Starting phenix.real_space_refine on Wed Feb 4 22:42:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l1q_62752/02_2026/9l1q_62752.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l1q_62752/02_2026/9l1q_62752.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9l1q_62752/02_2026/9l1q_62752.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l1q_62752/02_2026/9l1q_62752.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9l1q_62752/02_2026/9l1q_62752.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l1q_62752/02_2026/9l1q_62752.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 8413 2.51 5 N 2274 2.21 5 O 2605 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13358 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1704 Classifications: {'peptide': 217} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 204} Chain: "B" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1704 Classifications: {'peptide': 217} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 204} Chain: "E" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1624 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 203} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "F" Number of atoms: 1598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1598 Classifications: {'peptide': 212} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 201} Chain: "H" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1710 Classifications: {'peptide': 225} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 211} Chain: "L" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1654 Classifications: {'peptide': 214} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 202} Chain: "h" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1710 Classifications: {'peptide': 225} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 211} Chain: "l" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1654 Classifications: {'peptide': 214} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 202} Time building chain proxies: 2.85, per 1000 atoms: 0.21 Number of scatterers: 13358 At special positions: 0 Unit cell: (221.748, 151.093, 106.526, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 2605 8.00 N 2274 7.00 C 8413 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 51 " - pdb=" SG CYS A 125 " distance=2.12 Simple disulfide: pdb=" SG CYS A 165 " - pdb=" SG CYS A 219 " distance=2.11 Simple disulfide: pdb=" SG CYS B 51 " - pdb=" SG CYS B 125 " distance=1.94 Simple disulfide: pdb=" SG CYS B 165 " - pdb=" SG CYS B 219 " distance=2.14 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 126 " distance=2.07 Simple disulfide: pdb=" SG CYS E 166 " - pdb=" SG CYS E 220 " distance=2.09 Simple disulfide: pdb=" SG CYS F 52 " - pdb=" SG CYS F 126 " distance=2.11 Simple disulfide: pdb=" SG CYS F 166 " - pdb=" SG CYS F 220 " distance=2.18 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.07 Simple disulfide: pdb=" SG CYS H 149 " - pdb=" SG CYS H 205 " distance=2.01 Simple disulfide: pdb=" SG CYS H 225 " - pdb=" SG CYS L 214 " distance=2.09 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.19 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.07 Simple disulfide: pdb=" SG CYS h 22 " - pdb=" SG CYS h 96 " distance=2.00 Simple disulfide: pdb=" SG CYS h 149 " - pdb=" SG CYS h 205 " distance=2.96 Simple disulfide: pdb=" SG CYS h 225 " - pdb=" SG CYS l 214 " distance=2.46 Simple disulfide: pdb=" SG CYS l 23 " - pdb=" SG CYS l 88 " distance=2.20 Simple disulfide: pdb=" SG CYS l 134 " - pdb=" SG CYS l 194 " distance=2.00 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: 1.10 Conformation dependent library (CDL) restraints added in 592.5 milliseconds 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3192 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 38 sheets defined 4.0% alpha, 36.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'B' and resid 85 through 88 removed outlier: 3.947A pdb=" N GLN B 88 " --> pdb=" O THR B 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 85 through 88' Processing helix chain 'B' and resid 197 through 199 No H-bonds generated for 'chain 'B' and resid 197 through 199' Processing helix chain 'E' and resid 117 through 121 removed outlier: 3.515A pdb=" N SER E 121 " --> pdb=" O ALA E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 242 removed outlier: 3.990A pdb=" N PHE E 241 " --> pdb=" O ALA E 238 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE E 242 " --> pdb=" O ASP E 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 238 through 242' Processing helix chain 'F' and resid 90 through 94 removed outlier: 3.557A pdb=" N ARG F 94 " --> pdb=" O ALA F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 121 Processing helix chain 'F' and resid 239 through 242 removed outlier: 3.912A pdb=" N PHE F 242 " --> pdb=" O ASP F 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 239 through 242' Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.934A pdb=" N ARG H 31 " --> pdb=" O ILE H 28 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 137 through 142 removed outlier: 4.113A pdb=" N SER H 141 " --> pdb=" O SER H 137 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 127 removed outlier: 3.727A pdb=" N LEU L 125 " --> pdb=" O ASP L 122 " (cutoff:3.500A) Processing helix chain 'h' and resid 61 through 65 Processing helix chain 'h' and resid 87 through 91 removed outlier: 3.928A pdb=" N THR h 91 " --> pdb=" O SER h 88 " (cutoff:3.500A) Processing helix chain 'h' and resid 136 through 141 removed outlier: 4.205A pdb=" N THR h 140 " --> pdb=" O SER h 136 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N SER h 141 " --> pdb=" O SER h 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 136 through 141' Processing helix chain 'l' and resid 183 through 188 removed outlier: 3.848A pdb=" N LYS l 188 " --> pdb=" O ALA l 184 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 48 removed outlier: 3.597A pdb=" N THR A 47 " --> pdb=" O ILE A 112 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 52 removed outlier: 4.045A pdb=" N VAL A 108 " --> pdb=" O CYS A 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 74 through 78 removed outlier: 6.699A pdb=" N TRP A 66 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N VAL A 77 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL A 64 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR A 126 " --> pdb=" O ARG A 65 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 156 through 157 Processing sheet with id=AA5, first strand: chain 'A' and resid 165 through 170 removed outlier: 3.599A pdb=" N VAL A 203 " --> pdb=" O SER A 167 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY A 169 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N PHE A 201 " --> pdb=" O GLY A 169 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 175 through 179 Processing sheet with id=AA7, first strand: chain 'B' and resid 32 through 33 removed outlier: 3.741A pdb=" N HIS B 52 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE B 112 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 39 through 41 Processing sheet with id=AA9, first strand: chain 'B' and resid 82 through 83 removed outlier: 3.863A pdb=" N LYS B 79 " --> pdb=" O ARG B 82 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TRP B 66 " --> pdb=" O PHE B 76 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 150 through 151 removed outlier: 3.530A pdb=" N LEU B 150 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ILE B 166 " --> pdb=" O THR B 205 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N THR B 205 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ARG B 168 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N VAL B 203 " --> pdb=" O ARG B 168 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TRP B 170 " --> pdb=" O PHE B 201 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 175 through 179 Processing sheet with id=AB3, first strand: chain 'E' and resid 33 through 34 removed outlier: 3.639A pdb=" N ALA E 48 " --> pdb=" O ILE E 113 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 40 through 43 removed outlier: 6.298A pdb=" N ILE E 40 " --> pdb=" O LYS E 142 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ALA E 144 " --> pdb=" O ILE E 40 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA E 42 " --> pdb=" O ALA E 144 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N SER E 69 " --> pdb=" O VAL E 75 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL E 75 " --> pdb=" O SER E 69 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 190 through 191 removed outlier: 3.866A pdb=" N VAL E 195 " --> pdb=" O GLU E 203 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 190 through 191 removed outlier: 5.364A pdb=" N TYR E 202 " --> pdb=" O GLY E 170 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N LEU F 229 " --> pdb=" O SER F 224 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N SER F 224 " --> pdb=" O LEU F 229 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 176 through 180 removed outlier: 3.733A pdb=" N LYS E 231 " --> pdb=" O ILE E 222 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N VAL F 152 " --> pdb=" O THR E 232 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N SER E 234 " --> pdb=" O VAL F 152 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N VAL F 154 " --> pdb=" O SER E 234 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N SER E 236 " --> pdb=" O VAL F 154 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N TYR F 202 " --> pdb=" O GLY F 170 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA F 203 " --> pdb=" O VAL F 195 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL F 195 " --> pdb=" O ALA F 203 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 40 through 41 removed outlier: 6.757A pdb=" N ILE F 40 " --> pdb=" O LYS F 142 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE F 128 " --> pdb=" O GLU F 135 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA F 137 " --> pdb=" O CYS F 126 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N CYS F 126 " --> pdb=" O ALA F 137 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL F 139 " --> pdb=" O TYR F 124 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 100 through 103 removed outlier: 3.660A pdb=" N ASP F 102 " --> pdb=" O LYS F 108 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N LYS F 108 " --> pdb=" O ASP F 102 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.521A pdb=" N VAL H 18 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.547A pdb=" N GLU H 10 " --> pdb=" O THR H 119 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LYS H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N TRP H 47 " --> pdb=" O LYS H 38 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.547A pdb=" N GLU H 10 " --> pdb=" O THR H 119 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N CYS H 96 " --> pdb=" O TRP H 112 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N TRP H 112 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ARG H 98 " --> pdb=" O ASP H 110 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 129 through 132 removed outlier: 5.479A pdb=" N TYR H 185 " --> pdb=" O ASP H 153 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 129 through 132 removed outlier: 5.479A pdb=" N TYR H 185 " --> pdb=" O ASP H 153 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU H 184 " --> pdb=" O GLN H 180 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 159 through 163 removed outlier: 3.627A pdb=" N THR H 160 " --> pdb=" O ASN H 208 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.641A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 4 through 7 removed outlier: 6.760A pdb=" N THR L 69 " --> pdb=" O ALA L 25 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 10 through 12 removed outlier: 7.300A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 129 through 139 removed outlier: 3.624A pdb=" N LEU L 181 " --> pdb=" O ALA L 130 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU L 175 " --> pdb=" O LEU L 136 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN L 138 " --> pdb=" O TYR L 173 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER L 174 " --> pdb=" O THR L 164 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 144 through 150 removed outlier: 4.159A pdb=" N LYS L 145 " --> pdb=" O THR L 197 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS L 149 " --> pdb=" O ALA L 193 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR L 192 " --> pdb=" O PHE L 209 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS L 207 " --> pdb=" O CYS L 194 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL L 196 " --> pdb=" O VAL L 205 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'h' and resid 18 through 23 removed outlier: 4.179A pdb=" N THR h 78 " --> pdb=" O ASP h 73 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP h 73 " --> pdb=" O THR h 78 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'h' and resid 49 through 51 removed outlier: 3.592A pdb=" N ARG h 98 " --> pdb=" O TYR h 111 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TYR h 111 " --> pdb=" O ARG h 98 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'h' and resid 49 through 51 Processing sheet with id=AD6, first strand: chain 'h' and resid 129 through 132 removed outlier: 3.692A pdb=" N LEU h 150 " --> pdb=" O PHE h 131 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASP h 153 " --> pdb=" O TYR h 185 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N TYR h 185 " --> pdb=" O ASP h 153 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'h' and resid 160 through 163 removed outlier: 3.816A pdb=" N CYS h 205 " --> pdb=" O LYS h 218 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR h 214 " --> pdb=" O HIS h 209 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'l' and resid 4 through 7 removed outlier: 11.676A pdb=" N CYS l 23 " --> pdb=" O THR l 74 " (cutoff:3.500A) removed outlier: 10.855A pdb=" N THR l 74 " --> pdb=" O CYS l 23 " (cutoff:3.500A) removed outlier: 12.252A pdb=" N ALA l 25 " --> pdb=" O THR l 72 " (cutoff:3.500A) removed outlier: 11.983A pdb=" N THR l 72 " --> pdb=" O ALA l 25 " (cutoff:3.500A) removed outlier: 11.088A pdb=" N GLN l 27 " --> pdb=" O ASP l 70 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ASP l 70 " --> pdb=" O GLN l 27 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'l' and resid 10 through 11 removed outlier: 6.854A pdb=" N LEU l 33 " --> pdb=" O TYR l 49 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N TYR l 49 " --> pdb=" O LEU l 33 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N TRP l 35 " --> pdb=" O LEU l 47 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'l' and resid 116 through 118 removed outlier: 3.752A pdb=" N PHE l 118 " --> pdb=" O VAL l 133 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL l 133 " --> pdb=" O PHE l 118 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR l 178 " --> pdb=" O GLN l 160 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'l' and resid 145 through 150 removed outlier: 3.725A pdb=" N CYS l 194 " --> pdb=" O LYS l 207 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS l 207 " --> pdb=" O CYS l 194 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL l 196 " --> pdb=" O VAL l 205 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL l 205 " --> pdb=" O VAL l 196 " (cutoff:3.500A) 393 hydrogen bonds defined for protein. 957 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: 1.98 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.31: 2700 1.31 - 1.48: 5324 1.48 - 1.65: 5532 1.65 - 1.82: 54 1.82 - 1.99: 45 Bond restraints: 13655 Sorted by residual: bond pdb=" CA THR H 105 " pdb=" C THR H 105 " ideal model delta sigma weight residual 1.519 1.622 -0.103 9.50e-03 1.11e+04 1.17e+02 bond pdb=" C PHE F 55 " pdb=" O PHE F 55 " ideal model delta sigma weight residual 1.246 1.155 0.091 9.20e-03 1.18e+04 9.87e+01 bond pdb=" CA PRO F 240 " pdb=" C PRO F 240 " ideal model delta sigma weight residual 1.520 1.612 -0.091 9.50e-03 1.11e+04 9.24e+01 bond pdb=" CA CYS E 52 " pdb=" C CYS E 52 " ideal model delta sigma weight residual 1.521 1.636 -0.115 1.20e-02 6.94e+03 9.22e+01 bond pdb=" SD MET E 63 " pdb=" CE MET E 63 " ideal model delta sigma weight residual 1.791 1.553 0.238 2.50e-02 1.60e+03 9.08e+01 ... (remaining 13650 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.97: 14045 2.97 - 5.94: 3330 5.94 - 8.91: 954 8.91 - 11.88: 181 11.88 - 14.84: 18 Bond angle restraints: 18528 Sorted by residual: angle pdb=" N ILE B 236 " pdb=" CA ILE B 236 " pdb=" C ILE B 236 " ideal model delta sigma weight residual 107.56 122.40 -14.84 9.10e-01 1.21e+00 2.66e+02 angle pdb=" N LYS L 50 " pdb=" CA LYS L 50 " pdb=" C LYS L 50 " ideal model delta sigma weight residual 113.23 99.07 14.16 1.22e+00 6.72e-01 1.35e+02 angle pdb=" OD1 ASN E 181 " pdb=" CG ASN E 181 " pdb=" ND2 ASN E 181 " ideal model delta sigma weight residual 122.60 112.06 10.54 1.00e+00 1.00e+00 1.11e+02 angle pdb=" N SER H 137 " pdb=" CA SER H 137 " pdb=" C SER H 137 " ideal model delta sigma weight residual 113.97 100.92 13.05 1.28e+00 6.10e-01 1.04e+02 angle pdb=" OE1 GLN E 176 " pdb=" CD GLN E 176 " pdb=" NE2 GLN E 176 " ideal model delta sigma weight residual 122.60 112.65 9.95 1.00e+00 1.00e+00 9.89e+01 ... (remaining 18523 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 7495 17.97 - 35.93: 638 35.93 - 53.90: 67 53.90 - 71.87: 20 71.87 - 89.83: 13 Dihedral angle restraints: 8233 sinusoidal: 3236 harmonic: 4997 Sorted by residual: dihedral pdb=" CA ARG B 65 " pdb=" C ARG B 65 " pdb=" N TRP B 66 " pdb=" CA TRP B 66 " ideal model delta harmonic sigma weight residual 180.00 135.71 44.29 0 5.00e+00 4.00e-02 7.85e+01 dihedral pdb=" CA SER A 69 " pdb=" C SER A 69 " pdb=" N GLN A 70 " pdb=" CA GLN A 70 " ideal model delta harmonic sigma weight residual -180.00 -138.54 -41.46 0 5.00e+00 4.00e-02 6.88e+01 dihedral pdb=" CA PRO B 195 " pdb=" C PRO B 195 " pdb=" N ASP B 196 " pdb=" CA ASP B 196 " ideal model delta harmonic sigma weight residual 180.00 140.80 39.20 0 5.00e+00 4.00e-02 6.15e+01 ... (remaining 8230 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.199: 1447 0.199 - 0.397: 525 0.397 - 0.596: 65 0.596 - 0.794: 18 0.794 - 0.993: 6 Chirality restraints: 2061 Sorted by residual: chirality pdb=" CG LEU F 72 " pdb=" CB LEU F 72 " pdb=" CD1 LEU F 72 " pdb=" CD2 LEU F 72 " both_signs ideal model delta sigma weight residual False -2.59 -1.60 -0.99 2.00e-01 2.50e+01 2.46e+01 chirality pdb=" CB ILE l 117 " pdb=" CA ILE l 117 " pdb=" CG1 ILE l 117 " pdb=" CG2 ILE l 117 " both_signs ideal model delta sigma weight residual False 2.64 1.66 0.98 2.00e-01 2.50e+01 2.41e+01 chirality pdb=" CB THR F 57 " pdb=" CA THR F 57 " pdb=" OG1 THR F 57 " pdb=" CG2 THR F 57 " both_signs ideal model delta sigma weight residual False 2.55 1.59 0.96 2.00e-01 2.50e+01 2.30e+01 ... (remaining 2058 not shown) Planarity restraints: 2389 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 79 " 0.124 2.00e-02 2.50e+03 9.82e-02 1.93e+02 pdb=" CG TYR F 79 " 0.079 2.00e-02 2.50e+03 pdb=" CD1 TYR F 79 " -0.131 2.00e-02 2.50e+03 pdb=" CD2 TYR F 79 " -0.128 2.00e-02 2.50e+03 pdb=" CE1 TYR F 79 " -0.047 2.00e-02 2.50e+03 pdb=" CE2 TYR F 79 " -0.068 2.00e-02 2.50e+03 pdb=" CZ TYR F 79 " 0.076 2.00e-02 2.50e+03 pdb=" OH TYR F 79 " 0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR h 33 " -0.133 2.00e-02 2.50e+03 9.57e-02 1.83e+02 pdb=" CG TYR h 33 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR h 33 " 0.127 2.00e-02 2.50e+03 pdb=" CD2 TYR h 33 " 0.142 2.00e-02 2.50e+03 pdb=" CE1 TYR h 33 " 0.034 2.00e-02 2.50e+03 pdb=" CE2 TYR h 33 " 0.042 2.00e-02 2.50e+03 pdb=" CZ TYR h 33 " -0.090 2.00e-02 2.50e+03 pdb=" OH TYR h 33 " -0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP L 35 " -0.065 2.00e-02 2.50e+03 7.89e-02 1.56e+02 pdb=" CG TRP L 35 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP L 35 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP L 35 " 0.165 2.00e-02 2.50e+03 pdb=" NE1 TRP L 35 " -0.035 2.00e-02 2.50e+03 pdb=" CE2 TRP L 35 " 0.066 2.00e-02 2.50e+03 pdb=" CE3 TRP L 35 " 0.095 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 35 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 35 " -0.092 2.00e-02 2.50e+03 pdb=" CH2 TRP L 35 " -0.068 2.00e-02 2.50e+03 ... (remaining 2386 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2716 2.79 - 3.31: 12309 3.31 - 3.84: 20240 3.84 - 4.37: 23838 4.37 - 4.90: 41224 Nonbonded interactions: 100327 Sorted by model distance: nonbonded pdb=" N ARG A 68 " pdb=" O ARG A 68 " model vdw 2.257 2.496 nonbonded pdb=" N ARG h 40 " pdb=" O ARG h 40 " model vdw 2.368 2.496 nonbonded pdb=" N ARG H 40 " pdb=" O ARG H 40 " model vdw 2.400 2.496 nonbonded pdb=" N ALA H 134 " pdb=" O ALA H 134 " model vdw 2.417 2.496 nonbonded pdb=" N ILE F 237 " pdb=" O ILE F 237 " model vdw 2.425 2.496 ... (remaining 100322 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = (chain 'E' and (resid 32 through 148 or resid 150 through 152 or resid 154 throu \ gh 157 or resid 159 through 181 or resid 183 through 188 or resid 190 through 20 \ 2 or resid 204 through 212 or resid 214 through 220 or resid 222 through 223 or \ resid 225 through 243)) selection = (chain 'F' and (resid 32 through 148 or resid 150 through 152 or resid 154 throu \ gh 157 or resid 159 through 181 or resid 183 through 188 or resid 190 through 20 \ 2 or resid 204 through 212 or resid 214 through 220 or resid 222 through 223 or \ resid 225 through 243)) } ncs_group { reference = chain 'H' selection = chain 'h' } ncs_group { reference = chain 'L' selection = chain 'l' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.280 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: 0.290 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.220 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5921 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 : 0.040 0.925 13673 Z= 2.462 Angle : 2.881 26.964 18564 Z= 1.874 Chirality : 0.201 0.993 2061 Planarity : 0.024 0.138 2389 Dihedral : 13.582 89.833 4987 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Rotamer: Outliers : 0.13 % Allowed : 0.54 % Favored : 99.33 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 7.61 % Cis-general : 0.00 % Twisted Proline : 10.87 % Twisted General : 2.32 % 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: -2.23 (0.19), residues: 1723 helix: -4.57 (0.29), residues: 12 sheet: -0.82 (0.20), residues: 708 loop : -1.99 (0.18), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.073 0.009 ARG B 105 TYR 0.142 0.029 TYR h 33 PHE 0.117 0.028 PHE B 240 TRP 0.165 0.033 TRP L 35 HIS 0.086 0.018 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.03898 (13655) covalent geometry : angle 2.86424 (18528) SS BOND : bond 0.25503 ( 18) SS BOND : angle 7.53576 ( 36) hydrogen bonds : bond 0.27046 ( 360) hydrogen bonds : angle 10.74858 ( 957) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 236 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 MET cc_start: 0.3287 (ttm) cc_final: 0.2574 (ttm) REVERT: H 43 GLN cc_start: 0.8503 (mp10) cc_final: 0.8276 (mp10) REVERT: H 154 TYR cc_start: 0.6371 (p90) cc_final: 0.5908 (p90) REVERT: L 36 TYR cc_start: 0.8442 (m-10) cc_final: 0.8236 (m-10) REVERT: L 49 TYR cc_start: 0.8679 (p90) cc_final: 0.8476 (p90) REVERT: L 92 GLN cc_start: 0.8307 (tt0) cc_final: 0.8087 (tt0) REVERT: L 195 GLU cc_start: 0.4443 (mm-30) cc_final: 0.4168 (mm-30) outliers start: 2 outliers final: 1 residues processed: 238 average time/residue: 0.0957 time to fit residues: 33.9135 Evaluate side-chains 177 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 176 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 163 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 HIS E 89 GLN E 178 GLN F 53 HIS F 151 HIS ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 3 GLN h 6 GLN l 6 GLN ** l 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 37 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.225133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.216821 restraints weight = 23579.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.215552 restraints weight = 37893.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.215105 restraints weight = 40250.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.214422 restraints weight = 40098.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.213985 restraints weight = 39464.904| |-----------------------------------------------------------------------------| r_work (final): 0.4486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5856 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13673 Z= 0.156 Angle : 0.741 7.673 18564 Z= 0.385 Chirality : 0.048 0.172 2061 Planarity : 0.007 0.087 2389 Dihedral : 6.649 42.800 1881 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.64 % Favored : 95.30 % Rotamer: Outliers : 1.68 % Allowed : 4.72 % Favored : 93.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.48 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.20), residues: 1723 helix: -3.50 (1.70), residues: 6 sheet: -0.60 (0.19), residues: 732 loop : -1.64 (0.19), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 85 TYR 0.022 0.002 TYR F 202 PHE 0.020 0.002 PHE l 116 TRP 0.026 0.002 TRP h 47 HIS 0.004 0.001 HIS H 209 Details of bonding type rmsd covalent geometry : bond 0.00349 (13655) covalent geometry : angle 0.73937 (18528) SS BOND : bond 0.00453 ( 18) SS BOND : angle 1.38419 ( 36) hydrogen bonds : bond 0.04254 ( 360) hydrogen bonds : angle 7.57691 ( 957) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 216 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 241 MET cc_start: 0.3478 (tpt) cc_final: 0.3204 (tpp) REVERT: E 136 LYS cc_start: 0.8709 (pttt) cc_final: 0.8048 (ptpp) REVERT: F 210 MET cc_start: 0.3670 (ttp) cc_final: 0.3441 (ttm) REVERT: L 36 TYR cc_start: 0.8608 (m-10) cc_final: 0.7954 (m-10) REVERT: L 49 TYR cc_start: 0.8685 (p90) cc_final: 0.8426 (p90) REVERT: L 50 LYS cc_start: 0.7851 (ttpt) cc_final: 0.7352 (tttt) REVERT: L 149 LYS cc_start: 0.5348 (ptpt) cc_final: 0.5026 (mttp) outliers start: 25 outliers final: 17 residues processed: 224 average time/residue: 0.1032 time to fit residues: 33.9870 Evaluate side-chains 192 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 175 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 156 HIS Chi-restraints excluded: chain E residue 163 HIS Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 83 LYS Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain l residue 11 LEU Chi-restraints excluded: chain l residue 26 SER Chi-restraints excluded: chain l residue 74 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 139 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 154 optimal weight: 2.9990 chunk 136 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 6 optimal weight: 0.2980 chunk 126 optimal weight: 0.0870 chunk 122 optimal weight: 4.9990 overall best weight: 1.4762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS L 28 ASN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 173 HIS ** l 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 198 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.218703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.209962 restraints weight = 23556.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.208139 restraints weight = 37720.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.207800 restraints weight = 41281.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.207698 restraints weight = 30675.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.207143 restraints weight = 32139.481| |-----------------------------------------------------------------------------| r_work (final): 0.4416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6048 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13673 Z= 0.190 Angle : 0.727 9.109 18564 Z= 0.377 Chirality : 0.047 0.167 2061 Planarity : 0.006 0.057 2389 Dihedral : 6.154 47.141 1881 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 2.90 % Allowed : 7.75 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.48 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.81 (0.20), residues: 1723 helix: -4.19 (0.82), residues: 6 sheet: -0.64 (0.19), residues: 749 loop : -1.65 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 112 TYR 0.020 0.002 TYR A 126 PHE 0.020 0.002 PHE F 241 TRP 0.026 0.002 TRP l 35 HIS 0.005 0.001 HIS E 151 Details of bonding type rmsd covalent geometry : bond 0.00425 (13655) covalent geometry : angle 0.72550 (18528) SS BOND : bond 0.00595 ( 18) SS BOND : angle 1.39330 ( 36) hydrogen bonds : bond 0.04025 ( 360) hydrogen bonds : angle 7.28391 ( 957) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 208 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 36 TYR cc_start: 0.8764 (m-10) cc_final: 0.8345 (m-80) REVERT: L 48 ILE cc_start: 0.8773 (mm) cc_final: 0.8512 (mt) REVERT: L 50 LYS cc_start: 0.7934 (ttpt) cc_final: 0.7422 (tttt) REVERT: L 149 LYS cc_start: 0.5862 (ptpt) cc_final: 0.5458 (mttp) outliers start: 43 outliers final: 34 residues processed: 226 average time/residue: 0.1134 time to fit residues: 36.2594 Evaluate side-chains 214 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 180 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 156 HIS Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 163 HIS Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 53 HIS Chi-restraints excluded: chain F residue 83 LYS Chi-restraints excluded: chain F residue 88 ARG Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 97 SER Chi-restraints excluded: chain H residue 99 GLU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain h residue 46 GLU Chi-restraints excluded: chain l residue 2 ILE Chi-restraints excluded: chain l residue 26 SER Chi-restraints excluded: chain l residue 48 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 27 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 116 optimal weight: 0.2980 chunk 80 optimal weight: 7.9990 chunk 31 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 121 optimal weight: 6.9990 chunk 138 optimal weight: 4.9990 chunk 141 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 174 GLN L 28 ASN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 27 GLN ** 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 = 0.4525 r_free = 0.4525 target = 0.218269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.210080 restraints weight = 23081.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.208202 restraints weight = 36453.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.207335 restraints weight = 41371.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.206924 restraints weight = 41432.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.206597 restraints weight = 34995.923| |-----------------------------------------------------------------------------| r_work (final): 0.4403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6055 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13673 Z= 0.157 Angle : 0.676 8.603 18564 Z= 0.348 Chirality : 0.046 0.150 2061 Planarity : 0.006 0.092 2389 Dihedral : 5.764 47.457 1881 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 3.37 % Allowed : 10.51 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.48 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.78 (0.20), residues: 1723 helix: -3.55 (1.31), residues: 6 sheet: -0.66 (0.19), residues: 757 loop : -1.60 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 112 TYR 0.012 0.001 TYR A 126 PHE 0.019 0.002 PHE L 139 TRP 0.030 0.002 TRP A 66 HIS 0.004 0.001 HIS E 151 Details of bonding type rmsd covalent geometry : bond 0.00350 (13655) covalent geometry : angle 0.67472 (18528) SS BOND : bond 0.00462 ( 18) SS BOND : angle 1.05073 ( 36) hydrogen bonds : bond 0.03641 ( 360) hydrogen bonds : angle 6.83433 ( 957) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 194 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 TYR cc_start: 0.4670 (OUTLIER) cc_final: 0.4339 (t80) REVERT: A 176 THR cc_start: 0.6664 (t) cc_final: 0.6322 (m) REVERT: H 85 ARG cc_start: 0.5988 (OUTLIER) cc_final: 0.5464 (ttp80) REVERT: L 36 TYR cc_start: 0.8739 (m-10) cc_final: 0.8217 (m-10) REVERT: L 48 ILE cc_start: 0.8759 (mm) cc_final: 0.8550 (mt) REVERT: L 149 LYS cc_start: 0.5855 (OUTLIER) cc_final: 0.5551 (mttp) REVERT: L 198 HIS cc_start: 0.3236 (t70) cc_final: 0.2872 (p90) outliers start: 50 outliers final: 35 residues processed: 218 average time/residue: 0.1002 time to fit residues: 31.5454 Evaluate side-chains 219 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 181 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 123 TYR Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 156 HIS Chi-restraints excluded: chain E residue 163 HIS Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 53 HIS Chi-restraints excluded: chain F residue 88 ARG Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 85 ARG Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 97 SER Chi-restraints excluded: chain H residue 99 GLU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 149 LYS Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain h residue 46 GLU Chi-restraints excluded: chain h residue 83 LEU Chi-restraints excluded: chain h residue 174 THR Chi-restraints excluded: chain l residue 2 ILE Chi-restraints excluded: chain l residue 26 SER Chi-restraints excluded: chain l residue 48 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 132 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 12 optimal weight: 0.4980 chunk 166 optimal weight: 10.0000 chunk 63 optimal weight: 0.1980 chunk 13 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 81 optimal weight: 0.0570 chunk 58 optimal weight: 0.3980 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 28 ASN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 173 HIS ** l 27 GLN ** 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 = 0.4554 r_free = 0.4554 target = 0.221162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.213265 restraints weight = 23245.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.211527 restraints weight = 35964.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.210751 restraints weight = 41088.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.210184 restraints weight = 38495.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.209702 restraints weight = 37141.512| |-----------------------------------------------------------------------------| r_work (final): 0.4435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5975 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13673 Z= 0.116 Angle : 0.631 7.395 18564 Z= 0.322 Chirality : 0.045 0.156 2061 Planarity : 0.005 0.067 2389 Dihedral : 5.374 45.885 1881 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.03 % Allowed : 12.47 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.48 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.66 (0.20), residues: 1723 helix: -3.18 (1.64), residues: 6 sheet: -0.58 (0.19), residues: 746 loop : -1.53 (0.20), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 112 TYR 0.017 0.001 TYR l 140 PHE 0.016 0.001 PHE l 71 TRP 0.020 0.002 TRP h 47 HIS 0.004 0.001 HIS L 24 Details of bonding type rmsd covalent geometry : bond 0.00260 (13655) covalent geometry : angle 0.63019 (18528) SS BOND : bond 0.00376 ( 18) SS BOND : angle 0.82106 ( 36) hydrogen bonds : bond 0.03166 ( 360) hydrogen bonds : angle 6.37920 ( 957) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 184 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 THR cc_start: 0.6799 (t) cc_final: 0.6525 (m) REVERT: L 36 TYR cc_start: 0.8598 (m-10) cc_final: 0.8153 (m-10) REVERT: L 48 ILE cc_start: 0.8764 (mm) cc_final: 0.8564 (mt) REVERT: L 149 LYS cc_start: 0.5624 (OUTLIER) cc_final: 0.5304 (mttp) REVERT: L 198 HIS cc_start: 0.3205 (t70) cc_final: 0.2831 (p90) outliers start: 45 outliers final: 33 residues processed: 204 average time/residue: 0.1027 time to fit residues: 31.0165 Evaluate side-chains 209 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 175 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 156 HIS Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 163 HIS Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 88 ARG Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 97 SER Chi-restraints excluded: chain H residue 99 GLU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 149 LYS Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain h residue 46 GLU Chi-restraints excluded: chain h residue 174 THR Chi-restraints excluded: chain l residue 2 ILE Chi-restraints excluded: chain l residue 48 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 99 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 chunk 59 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 ASN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 6 GLN h 173 HIS h 209 HIS ** l 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.215032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.206667 restraints weight = 23046.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.205479 restraints weight = 34511.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.205076 restraints weight = 36036.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.204554 restraints weight = 34224.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.204331 restraints weight = 36801.437| |-----------------------------------------------------------------------------| r_work (final): 0.4385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6125 moved from start: 0.3967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13673 Z= 0.191 Angle : 0.704 10.728 18564 Z= 0.366 Chirality : 0.047 0.155 2061 Planarity : 0.006 0.070 2389 Dihedral : 5.747 46.805 1881 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 3.64 % Allowed : 12.53 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.48 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.89 (0.20), residues: 1723 helix: -3.31 (1.18), residues: 12 sheet: -0.78 (0.19), residues: 755 loop : -1.63 (0.20), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 112 TYR 0.020 0.002 TYR A 171 PHE 0.020 0.002 PHE L 139 TRP 0.041 0.002 TRP A 66 HIS 0.005 0.001 HIS E 163 Details of bonding type rmsd covalent geometry : bond 0.00427 (13655) covalent geometry : angle 0.70262 (18528) SS BOND : bond 0.00553 ( 18) SS BOND : angle 1.11508 ( 36) hydrogen bonds : bond 0.03774 ( 360) hydrogen bonds : angle 6.82170 ( 957) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 185 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 TYR cc_start: 0.4765 (OUTLIER) cc_final: 0.4344 (t80) REVERT: A 176 THR cc_start: 0.6887 (t) cc_final: 0.6663 (m) REVERT: E 207 SER cc_start: 0.4967 (OUTLIER) cc_final: 0.4588 (t) REVERT: F 132 ASP cc_start: 0.6823 (m-30) cc_final: 0.6546 (m-30) REVERT: L 36 TYR cc_start: 0.8750 (m-10) cc_final: 0.8261 (m-10) REVERT: L 149 LYS cc_start: 0.6055 (OUTLIER) cc_final: 0.5702 (mttp) REVERT: L 198 HIS cc_start: 0.3560 (t70) cc_final: 0.3214 (p90) REVERT: h 46 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.6219 (pt0) outliers start: 54 outliers final: 39 residues processed: 215 average time/residue: 0.1089 time to fit residues: 34.5016 Evaluate side-chains 223 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 180 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 123 TYR Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 156 HIS Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 163 HIS Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 53 HIS Chi-restraints excluded: chain F residue 88 ARG Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 241 PHE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 97 SER Chi-restraints excluded: chain H residue 99 GLU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain L residue 149 LYS Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain h residue 46 GLU Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain h residue 174 THR Chi-restraints excluded: chain l residue 2 ILE Chi-restraints excluded: chain l residue 48 ILE Chi-restraints excluded: chain l residue 178 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 52 optimal weight: 0.9990 chunk 142 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 163 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 105 optimal weight: 0.5980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 ASN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 28 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.218229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.210148 restraints weight = 22948.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.207370 restraints weight = 36892.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.206309 restraints weight = 47670.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.205624 restraints weight = 41808.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.205205 restraints weight = 36680.170| |-----------------------------------------------------------------------------| r_work (final): 0.4388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6156 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13673 Z= 0.151 Angle : 0.676 9.926 18564 Z= 0.347 Chirality : 0.046 0.159 2061 Planarity : 0.005 0.070 2389 Dihedral : 5.539 45.958 1881 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 4.11 % Allowed : 12.47 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.48 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.85 (0.20), residues: 1723 helix: -3.31 (1.19), residues: 12 sheet: -0.77 (0.19), residues: 757 loop : -1.58 (0.20), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 112 TYR 0.014 0.001 TYR l 140 PHE 0.016 0.002 PHE L 139 TRP 0.032 0.002 TRP A 66 HIS 0.004 0.001 HIS E 163 Details of bonding type rmsd covalent geometry : bond 0.00342 (13655) covalent geometry : angle 0.67560 (18528) SS BOND : bond 0.00494 ( 18) SS BOND : angle 0.94671 ( 36) hydrogen bonds : bond 0.03412 ( 360) hydrogen bonds : angle 6.55977 ( 957) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 183 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 TYR cc_start: 0.4543 (OUTLIER) cc_final: 0.4208 (t80) REVERT: A 176 THR cc_start: 0.7239 (t) cc_final: 0.6937 (m) REVERT: L 6 GLN cc_start: 0.7713 (tt0) cc_final: 0.7274 (tt0) REVERT: L 36 TYR cc_start: 0.8729 (m-10) cc_final: 0.8221 (m-10) REVERT: L 149 LYS cc_start: 0.6089 (OUTLIER) cc_final: 0.5738 (mttp) REVERT: L 198 HIS cc_start: 0.3803 (t70) cc_final: 0.3132 (p90) REVERT: h 46 GLU cc_start: 0.6645 (OUTLIER) cc_final: 0.5895 (pt0) REVERT: l 104 LEU cc_start: 0.4952 (OUTLIER) cc_final: 0.4748 (mp) outliers start: 61 outliers final: 44 residues processed: 218 average time/residue: 0.1002 time to fit residues: 33.0475 Evaluate side-chains 228 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 180 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 123 TYR Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 156 HIS Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 163 HIS Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 53 HIS Chi-restraints excluded: chain F residue 83 LYS Chi-restraints excluded: chain F residue 88 ARG Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 97 SER Chi-restraints excluded: chain H residue 99 GLU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 149 LYS Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 30 THR Chi-restraints excluded: chain h residue 46 GLU Chi-restraints excluded: chain h residue 83 LEU Chi-restraints excluded: chain h residue 174 THR Chi-restraints excluded: chain l residue 2 ILE Chi-restraints excluded: chain l residue 20 THR Chi-restraints excluded: chain l residue 27 GLN Chi-restraints excluded: chain l residue 48 ILE Chi-restraints excluded: chain l residue 104 LEU Chi-restraints excluded: chain l residue 163 VAL Chi-restraints excluded: chain l residue 178 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 66 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 119 optimal weight: 2.9990 chunk 4 optimal weight: 0.0980 chunk 58 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 63 optimal weight: 0.2980 chunk 23 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 HIS H 6 GLN L 28 ASN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 137 ASN ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.220522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.212513 restraints weight = 22809.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.210834 restraints weight = 35605.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.209332 restraints weight = 38068.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.207793 restraints weight = 42017.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.207401 restraints weight = 38909.144| |-----------------------------------------------------------------------------| r_work (final): 0.4410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6122 moved from start: 0.4354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13673 Z= 0.132 Angle : 0.656 8.237 18564 Z= 0.335 Chirality : 0.045 0.154 2061 Planarity : 0.005 0.073 2389 Dihedral : 5.324 45.423 1881 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.71 % Allowed : 13.88 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.48 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.20), residues: 1723 helix: -3.18 (1.24), residues: 12 sheet: -0.67 (0.19), residues: 764 loop : -1.57 (0.20), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 112 TYR 0.013 0.001 TYR l 96 PHE 0.021 0.002 PHE A 240 TRP 0.028 0.002 TRP A 66 HIS 0.004 0.001 HIS E 163 Details of bonding type rmsd covalent geometry : bond 0.00298 (13655) covalent geometry : angle 0.65520 (18528) SS BOND : bond 0.00452 ( 18) SS BOND : angle 0.86806 ( 36) hydrogen bonds : bond 0.03171 ( 360) hydrogen bonds : angle 6.28294 ( 957) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 181 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 MET cc_start: 0.2613 (ttp) cc_final: 0.2280 (mtp) REVERT: A 176 THR cc_start: 0.7132 (t) cc_final: 0.6809 (m) REVERT: A 217 MET cc_start: 0.6302 (tmm) cc_final: 0.5743 (tmm) REVERT: L 6 GLN cc_start: 0.7759 (tt0) cc_final: 0.7287 (tt0) REVERT: L 36 TYR cc_start: 0.8673 (m-10) cc_final: 0.8191 (m-10) REVERT: L 149 LYS cc_start: 0.6081 (OUTLIER) cc_final: 0.5734 (mttp) REVERT: L 198 HIS cc_start: 0.3725 (t70) cc_final: 0.2953 (p90) REVERT: h 46 GLU cc_start: 0.6618 (OUTLIER) cc_final: 0.5799 (pt0) outliers start: 55 outliers final: 41 residues processed: 213 average time/residue: 0.1077 time to fit residues: 34.2654 Evaluate side-chains 215 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 172 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 156 HIS Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 163 HIS Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 53 HIS Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 83 LYS Chi-restraints excluded: chain F residue 88 ARG Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 97 SER Chi-restraints excluded: chain H residue 99 GLU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 149 LYS Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 46 GLU Chi-restraints excluded: chain h residue 83 LEU Chi-restraints excluded: chain h residue 174 THR Chi-restraints excluded: chain l residue 2 ILE Chi-restraints excluded: chain l residue 20 THR Chi-restraints excluded: chain l residue 27 GLN Chi-restraints excluded: chain l residue 163 VAL Chi-restraints excluded: chain l residue 178 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 99 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 44 optimal weight: 0.4980 chunk 67 optimal weight: 0.5980 chunk 151 optimal weight: 3.9990 chunk 117 optimal weight: 0.0070 chunk 38 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 HIS B 223 ASN L 28 ASN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.220365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.210645 restraints weight = 23205.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.209344 restraints weight = 32769.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.208489 restraints weight = 29879.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.207450 restraints weight = 30736.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.206982 restraints weight = 30170.949| |-----------------------------------------------------------------------------| r_work (final): 0.4418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6098 moved from start: 0.4492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13673 Z= 0.125 Angle : 0.648 8.328 18564 Z= 0.331 Chirality : 0.045 0.152 2061 Planarity : 0.005 0.071 2389 Dihedral : 5.206 45.232 1881 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 3.37 % Allowed : 14.76 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.48 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.72 (0.20), residues: 1723 helix: -3.69 (0.87), residues: 18 sheet: -0.65 (0.19), residues: 751 loop : -1.50 (0.20), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 112 TYR 0.019 0.001 TYR A 126 PHE 0.024 0.002 PHE F 133 TRP 0.030 0.002 TRP h 47 HIS 0.003 0.001 HIS E 163 Details of bonding type rmsd covalent geometry : bond 0.00286 (13655) covalent geometry : angle 0.64810 (18528) SS BOND : bond 0.00436 ( 18) SS BOND : angle 0.82815 ( 36) hydrogen bonds : bond 0.03066 ( 360) hydrogen bonds : angle 6.15864 ( 957) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 181 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 THR cc_start: 0.7072 (t) cc_final: 0.6781 (m) REVERT: A 194 MET cc_start: 0.3380 (mpp) cc_final: 0.3044 (ptm) REVERT: A 217 MET cc_start: 0.6227 (tmm) cc_final: 0.5666 (tmm) REVERT: L 6 GLN cc_start: 0.7746 (tt0) cc_final: 0.7287 (tt0) REVERT: L 36 TYR cc_start: 0.8649 (m-10) cc_final: 0.8175 (m-10) REVERT: L 149 LYS cc_start: 0.6117 (OUTLIER) cc_final: 0.5743 (mttp) REVERT: L 198 HIS cc_start: 0.3307 (t70) cc_final: 0.2756 (p90) REVERT: h 46 GLU cc_start: 0.6574 (OUTLIER) cc_final: 0.5748 (pt0) outliers start: 50 outliers final: 43 residues processed: 212 average time/residue: 0.0936 time to fit residues: 30.2250 Evaluate side-chains 221 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 176 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 156 HIS Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 163 HIS Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 53 HIS Chi-restraints excluded: chain F residue 83 LYS Chi-restraints excluded: chain F residue 88 ARG Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 97 SER Chi-restraints excluded: chain H residue 99 GLU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain L residue 149 LYS Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 46 GLU Chi-restraints excluded: chain h residue 83 LEU Chi-restraints excluded: chain h residue 174 THR Chi-restraints excluded: chain l residue 2 ILE Chi-restraints excluded: chain l residue 20 THR Chi-restraints excluded: chain l residue 27 GLN Chi-restraints excluded: chain l residue 163 VAL Chi-restraints excluded: chain l residue 178 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 69 optimal weight: 0.0170 chunk 11 optimal weight: 10.0000 chunk 41 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 135 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 126 optimal weight: 6.9990 chunk 166 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 168 optimal weight: 0.0370 overall best weight: 1.4100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 28 ASN L 79 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 164 ASN ** l 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.220670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.209064 restraints weight = 22983.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.206082 restraints weight = 33409.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.205387 restraints weight = 38791.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.205132 restraints weight = 35057.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.204713 restraints weight = 31322.895| |-----------------------------------------------------------------------------| r_work (final): 0.4345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6266 moved from start: 0.4731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13673 Z= 0.176 Angle : 0.704 10.010 18564 Z= 0.362 Chirality : 0.047 0.158 2061 Planarity : 0.006 0.062 2389 Dihedral : 5.569 45.454 1881 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 3.17 % Allowed : 15.23 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.48 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.88 (0.20), residues: 1723 helix: -3.79 (0.71), residues: 18 sheet: -0.77 (0.19), residues: 756 loop : -1.59 (0.20), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 112 TYR 0.018 0.002 TYR A 126 PHE 0.022 0.002 PHE L 139 TRP 0.038 0.002 TRP h 47 HIS 0.005 0.001 HIS E 163 Details of bonding type rmsd covalent geometry : bond 0.00400 (13655) covalent geometry : angle 0.70268 (18528) SS BOND : bond 0.00551 ( 18) SS BOND : angle 1.09907 ( 36) hydrogen bonds : bond 0.03558 ( 360) hydrogen bonds : angle 6.56782 ( 957) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 189 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 MET cc_start: 0.2679 (ttp) cc_final: 0.2333 (mtp) REVERT: A 176 THR cc_start: 0.7203 (t) cc_final: 0.6868 (m) REVERT: A 217 MET cc_start: 0.6341 (tmm) cc_final: 0.5724 (tmm) REVERT: L 6 GLN cc_start: 0.7755 (tt0) cc_final: 0.7267 (tt0) REVERT: L 36 TYR cc_start: 0.8797 (m-10) cc_final: 0.8407 (m-80) REVERT: L 149 LYS cc_start: 0.6443 (OUTLIER) cc_final: 0.6068 (mttp) REVERT: h 46 GLU cc_start: 0.6863 (OUTLIER) cc_final: 0.6062 (pt0) outliers start: 47 outliers final: 41 residues processed: 218 average time/residue: 0.1078 time to fit residues: 34.4198 Evaluate side-chains 225 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 182 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 156 HIS Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 163 HIS Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 53 HIS Chi-restraints excluded: chain F residue 83 LYS Chi-restraints excluded: chain F residue 88 ARG Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 97 SER Chi-restraints excluded: chain H residue 99 GLU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 149 LYS Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 46 GLU Chi-restraints excluded: chain h residue 83 LEU Chi-restraints excluded: chain h residue 174 THR Chi-restraints excluded: chain l residue 2 ILE Chi-restraints excluded: chain l residue 20 THR Chi-restraints excluded: chain l residue 163 VAL Chi-restraints excluded: chain l residue 178 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 52 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 chunk 30 optimal weight: 0.7980 chunk 149 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 159 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN L 28 ASN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 27 GLN ** 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 = 0.4535 r_free = 0.4535 target = 0.220081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.211402 restraints weight = 22927.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.209357 restraints weight = 40241.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.209071 restraints weight = 41090.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.208102 restraints weight = 40864.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.208625 restraints weight = 35813.987| |-----------------------------------------------------------------------------| r_work (final): 0.4408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6133 moved from start: 0.4859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13673 Z= 0.153 Angle : 0.697 13.531 18564 Z= 0.353 Chirality : 0.046 0.152 2061 Planarity : 0.005 0.056 2389 Dihedral : 5.447 44.835 1881 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 3.03 % Allowed : 15.63 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.48 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.90 (0.20), residues: 1723 helix: -4.04 (0.56), residues: 24 sheet: -0.84 (0.19), residues: 750 loop : -1.52 (0.20), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 112 TYR 0.017 0.002 TYR A 126 PHE 0.022 0.002 PHE F 133 TRP 0.039 0.002 TRP h 47 HIS 0.004 0.001 HIS L 198 Details of bonding type rmsd covalent geometry : bond 0.00351 (13655) covalent geometry : angle 0.69663 (18528) SS BOND : bond 0.00503 ( 18) SS BOND : angle 0.98262 ( 36) hydrogen bonds : bond 0.03301 ( 360) hydrogen bonds : angle 6.38764 ( 957) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2029.03 seconds wall clock time: 35 minutes 58.19 seconds (2158.19 seconds total)