: 0.9990 chunk 232 optimal weight: 9.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 110 GLN ** I 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.119790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.084243 restraints weight = 29944.698| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.78 r_work: 0.3008 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17702 Z= 0.133 Angle : 0.543 6.422 24108 Z= 0.268 Chirality : 0.040 0.149 2956 Planarity : 0.003 0.033 3075 Dihedral : 5.199 59.207 2597 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.20 % Allowed : 16.79 % Favored : 81.01 % 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: 0.46 (0.20), residues: 2046 helix: 2.15 (0.18), residues: 895 sheet: -1.98 (0.28), residues: 308 loop : -0.78 (0.22), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 89 TYR 0.017 0.001 TYR G 222 PHE 0.022 0.001 PHE C 118 TRP 0.014 0.001 TRP G 195 HIS 0.005 0.000 HIS I 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (17702) covalent geometry : angle 0.54318 / 0.27 (24108) hydrogen bonds : bond 0.04247 / 2.81 ( 1074) hydrogen bonds : angle 4.73762 / 3.31 ( 3168) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 331 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 HIS cc_start: 0.8187 (t70) cc_final: 0.7562 (t70) REVERT: A 132 ASP cc_start: 0.8600 (m-30) cc_final: 0.8004 (m-30) REVERT: B 115 ASN cc_start: 0.7916 (m-40) cc_final: 0.7480 (t0) REVERT: B 118 PHE cc_start: 0.6668 (p90) cc_final: 0.6376 (t80) REVERT: B 132 ASP cc_start: 0.8424 (t0) cc_final: 0.8085 (t0) REVERT: B 138 LYS cc_start: 0.8352 (mppt) cc_final: 0.8108 (mptt) REVERT: C 76 LYS cc_start: 0.9126 (ttpp) cc_final: 0.8926 (mptt) REVERT: C 132 ASP cc_start: 0.8428 (m-30) cc_final: 0.7964 (m-30) REVERT: C 138 LYS cc_start: 0.8721 (mttp) cc_final: 0.8343 (mtpp) REVERT: D 7 GLU cc_start: 0.8463 (mm-30) cc_final: 0.8042 (mm-30) REVERT: D 87 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7397 (mt-10) REVERT: D 129 LYS cc_start: 0.8523 (pttm) cc_final: 0.8070 (mmmt) REVERT: E 55 ARG cc_start: 0.8373 (mmm160) cc_final: 0.7938 (mmp80) REVERT: F 53 LYS cc_start: 0.8657 (mttp) cc_final: 0.7941 (ttmm) REVERT: F 115 ASN cc_start: 0.8485 (t0) cc_final: 0.8118 (t0) REVERT: F 149 GLN cc_start: 0.9030 (tm-30) cc_final: 0.8648 (tm-30) REVERT: G 127 GLU cc_start: 0.8416 (mm-30) cc_final: 0.8088 (mm-30) REVERT: G 189 MET cc_start: 0.8995 (ttm) cc_final: 0.8752 (ttm) REVERT: H 18 ARG cc_start: 0.8335 (ttm170) cc_final: 0.7859 (mtp85) REVERT: H 98 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7744 (mm-30) REVERT: H 223 ASP cc_start: 0.8732 (t0) cc_final: 0.8437 (t0) REVERT: I 10 ASP cc_start: 0.8152 (t0) cc_final: 0.7551 (t0) REVERT: I 13 ASP cc_start: 0.8503 (m-30) cc_final: 0.7340 (t0) REVERT: I 130 GLU cc_start: 0.8888 (tp30) cc_final: 0.8231 (tp30) REVERT: I 144 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8110 (tm-30) REVERT: I 220 ASP cc_start: 0.8149 (t0) cc_final: 0.7595 (t70) REVERT: I 221 LYS cc_start: 0.8657 (mtmm) cc_final: 0.8382 (mtpp) REVERT: J 26 ASN cc_start: 0.9382 (t0) cc_final: 0.8886 (t0) REVERT: J 64 GLU cc_start: 0.8265 (pm20) cc_final: 0.7723 (pm20) REVERT: J 130 GLU cc_start: 0.8969 (tp30) cc_final: 0.8493 (tp30) REVERT: J 220 ASP cc_start: 0.8404 (t0) cc_final: 0.8112 (t0) REVERT: J 221 LYS cc_start: 0.8794 (mtmt) cc_final: 0.8238 (mtmt) REVERT: K 30 GLU cc_start: 0.9101 (mt-10) cc_final: 0.8663 (mt-10) REVERT: K 31 MET cc_start: 0.8426 (ptm) cc_final: 0.7645 (ppp) REVERT: K 80 LYS cc_start: 0.8708 (ttmm) cc_final: 0.8429 (tmtt) REVERT: K 86 LYS cc_start: 0.9090 (ttpp) cc_final: 0.8840 (tppt) REVERT: L 22 GLN cc_start: 0.7932 (mp10) cc_final: 0.7535 (mp10) REVERT: L 31 MET cc_start: 0.6877 (ptp) cc_final: 0.6610 (ptm) REVERT: L 34 GLU cc_start: 0.7976 (pm20) cc_final: 0.7502 (pm20) outliers start: 37 outliers final: 31 residues processed: 352 average time/residue: 0.1622 time to fit residues: 81.5529 Evaluate side-chains 356 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 325 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain B residue 141 MET Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 66 ILE Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain I residue 17 THR Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain I residue 115 GLN Chi-restraints excluded: chain I residue 189 GLU Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 170 GLU Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain L residue 50 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 192 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 56 optimal weight: 7.9990 chunk 146 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 217 optimal weight: 20.0000 chunk 158 optimal weight: 5.9990 chunk 189 optimal weight: 7.9990 chunk 205 optimal weight: 40.0000 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 110 GLN G 40 HIS ** I 113 HIS ** 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 = 0.3696 r_free = 0.3696 target = 0.117686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.081488 restraints weight = 30405.319| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.80 r_work: 0.2963 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 17702 Z= 0.203 Angle : 0.587 7.257 24108 Z= 0.290 Chirality : 0.041 0.163 2956 Planarity : 0.004 0.036 3075 Dihedral : 5.294 59.718 2597 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.56 % Allowed : 17.38 % Favored : 80.06 % 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: 0.46 (0.20), residues: 2046 helix: 2.08 (0.18), residues: 896 sheet: -1.86 (0.28), residues: 307 loop : -0.76 (0.23), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 89 TYR 0.020 0.001 TYR G 222 PHE 0.024 0.001 PHE C 118 TRP 0.012 0.001 TRP G 195 HIS 0.006 0.001 HIS I 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.20 (17702) covalent geometry : angle 0.58707 / 0.29 (24108) hydrogen bonds : bond 0.04442 / 2.95 ( 1074) hydrogen bonds : angle 4.79780 / 3.36 ( 3168) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 321 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 ASP cc_start: 0.8577 (m-30) cc_final: 0.7979 (m-30) REVERT: B 115 ASN cc_start: 0.7964 (m-40) cc_final: 0.7478 (t0) REVERT: B 118 PHE cc_start: 0.6697 (p90) cc_final: 0.6417 (t80) REVERT: B 132 ASP cc_start: 0.8441 (t0) cc_final: 0.8081 (t0) REVERT: B 138 LYS cc_start: 0.8327 (mppt) cc_final: 0.8089 (mptt) REVERT: C 132 ASP cc_start: 0.8435 (m-30) cc_final: 0.8195 (m-30) REVERT: C 138 LYS cc_start: 0.8766 (mttp) cc_final: 0.8376 (mtpp) REVERT: C 141 MET cc_start: 0.8159 (ptp) cc_final: 0.7933 (ptp) REVERT: D 5 LYS cc_start: 0.7716 (tttm) cc_final: 0.7276 (tptt) REVERT: D 7 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8055 (mm-30) REVERT: D 129 LYS cc_start: 0.8523 (pttm) cc_final: 0.8060 (mptt) REVERT: E 55 ARG cc_start: 0.8445 (mmm160) cc_final: 0.8110 (mmp80) REVERT: F 70 ASP cc_start: 0.8361 (t0) cc_final: 0.8087 (t0) REVERT: F 115 ASN cc_start: 0.8457 (t0) cc_final: 0.8072 (t0) REVERT: F 149 GLN cc_start: 0.9050 (tm-30) cc_final: 0.8678 (tm-30) REVERT: G 127 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8196 (mm-30) REVERT: H 18 ARG cc_start: 0.8384 (ttm170) cc_final: 0.8004 (mtp85) REVERT: H 223 ASP cc_start: 0.8771 (t0) cc_final: 0.8471 (t0) REVERT: I 10 ASP cc_start: 0.8165 (t0) cc_final: 0.7514 (t0) REVERT: I 130 GLU cc_start: 0.8977 (tp30) cc_final: 0.8355 (tp30) REVERT: I 144 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8084 (tm-30) REVERT: I 220 ASP cc_start: 0.8187 (t0) cc_final: 0.7626 (t70) REVERT: I 221 LYS cc_start: 0.8737 (mtmm) cc_final: 0.8458 (mtpp) REVERT: J 64 GLU cc_start: 0.8304 (pm20) cc_final: 0.7773 (pm20) REVERT: J 130 GLU cc_start: 0.9001 (tp30) cc_final: 0.8550 (tp30) REVERT: J 220 ASP cc_start: 0.8436 (t0) cc_final: 0.8132 (t0) REVERT: J 221 LYS cc_start: 0.8802 (mtmt) cc_final: 0.8215 (mtmt) REVERT: J 262 HIS cc_start: 0.7474 (OUTLIER) cc_final: 0.6744 (m-70) REVERT: K 30 GLU cc_start: 0.9102 (mt-10) cc_final: 0.8645 (mt-10) REVERT: K 31 MET cc_start: 0.8473 (ptm) cc_final: 0.7609 (ppp) REVERT: K 80 LYS cc_start: 0.8744 (ttmm) cc_final: 0.8445 (tmtt) REVERT: K 86 LYS cc_start: 0.9100 (ttpp) cc_final: 0.8850 (tppt) REVERT: L 22 GLN cc_start: 0.8070 (mp10) cc_final: 0.7648 (mp10) REVERT: L 33 GLU cc_start: 0.7395 (pm20) cc_final: 0.7060 (pm20) REVERT: L 34 GLU cc_start: 0.7986 (pm20) cc_final: 0.7617 (pm20) outliers start: 43 outliers final: 37 residues processed: 350 average time/residue: 0.1658 time to fit residues: 82.4553 Evaluate side-chains 356 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 318 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain B residue 141 MET Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 66 ILE Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 189 MET Chi-restraints excluded: chain H residue 203 LEU Chi-restraints excluded: chain I residue 17 THR Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain I residue 115 GLN Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 189 GLU Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 170 GLU Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 262 HIS Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain L residue 50 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 222 optimal weight: 40.0000 chunk 0 optimal weight: 7.9990 chunk 126 optimal weight: 0.9980 chunk 120 optimal weight: 4.9990 chunk 212 optimal weight: 30.0000 chunk 159 optimal weight: 0.9990 chunk 214 optimal weight: 20.0000 chunk 21 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 176 optimal weight: 0.9990 chunk 117 optimal weight: 0.5980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 110 GLN G 40 HIS ** I 113 HIS ** 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 = 0.3725 r_free = 0.3725 target = 0.120141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.084306 restraints weight = 29995.323| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.80 r_work: 0.2997 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17702 Z= 0.137 Angle : 0.557 7.035 24108 Z= 0.275 Chirality : 0.040 0.164 2956 Planarity : 0.003 0.035 3075 Dihedral : 5.215 57.998 2597 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.50 % Allowed : 17.56 % Favored : 79.94 % 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: 0.63 (0.20), residues: 2046 helix: 2.22 (0.18), residues: 898 sheet: -1.84 (0.28), residues: 307 loop : -0.64 (0.22), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 89 TYR 0.019 0.001 TYR G 222 PHE 0.022 0.001 PHE C 118 TRP 0.025 0.001 TRP G 195 HIS 0.006 0.001 HIS I 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (17702) covalent geometry : angle 0.55651 / 0.28 (24108) hydrogen bonds : bond 0.04185 / 2.78 ( 1074) hydrogen bonds : angle 4.68551 / 3.28 ( 3168) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 325 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 LYS cc_start: 0.7616 (pttp) cc_final: 0.7136 (tptp) REVERT: A 92 HIS cc_start: 0.8163 (t70) cc_final: 0.7464 (t70) REVERT: A 132 ASP cc_start: 0.8547 (m-30) cc_final: 0.7920 (m-30) REVERT: B 115 ASN cc_start: 0.7897 (m-40) cc_final: 0.7434 (t0) REVERT: B 118 PHE cc_start: 0.6674 (p90) cc_final: 0.6393 (t80) REVERT: B 132 ASP cc_start: 0.8404 (t0) cc_final: 0.8047 (t0) REVERT: B 138 LYS cc_start: 0.8232 (mppt) cc_final: 0.7986 (mptt) REVERT: C 89 ARG cc_start: 0.9105 (ttp-110) cc_final: 0.8469 (mtm-85) REVERT: C 132 ASP cc_start: 0.8380 (m-30) cc_final: 0.7886 (m-30) REVERT: C 138 LYS cc_start: 0.8678 (mttp) cc_final: 0.8283 (mtpp) REVERT: D 7 GLU cc_start: 0.8418 (mm-30) cc_final: 0.8005 (mm-30) REVERT: D 87 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7254 (mt-10) REVERT: D 129 LYS cc_start: 0.8410 (pttm) cc_final: 0.7956 (mmmt) REVERT: E 55 ARG cc_start: 0.8408 (mmm160) cc_final: 0.8048 (mmp80) REVERT: F 89 ARG cc_start: 0.8607 (mtm-85) cc_final: 0.8368 (mtm-85) REVERT: F 115 ASN cc_start: 0.8425 (t0) cc_final: 0.8046 (t0) REVERT: F 149 GLN cc_start: 0.9013 (tm-30) cc_final: 0.8655 (tm-30) REVERT: G 127 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8067 (mm-30) REVERT: H 18 ARG cc_start: 0.8300 (ttm170) cc_final: 0.7830 (mtp85) REVERT: H 223 ASP cc_start: 0.8743 (t0) cc_final: 0.8449 (t0) REVERT: I 10 ASP cc_start: 0.8135 (t0) cc_final: 0.7411 (t0) REVERT: I 130 GLU cc_start: 0.8871 (tp30) cc_final: 0.8242 (tp30) REVERT: I 144 GLU cc_start: 0.8389 (mt-10) cc_final: 0.8024 (tm-30) REVERT: I 220 ASP cc_start: 0.8215 (t0) cc_final: 0.7617 (t0) REVERT: I 221 LYS cc_start: 0.8628 (mtmm) cc_final: 0.8316 (mtpp) REVERT: J 26 ASN cc_start: 0.9334 (t0) cc_final: 0.9071 (t0) REVERT: J 64 GLU cc_start: 0.8207 (pm20) cc_final: 0.7666 (pm20) REVERT: J 130 GLU cc_start: 0.8984 (tp30) cc_final: 0.8521 (tp30) REVERT: J 220 ASP cc_start: 0.8456 (t0) cc_final: 0.8128 (t0) REVERT: J 221 LYS cc_start: 0.8702 (mtmt) cc_final: 0.8142 (mtmt) REVERT: K 30 GLU cc_start: 0.9092 (mt-10) cc_final: 0.8620 (mt-10) REVERT: K 31 MET cc_start: 0.8396 (ptm) cc_final: 0.7550 (ppp) REVERT: K 80 LYS cc_start: 0.8701 (ttmm) cc_final: 0.8318 (mtmm) REVERT: K 86 LYS cc_start: 0.9075 (ttpp) cc_final: 0.8810 (tppt) REVERT: L 22 GLN cc_start: 0.7971 (mp10) cc_final: 0.7583 (mp10) REVERT: L 33 GLU cc_start: 0.7376 (pm20) cc_final: 0.7037 (pm20) outliers start: 42 outliers final: 38 residues processed: 349 average time/residue: 0.1656 time to fit residues: 82.2571 Evaluate side-chains 358 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 320 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain B residue 141 MET Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 197 MET Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 66 ILE Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 189 MET Chi-restraints excluded: chain I residue 17 THR Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain I residue 115 GLN Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 189 GLU Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 170 GLU Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain L residue 50 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 71 optimal weight: 7.9990 chunk 130 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 177 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 232 optimal weight: 10.0000 chunk 225 optimal weight: 30.0000 chunk 140 optimal weight: 6.9990 chunk 139 optimal weight: 4.9990 chunk 84 optimal weight: 8.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 110 GLN G 40 HIS ** I 113 HIS ** 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 = 0.3695 r_free = 0.3695 target = 0.118077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.082047 restraints weight = 29854.681| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.78 r_work: 0.2966 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17702 Z= 0.190 Angle : 0.592 7.006 24108 Z= 0.293 Chirality : 0.041 0.181 2956 Planarity : 0.004 0.035 3075 Dihedral : 5.243 59.416 2597 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.50 % Allowed : 17.80 % Favored : 79.70 % 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: 0.63 (0.20), residues: 2046 helix: 2.21 (0.18), residues: 894 sheet: -1.72 (0.28), residues: 312 loop : -0.65 (0.23), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 89 TYR 0.021 0.001 TYR G 222 PHE 0.024 0.001 PHE C 118 TRP 0.016 0.001 TRP G 195 HIS 0.007 0.001 HIS I 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.19 (17702) covalent geometry : angle 0.59154 / 0.29 (24108) hydrogen bonds : bond 0.04352 / 2.89 ( 1074) hydrogen bonds : angle 4.73168 / 3.31 ( 3168) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 318 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 LYS cc_start: 0.7645 (pttp) cc_final: 0.7146 (tptp) REVERT: A 132 ASP cc_start: 0.8518 (m-30) cc_final: 0.7872 (m-30) REVERT: B 115 ASN cc_start: 0.7893 (m-40) cc_final: 0.7394 (t0) REVERT: B 118 PHE cc_start: 0.6696 (p90) cc_final: 0.6398 (t80) REVERT: B 132 ASP cc_start: 0.8414 (t0) cc_final: 0.8054 (t0) REVERT: B 138 LYS cc_start: 0.8229 (mppt) cc_final: 0.8018 (mptt) REVERT: C 132 ASP cc_start: 0.8377 (m-30) cc_final: 0.7871 (m-30) REVERT: C 138 LYS cc_start: 0.8708 (mttp) cc_final: 0.8307 (mtpp) REVERT: C 141 MET cc_start: 0.8148 (ptp) cc_final: 0.7921 (ptp) REVERT: D 5 LYS cc_start: 0.7621 (tttm) cc_final: 0.7184 (tptt) REVERT: D 7 GLU cc_start: 0.8412 (mm-30) cc_final: 0.8002 (mm-30) REVERT: D 87 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7305 (mt-10) REVERT: D 129 LYS cc_start: 0.8420 (pttm) cc_final: 0.7992 (mmmt) REVERT: E 55 ARG cc_start: 0.8441 (mmm160) cc_final: 0.8079 (mmp80) REVERT: F 70 ASP cc_start: 0.8367 (t0) cc_final: 0.8122 (t0) REVERT: F 89 ARG cc_start: 0.8527 (mtm-85) cc_final: 0.8238 (mtm-85) REVERT: F 115 ASN cc_start: 0.8398 (t0) cc_final: 0.8002 (t0) REVERT: F 149 GLN cc_start: 0.9041 (tm-30) cc_final: 0.8679 (tm-30) REVERT: G 127 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8164 (mm-30) REVERT: H 18 ARG cc_start: 0.8324 (ttm170) cc_final: 0.7944 (mtp85) REVERT: H 223 ASP cc_start: 0.8737 (t0) cc_final: 0.8442 (t0) REVERT: I 10 ASP cc_start: 0.8127 (t0) cc_final: 0.7360 (t0) REVERT: I 130 GLU cc_start: 0.8943 (tp30) cc_final: 0.8317 (tp30) REVERT: I 144 GLU cc_start: 0.8410 (mt-10) cc_final: 0.8009 (tm-30) REVERT: I 220 ASP cc_start: 0.8259 (t0) cc_final: 0.7603 (t0) REVERT: I 221 LYS cc_start: 0.8708 (mtmm) cc_final: 0.8414 (mtpp) REVERT: J 26 ASN cc_start: 0.9321 (t0) cc_final: 0.9043 (t0) REVERT: J 64 GLU cc_start: 0.8240 (pm20) cc_final: 0.7674 (pm20) REVERT: J 130 GLU cc_start: 0.8994 (tp30) cc_final: 0.8526 (tp30) REVERT: J 220 ASP cc_start: 0.8479 (t0) cc_final: 0.8160 (t0) REVERT: J 221 LYS cc_start: 0.8714 (mtmt) cc_final: 0.8121 (mtmt) REVERT: K 30 GLU cc_start: 0.9105 (mt-10) cc_final: 0.8625 (mt-10) REVERT: K 31 MET cc_start: 0.8437 (ptm) cc_final: 0.7554 (ppp) REVERT: K 80 LYS cc_start: 0.8727 (ttmm) cc_final: 0.8331 (mtmm) REVERT: K 86 LYS cc_start: 0.9093 (ttpp) cc_final: 0.8823 (tppt) REVERT: L 22 GLN cc_start: 0.8006 (mp10) cc_final: 0.7601 (mp10) outliers start: 42 outliers final: 42 residues processed: 344 average time/residue: 0.1696 time to fit residues: 82.2070 Evaluate side-chains 356 residues out of total 1719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 314 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain B residue 141 MET Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain G residue 40 HIS Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 194 ASP Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 66 ILE Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 189 MET Chi-restraints excluded: chain I residue 17 THR Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain I residue 115 GLN Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 167 MET Chi-restraints excluded: chain I residue 189 GLU Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 170 GLU Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain L residue 50 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 69 optimal weight: 20.0000 chunk 199 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 224 optimal weight: 20.0000 chunk 213 optimal weight: 30.0000 chunk 222 optimal weight: 40.0000 chunk 139 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 chunk 203 optimal weight: 50.0000 chunk 11 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 110 GLN G 40 HIS ** I 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 191 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.115377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.079238 restraints weight = 30723.762| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.79 r_work: 0.2919 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 17702 Z= 0.300 Angle : 0.670 6.835 24108 Z= 0.332 Chirality : 0.044 0.188 2956 Planarity : 0.004 0.038 3075 Dihedral : 5.435 58.513 2597 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.74 % Allowed : 17.80 % Favored : 79.46 % 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: 0.33 (0.19), residues: 2046 helix: 1.87 (0.17), residues: 894 sheet: -1.89 (0.27), residues: 325 loop : -0.66 (0.23), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 77 TYR 0.026 0.002 TYR G 222 PHE 0.027 0.002 PHE C 118 TRP 0.016 0.001 TRP G 195 HIS 0.018 0.001 HIS G 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00712 / 0.30 (17702) covalent geometry : angle 0.67039 / 0.33 (24108) hydrogen bonds : bond 0.04677 / 3.10 ( 1074) hydrogen bonds : angle 4.89190 / 3.43 ( 3168) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4430.45 seconds wall clock time: 76 minutes 30.82 seconds (4590.82 seconds total)