Starting phenix.real_space_refine on Sun Aug 9 16:33:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/36is_77603/08_2026/36is_77603.cif Found real_map, /net/cci-nas-00/data/ceres_data/36is_77603/08_2026/36is_77603.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/36is_77603/08_2026/36is_77603.map" default_real_map = "/net/cci-nas-00/data/ceres_data/36is_77603/08_2026/36is_77603.map" model { file = "/net/cci-nas-00/data/ceres_data/36is_77603/08_2026/36is_77603.cif" } default_model = "/net/cci-nas-00/data/ceres_data/36is_77603/08_2026/36is_77603.cif" } resolution = 4.3 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= 0.018 sd= 0.375 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 253 5.16 5 C 23229 2.51 5 N 5630 2.21 5 O 6026 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35138 Number of models: 1 Model: "" Number of chains: 20 Chain: "A1" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1623 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 15, 'TRANS': 193} Chain: "B1" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1623 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 15, 'TRANS': 193} Chain: "C1" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1623 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 15, 'TRANS': 193} Chain: "D1" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1623 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 15, 'TRANS': 193} Chain: "E1" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1623 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 15, 'TRANS': 193} Chain: "F1" Number of atoms: 1925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1925 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 15, 'TRANS': 234} Chain: "G1" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 670 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "H1" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 670 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "I1" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 670 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "J1" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 670 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "K1" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1637 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 12, 'TRANS': 201} Chain: "A2" Number of atoms: 2309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2309 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 9, 'TRANS': 301} Chain: "B2" Number of atoms: 2309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2309 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 9, 'TRANS': 301} Chain: "C2" Number of atoms: 2309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2309 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 9, 'TRANS': 301} Chain: "D2" Number of atoms: 2309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2309 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 9, 'TRANS': 301} Chain: "E2" Number of atoms: 2309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2309 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 9, 'TRANS': 301} Chain: "F2" Number of atoms: 2309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2309 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 9, 'TRANS': 301} Chain: "G2" Number of atoms: 2309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2309 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 9, 'TRANS': 301} Chain: "H2" Number of atoms: 2309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2309 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 9, 'TRANS': 301} Chain: "I2" Number of atoms: 2309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2309 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 9, 'TRANS': 301} Time building chain proxies: 7.55, per 1000 atoms: 0.21 Number of scatterers: 35138 At special positions: 0 Unit cell: (137.55, 135.45, 185.85, 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 253 16.00 O 6026 8.00 N 5630 7.00 C 23229 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.30 Conformation dependent library (CDL) restraints added in 1.6 seconds 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8532 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 0 sheets defined 86.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A1' and resid 41 through 53 removed outlier: 3.621A pdb=" N PHEA1 53 " --> pdb=" O THRA1 49 " (cutoff:3.500A) Processing helix chain 'A1' and resid 53 through 62 removed outlier: 3.772A pdb=" N THRA1 62 " --> pdb=" O LEUA1 58 " (cutoff:3.500A) Processing helix chain 'A1' and resid 63 through 77 Processing helix chain 'A1' and resid 85 through 112 removed outlier: 3.563A pdb=" N LEUA1 89 " --> pdb=" O PROA1 85 " (cutoff:3.500A) Proline residue: A1 103 - end of helix Processing helix chain 'A1' and resid 112 through 118 Processing helix chain 'A1' and resid 124 through 141 removed outlier: 4.239A pdb=" N ASPA1 128 " --> pdb=" O GLNA1 124 " (cutoff:3.500A) Proline residue: A1 133 - end of helix removed outlier: 3.648A pdb=" N GLNA1 141 " --> pdb=" O PHEA1 137 " (cutoff:3.500A) Processing helix chain 'A1' and resid 143 through 155 removed outlier: 3.665A pdb=" N LEUA1 147 " --> pdb=" O ARGA1 143 " (cutoff:3.500A) Processing helix chain 'A1' and resid 161 through 165 removed outlier: 3.562A pdb=" N VALA1 165 " --> pdb=" O PROA1 162 " (cutoff:3.500A) Processing helix chain 'A1' and resid 169 through 207 Proline residue: A1 192 - end of helix removed outlier: 3.688A pdb=" N ILEA1 196 " --> pdb=" O PROA1 192 " (cutoff:3.500A) Processing helix chain 'A1' and resid 213 through 229 removed outlier: 3.909A pdb=" N ILEA1 217 " --> pdb=" O PROA1 213 " (cutoff:3.500A) Proline residue: A1 220 - end of helix Processing helix chain 'A1' and resid 230 through 245 removed outlier: 3.764A pdb=" N PHEA1 243 " --> pdb=" O LEUA1 239 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYRA1 244 " --> pdb=" O ALAA1 240 " (cutoff:3.500A) Processing helix chain 'B1' and resid 40 through 52 removed outlier: 3.621A pdb=" N THRB1 52 " --> pdb=" O ILEB1 48 " (cutoff:3.500A) Processing helix chain 'B1' and resid 53 through 62 removed outlier: 3.957A pdb=" N THRB1 62 " --> pdb=" O LEUB1 58 " (cutoff:3.500A) Processing helix chain 'B1' and resid 63 through 77 Processing helix chain 'B1' and resid 78 through 80 No H-bonds generated for 'chain 'B1' and resid 78 through 80' Processing helix chain 'B1' and resid 88 through 112 Proline residue: B1 103 - end of helix Processing helix chain 'B1' and resid 112 through 118 Processing helix chain 'B1' and resid 124 through 141 removed outlier: 3.835A pdb=" N ASPB1 128 " --> pdb=" O GLNB1 124 " (cutoff:3.500A) Proline residue: B1 133 - end of helix removed outlier: 3.626A pdb=" N GLNB1 141 " --> pdb=" O PHEB1 137 " (cutoff:3.500A) Processing helix chain 'B1' and resid 143 through 155 removed outlier: 3.656A pdb=" N LEUB1 147 " --> pdb=" O ARGB1 143 " (cutoff:3.500A) Processing helix chain 'B1' and resid 161 through 165 Processing helix chain 'B1' and resid 166 through 207 Proline residue: B1 172 - end of helix Proline residue: B1 192 - end of helix Processing helix chain 'B1' and resid 213 through 229 removed outlier: 4.185A pdb=" N ILEB1 217 " --> pdb=" O PROB1 213 " (cutoff:3.500A) Proline residue: B1 220 - end of helix Processing helix chain 'B1' and resid 230 through 245 removed outlier: 3.805A pdb=" N PHEB1 243 " --> pdb=" O LEUB1 239 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYRB1 244 " --> pdb=" O ALAB1 240 " (cutoff:3.500A) Processing helix chain 'C1' and resid 40 through 53 removed outlier: 3.738A pdb=" N PHEC1 53 " --> pdb=" O THRC1 49 " (cutoff:3.500A) Processing helix chain 'C1' and resid 53 through 62 removed outlier: 3.542A pdb=" N THRC1 62 " --> pdb=" O LEUC1 58 " (cutoff:3.500A) Processing helix chain 'C1' and resid 63 through 77 Processing helix chain 'C1' and resid 78 through 80 No H-bonds generated for 'chain 'C1' and resid 78 through 80' Processing helix chain 'C1' and resid 88 through 112 Proline residue: C1 103 - end of helix Processing helix chain 'C1' and resid 112 through 118 removed outlier: 3.885A pdb=" N GLUC1 118 " --> pdb=" O GLNC1 114 " (cutoff:3.500A) Processing helix chain 'C1' and resid 124 through 141 removed outlier: 3.818A pdb=" N ASPC1 128 " --> pdb=" O GLNC1 124 " (cutoff:3.500A) Proline residue: C1 133 - end of helix removed outlier: 3.619A pdb=" N GLNC1 141 " --> pdb=" O PHEC1 137 " (cutoff:3.500A) Processing helix chain 'C1' and resid 143 through 155 removed outlier: 3.579A pdb=" N LEUC1 147 " --> pdb=" O ARGC1 143 " (cutoff:3.500A) Processing helix chain 'C1' and resid 161 through 165 Processing helix chain 'C1' and resid 166 through 207 Proline residue: C1 172 - end of helix Proline residue: C1 192 - end of helix Processing helix chain 'C1' and resid 213 through 229 removed outlier: 4.302A pdb=" N ILEC1 217 " --> pdb=" O PROC1 213 " (cutoff:3.500A) Proline residue: C1 220 - end of helix Processing helix chain 'C1' and resid 230 through 245 removed outlier: 3.987A pdb=" N PHEC1 243 " --> pdb=" O LEUC1 239 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N TYRC1 244 " --> pdb=" O ALAC1 240 " (cutoff:3.500A) Processing helix chain 'D1' and resid 41 through 53 Processing helix chain 'D1' and resid 53 through 62 removed outlier: 3.689A pdb=" N THRD1 62 " --> pdb=" O LEUD1 58 " (cutoff:3.500A) Processing helix chain 'D1' and resid 63 through 77 Processing helix chain 'D1' and resid 78 through 80 No H-bonds generated for 'chain 'D1' and resid 78 through 80' Processing helix chain 'D1' and resid 88 through 112 Proline residue: D1 103 - end of helix Processing helix chain 'D1' and resid 112 through 118 Processing helix chain 'D1' and resid 124 through 141 removed outlier: 3.629A pdb=" N ASPD1 128 " --> pdb=" O GLND1 124 " (cutoff:3.500A) Proline residue: D1 133 - end of helix removed outlier: 3.518A pdb=" N GLND1 141 " --> pdb=" O PHED1 137 " (cutoff:3.500A) Processing helix chain 'D1' and resid 143 through 155 Processing helix chain 'D1' and resid 161 through 165 removed outlier: 3.615A pdb=" N VALD1 165 " --> pdb=" O PROD1 162 " (cutoff:3.500A) Processing helix chain 'D1' and resid 166 through 207 Proline residue: D1 172 - end of helix Proline residue: D1 192 - end of helix Processing helix chain 'D1' and resid 213 through 229 removed outlier: 3.988A pdb=" N ILED1 217 " --> pdb=" O PROD1 213 " (cutoff:3.500A) Proline residue: D1 220 - end of helix Processing helix chain 'D1' and resid 230 through 242 Processing helix chain 'E1' and resid 40 through 53 removed outlier: 3.646A pdb=" N THRE1 52 " --> pdb=" O ILEE1 48 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHEE1 53 " --> pdb=" O THRE1 49 " (cutoff:3.500A) Processing helix chain 'E1' and resid 53 through 62 removed outlier: 3.606A pdb=" N THRE1 62 " --> pdb=" O LEUE1 58 " (cutoff:3.500A) Processing helix chain 'E1' and resid 63 through 77 Processing helix chain 'E1' and resid 88 through 113 Proline residue: E1 103 - end of helix Processing helix chain 'E1' and resid 113 through 118 Processing helix chain 'E1' and resid 124 through 141 removed outlier: 3.901A pdb=" N ASPE1 128 " --> pdb=" O GLNE1 124 " (cutoff:3.500A) Proline residue: E1 133 - end of helix Processing helix chain 'E1' and resid 143 through 155 removed outlier: 3.680A pdb=" N LEUE1 147 " --> pdb=" O ARGE1 143 " (cutoff:3.500A) Processing helix chain 'E1' and resid 161 through 165 Processing helix chain 'E1' and resid 166 through 207 Proline residue: E1 172 - end of helix Proline residue: E1 192 - end of helix Processing helix chain 'E1' and resid 213 through 229 removed outlier: 4.282A pdb=" N ILEE1 217 " --> pdb=" O PROE1 213 " (cutoff:3.500A) Proline residue: E1 220 - end of helix Processing helix chain 'E1' and resid 230 through 242 Processing helix chain 'F1' and resid 8 through 17 Processing helix chain 'F1' and resid 17 through 28 removed outlier: 3.553A pdb=" N ARGF1 22 " --> pdb=" O TRPF1 18 " (cutoff:3.500A) Processing helix chain 'F1' and resid 39 through 55 Processing helix chain 'F1' and resid 56 through 58 No H-bonds generated for 'chain 'F1' and resid 56 through 58' Processing helix chain 'F1' and resid 68 through 107 removed outlier: 3.589A pdb=" N PHEF1 90 " --> pdb=" O PHEF1 86 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ALAF1 91 " --> pdb=" O THRF1 87 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N PHEF1 92 " --> pdb=" O METF1 88 " (cutoff:3.500A) Processing helix chain 'F1' and resid 109 through 115 removed outlier: 3.525A pdb=" N PHEF1 113 " --> pdb=" O SERF1 109 " (cutoff:3.500A) Processing helix chain 'F1' and resid 123 through 140 Processing helix chain 'F1' and resid 141 through 157 removed outlier: 3.575A pdb=" N HISF1 155 " --> pdb=" O VALF1 151 " (cutoff:3.500A) Processing helix chain 'F1' and resid 166 through 208 removed outlier: 3.831A pdb=" N METF1 170 " --> pdb=" O SERF1 166 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLYF1 176 " --> pdb=" O LEUF1 172 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLYF1 177 " --> pdb=" O ALAF1 173 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LEUF1 178 " --> pdb=" O ARGF1 174 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILEF1 179 " --> pdb=" O ALAF1 175 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHEF1 180 " --> pdb=" O GLYF1 176 " (cutoff:3.500A) Proline residue: F1 189 - end of helix Processing helix chain 'F1' and resid 216 through 255 removed outlier: 3.567A pdb=" N LEUF1 220 " --> pdb=" O ILEF1 216 " (cutoff:3.500A) Proline residue: F1 234 - end of helix removed outlier: 4.261A pdb=" N ALAF1 237 " --> pdb=" O METF1 233 " (cutoff:3.500A) Proline residue: F1 238 - end of helix Processing helix chain 'G1' and resid 2 through 42 Proline residue: G1 23 - end of helix Processing helix chain 'G1' and resid 47 through 84 Proline residue: G1 53 - end of helix Proline residue: G1 67 - end of helix Processing helix chain 'G1' and resid 85 through 87 No H-bonds generated for 'chain 'G1' and resid 85 through 87' Processing helix chain 'H1' and resid 2 through 43 Proline residue: H1 23 - end of helix Processing helix chain 'H1' and resid 47 through 84 Proline residue: H1 53 - end of helix Proline residue: H1 67 - end of helix Processing helix chain 'H1' and resid 85 through 87 No H-bonds generated for 'chain 'H1' and resid 85 through 87' Processing helix chain 'I1' and resid 2 through 42 Proline residue: I1 23 - end of helix Processing helix chain 'I1' and resid 47 through 84 Proline residue: I1 53 - end of helix Proline residue: I1 67 - end of helix Processing helix chain 'I1' and resid 85 through 87 No H-bonds generated for 'chain 'I1' and resid 85 through 87' Processing helix chain 'J1' and resid 2 through 43 Proline residue: J1 23 - end of helix Processing helix chain 'J1' and resid 50 through 84 Proline residue: J1 67 - end of helix Processing helix chain 'J1' and resid 85 through 88 removed outlier: 3.981A pdb=" N ILEJ1 88 " --> pdb=" O PROJ1 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'J1' and resid 85 through 88' Processing helix chain 'K1' and resid 14 through 23 removed outlier: 3.881A pdb=" N GLUK1 23 " --> pdb=" O GLUK1 19 " (cutoff:3.500A) Processing helix chain 'K1' and resid 30 through 49 Processing helix chain 'K1' and resid 49 through 65 removed outlier: 3.523A pdb=" N LEUK1 53 " --> pdb=" O GLYK1 49 " (cutoff:3.500A) Processing helix chain 'K1' and resid 69 through 74 removed outlier: 3.905A pdb=" N ASNK1 73 " --> pdb=" O HISK1 69 " (cutoff:3.500A) Processing helix chain 'K1' and resid 76 through 107 Proline residue: K1 95 - end of helix Processing helix chain 'K1' and resid 108 through 112 removed outlier: 4.208A pdb=" N GLYK1 112 " --> pdb=" O VALK1 109 " (cutoff:3.500A) Processing helix chain 'K1' and resid 118 through 122 Processing helix chain 'K1' and resid 129 through 137 removed outlier: 4.046A pdb=" N GLYK1 133 " --> pdb=" O ASNK1 129 " (cutoff:3.500A) Processing helix chain 'K1' and resid 139 through 174 removed outlier: 3.611A pdb=" N GLYK1 143 " --> pdb=" O SERK1 139 " (cutoff:3.500A) Proline residue: K1 169 - end of helix Processing helix chain 'K1' and resid 175 through 177 No H-bonds generated for 'chain 'K1' and resid 175 through 177' Processing helix chain 'K1' and resid 178 through 201 removed outlier: 3.642A pdb=" N VALK1 201 " --> pdb=" O VALK1 197 " (cutoff:3.500A) Processing helix chain 'K1' and resid 201 through 220 Processing helix chain 'A2' and resid 22 through 37 Processing helix chain 'A2' and resid 40 through 64 removed outlier: 3.565A pdb=" N LEUA2 44 " --> pdb=" O PROA2 40 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEUA2 46 " --> pdb=" O PHEA2 42 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THRA2 49 " --> pdb=" O ASPA2 45 " (cutoff:3.500A) Processing helix chain 'A2' and resid 73 through 98 removed outlier: 3.613A pdb=" N ILEA2 77 " --> pdb=" O ALAA2 73 " (cutoff:3.500A) Processing helix chain 'A2' and resid 108 through 119 Processing helix chain 'A2' and resid 123 through 140 removed outlier: 6.163A pdb=" N VALA2 129 " --> pdb=" O ILEA2 125 " (cutoff:3.500A) Processing helix chain 'A2' and resid 140 through 173 Proline residue: A2 161 - end of helix removed outlier: 3.536A pdb=" N ALAA2 173 " --> pdb=" O ALAA2 169 " (cutoff:3.500A) Processing helix chain 'A2' and resid 177 through 231 removed outlier: 3.793A pdb=" N ASPA2 199 " --> pdb=" O TYRA2 195 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLYA2 200 " --> pdb=" O GLYA2 196 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N HISA2 231 " --> pdb=" O GLYA2 227 " (cutoff:3.500A) Processing helix chain 'A2' and resid 234 through 268 removed outlier: 3.740A pdb=" N ALAA2 238 " --> pdb=" O SERA2 234 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N SERA2 241 " --> pdb=" O SERA2 237 " (cutoff:3.500A) Proline residue: A2 256 - end of helix Processing helix chain 'A2' and resid 276 through 286 Processing helix chain 'A2' and resid 288 through 304 removed outlier: 3.866A pdb=" N META2 292 " --> pdb=" O ASNA2 288 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALAA2 295 " --> pdb=" O VALA2 291 " (cutoff:3.500A) Processing helix chain 'A2' and resid 310 through 327 Processing helix chain 'B2' and resid 22 through 37 Processing helix chain 'B2' and resid 40 through 64 removed outlier: 3.588A pdb=" N LEUB2 44 " --> pdb=" O PROB2 40 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LEUB2 46 " --> pdb=" O PHEB2 42 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THRB2 49 " --> pdb=" O ASPB2 45 " (cutoff:3.500A) Processing helix chain 'B2' and resid 73 through 98 removed outlier: 3.696A pdb=" N ILEB2 77 " --> pdb=" O ALAB2 73 " (cutoff:3.500A) Processing helix chain 'B2' and resid 108 through 119 Processing helix chain 'B2' and resid 123 through 139 removed outlier: 6.211A pdb=" N VALB2 129 " --> pdb=" O ILEB2 125 " (cutoff:3.500A) Processing helix chain 'B2' and resid 140 through 173 Proline residue: B2 161 - end of helix Processing helix chain 'B2' and resid 177 through 231 removed outlier: 3.796A pdb=" N ASPB2 199 " --> pdb=" O TYRB2 195 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLYB2 200 " --> pdb=" O GLYB2 196 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N HISB2 231 " --> pdb=" O GLYB2 227 " (cutoff:3.500A) Processing helix chain 'B2' and resid 234 through 268 removed outlier: 3.918A pdb=" N ALAB2 238 " --> pdb=" O SERB2 234 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N SERB2 241 " --> pdb=" O SERB2 237 " (cutoff:3.500A) Proline residue: B2 256 - end of helix Processing helix chain 'B2' and resid 276 through 286 Processing helix chain 'B2' and resid 289 through 304 removed outlier: 3.944A pdb=" N ALAB2 295 " --> pdb=" O VALB2 291 " (cutoff:3.500A) Processing helix chain 'B2' and resid 310 through 327 Processing helix chain 'C2' and resid 22 through 37 Processing helix chain 'C2' and resid 40 through 64 removed outlier: 3.532A pdb=" N LEUC2 44 " --> pdb=" O PROC2 40 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LEUC2 46 " --> pdb=" O PHEC2 42 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THRC2 49 " --> pdb=" O ASPC2 45 " (cutoff:3.500A) Processing helix chain 'C2' and resid 73 through 98 removed outlier: 3.550A pdb=" N ILEC2 77 " --> pdb=" O ALAC2 73 " (cutoff:3.500A) Processing helix chain 'C2' and resid 108 through 119 Processing helix chain 'C2' and resid 123 through 140 removed outlier: 6.112A pdb=" N VALC2 129 " --> pdb=" O ILEC2 125 " (cutoff:3.500A) Processing helix chain 'C2' and resid 140 through 173 Proline residue: C2 161 - end of helix Processing helix chain 'C2' and resid 177 through 231 removed outlier: 3.854A pdb=" N ASPC2 199 " --> pdb=" O TYRC2 195 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLYC2 200 " --> pdb=" O GLYC2 196 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N HISC2 231 " --> pdb=" O GLYC2 227 " (cutoff:3.500A) Processing helix chain 'C2' and resid 234 through 268 removed outlier: 3.707A pdb=" N ALAC2 238 " --> pdb=" O SERC2 234 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N SERC2 241 " --> pdb=" O SERC2 237 " (cutoff:3.500A) Proline residue: C2 256 - end of helix Processing helix chain 'C2' and resid 276 through 286 Processing helix chain 'C2' and resid 289 through 304 removed outlier: 4.051A pdb=" N ALAC2 295 " --> pdb=" O VALC2 291 " (cutoff:3.500A) Processing helix chain 'C2' and resid 310 through 327 Processing helix chain 'D2' and resid 22 through 37 Processing helix chain 'D2' and resid 40 through 64 removed outlier: 4.431A pdb=" N LEUD2 46 " --> pdb=" O PHED2 42 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THRD2 49 " --> pdb=" O ASPD2 45 " (cutoff:3.500A) Processing helix chain 'D2' and resid 73 through 98 removed outlier: 3.707A pdb=" N ILED2 77 " --> pdb=" O ALAD2 73 " (cutoff:3.500A) Processing helix chain 'D2' and resid 108 through 119 Processing helix chain 'D2' and resid 123 through 140 removed outlier: 6.190A pdb=" N VALD2 129 " --> pdb=" O ILED2 125 " (cutoff:3.500A) Processing helix chain 'D2' and resid 140 through 173 Proline residue: D2 161 - end of helix Processing helix chain 'D2' and resid 177 through 231 removed outlier: 3.744A pdb=" N ASPD2 199 " --> pdb=" O TYRD2 195 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLYD2 200 " --> pdb=" O GLYD2 196 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N HISD2 231 " --> pdb=" O GLYD2 227 " (cutoff:3.500A) Processing helix chain 'D2' and resid 234 through 268 removed outlier: 3.711A pdb=" N ALAD2 238 " --> pdb=" O SERD2 234 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N SERD2 241 " --> pdb=" O SERD2 237 " (cutoff:3.500A) Proline residue: D2 256 - end of helix Processing helix chain 'D2' and resid 276 through 286 Processing helix chain 'D2' and resid 289 through 304 removed outlier: 4.019A pdb=" N ALAD2 295 " --> pdb=" O VALD2 291 " (cutoff:3.500A) Processing helix chain 'D2' and resid 310 through 327 Processing helix chain 'E2' and resid 22 through 37 Processing helix chain 'E2' and resid 40 through 64 removed outlier: 3.663A pdb=" N LEUE2 44 " --> pdb=" O PROE2 40 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N LEUE2 46 " --> pdb=" O PHEE2 42 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THRE2 49 " --> pdb=" O ASPE2 45 " (cutoff:3.500A) Processing helix chain 'E2' and resid 73 through 98 removed outlier: 3.690A pdb=" N ILEE2 77 " --> pdb=" O ALAE2 73 " (cutoff:3.500A) Processing helix chain 'E2' and resid 108 through 119 Processing helix chain 'E2' and resid 123 through 140 removed outlier: 6.137A pdb=" N VALE2 129 " --> pdb=" O ILEE2 125 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VALE2 140 " --> pdb=" O ILEE2 136 " (cutoff:3.500A) Processing helix chain 'E2' and resid 140 through 173 Proline residue: E2 161 - end of helix Processing helix chain 'E2' and resid 177 through 231 removed outlier: 3.898A pdb=" N ASPE2 199 " --> pdb=" O TYRE2 195 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLYE2 200 " --> pdb=" O GLYE2 196 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N HISE2 231 " --> pdb=" O GLYE2 227 " (cutoff:3.500A) Processing helix chain 'E2' and resid 234 through 268 removed outlier: 3.820A pdb=" N ALAE2 238 " --> pdb=" O SERE2 234 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N SERE2 241 " --> pdb=" O SERE2 237 " (cutoff:3.500A) Proline residue: E2 256 - end of helix Processing helix chain 'E2' and resid 276 through 286 Processing helix chain 'E2' and resid 289 through 304 removed outlier: 4.147A pdb=" N ALAE2 295 " --> pdb=" O VALE2 291 " (cutoff:3.500A) Processing helix chain 'E2' and resid 310 through 327 Processing helix chain 'F2' and resid 22 through 37 Processing helix chain 'F2' and resid 40 through 64 removed outlier: 3.597A pdb=" N LEUF2 44 " --> pdb=" O PROF2 40 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEUF2 46 " --> pdb=" O PHEF2 42 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THRF2 49 " --> pdb=" O ASPF2 45 " (cutoff:3.500A) Processing helix chain 'F2' and resid 73 through 98 removed outlier: 3.635A pdb=" N ILEF2 77 " --> pdb=" O ALAF2 73 " (cutoff:3.500A) Processing helix chain 'F2' and resid 108 through 119 Processing helix chain 'F2' and resid 123 through 140 removed outlier: 6.238A pdb=" N VALF2 129 " --> pdb=" O ILEF2 125 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VALF2 140 " --> pdb=" O ILEF2 136 " (cutoff:3.500A) Processing helix chain 'F2' and resid 140 through 173 Proline residue: F2 161 - end of helix Processing helix chain 'F2' and resid 177 through 231 removed outlier: 3.854A pdb=" N ASPF2 199 " --> pdb=" O TYRF2 195 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLYF2 200 " --> pdb=" O GLYF2 196 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N HISF2 231 " --> pdb=" O GLYF2 227 " (cutoff:3.500A) Processing helix chain 'F2' and resid 234 through 268 removed outlier: 3.705A pdb=" N ALAF2 238 " --> pdb=" O SERF2 234 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N SERF2 241 " --> pdb=" O SERF2 237 " (cutoff:3.500A) Proline residue: F2 256 - end of helix Processing helix chain 'F2' and resid 276 through 286 Processing helix chain 'F2' and resid 289 through 304 removed outlier: 4.205A pdb=" N ALAF2 295 " --> pdb=" O VALF2 291 " (cutoff:3.500A) Processing helix chain 'F2' and resid 310 through 327 Processing helix chain 'G2' and resid 22 through 37 Processing helix chain 'G2' and resid 40 through 64 removed outlier: 4.543A pdb=" N LEUG2 46 " --> pdb=" O PHEG2 42 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THRG2 49 " --> pdb=" O ASPG2 45 " (cutoff:3.500A) Processing helix chain 'G2' and resid 73 through 98 removed outlier: 3.673A pdb=" N ILEG2 77 " --> pdb=" O ALAG2 73 " (cutoff:3.500A) Processing helix chain 'G2' and resid 108 through 117 Processing helix chain 'G2' and resid 123 through 140 removed outlier: 6.311A pdb=" N VALG2 129 " --> pdb=" O ILEG2 125 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VALG2 140 " --> pdb=" O ILEG2 136 " (cutoff:3.500A) Processing helix chain 'G2' and resid 140 through 173 Proline residue: G2 161 - end of helix Processing helix chain 'G2' and resid 177 through 231 removed outlier: 3.786A pdb=" N ASPG2 199 " --> pdb=" O TYRG2 195 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLYG2 200 " --> pdb=" O GLYG2 196 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N HISG2 231 " --> pdb=" O GLYG2 227 " (cutoff:3.500A) Processing helix chain 'G2' and resid 234 through 268 removed outlier: 3.701A pdb=" N ALAG2 238 " --> pdb=" O SERG2 234 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N SERG2 241 " --> pdb=" O SERG2 237 " (cutoff:3.500A) Proline residue: G2 256 - end of helix Processing helix chain 'G2' and resid 276 through 286 Processing helix chain 'G2' and resid 288 through 304 removed outlier: 4.048A pdb=" N METG2 292 " --> pdb=" O ASNG2 288 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALAG2 295 " --> pdb=" O VALG2 291 " (cutoff:3.500A) Processing helix chain 'G2' and resid 310 through 327 Processing helix chain 'H2' and resid 22 through 37 Processing helix chain 'H2' and resid 40 through 64 removed outlier: 3.715A pdb=" N LEUH2 44 " --> pdb=" O PROH2 40 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LEUH2 46 " --> pdb=" O PHEH2 42 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THRH2 49 " --> pdb=" O ASPH2 45 " (cutoff:3.500A) Processing helix chain 'H2' and resid 67 through 71 removed outlier: 3.793A pdb=" N PHEH2 71 " --> pdb=" O THRH2 68 " (cutoff:3.500A) Processing helix chain 'H2' and resid 73 through 99 removed outlier: 3.775A pdb=" N ILEH2 77 " --> pdb=" O ALAH2 73 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLUH2 99 " --> pdb=" O ILEH2 95 " (cutoff:3.500A) Processing helix chain 'H2' and resid 108 through 119 Processing helix chain 'H2' and resid 123 through 140 removed outlier: 6.211A pdb=" N VALH2 129 " --> pdb=" O ILEH2 125 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VALH2 140 " --> pdb=" O ILEH2 136 " (cutoff:3.500A) Processing helix chain 'H2' and resid 140 through 173 Proline residue: H2 161 - end of helix Processing helix chain 'H2' and resid 177 through 231 removed outlier: 3.929A pdb=" N ASPH2 199 " --> pdb=" O TYRH2 195 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLYH2 200 " --> pdb=" O GLYH2 196 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N HISH2 231 " --> pdb=" O GLYH2 227 " (cutoff:3.500A) Processing helix chain 'H2' and resid 234 through 268 removed outlier: 3.799A pdb=" N ALAH2 238 " --> pdb=" O SERH2 234 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N SERH2 241 " --> pdb=" O SERH2 237 " (cutoff:3.500A) Proline residue: H2 256 - end of helix Processing helix chain 'H2' and resid 276 through 286 Processing helix chain 'H2' and resid 288 through 304 removed outlier: 3.757A pdb=" N METH2 292 " --> pdb=" O ASNH2 288 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALAH2 295 " --> pdb=" O VALH2 291 " (cutoff:3.500A) Processing helix chain 'H2' and resid 310 through 327 Processing helix chain 'I2' and resid 22 through 37 Processing helix chain 'I2' and resid 40 through 64 removed outlier: 3.601A pdb=" N LEUI2 44 " --> pdb=" O PROI2 40 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEUI2 46 " --> pdb=" O PHEI2 42 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THRI2 49 " --> pdb=" O ASPI2 45 " (cutoff:3.500A) Processing helix chain 'I2' and resid 73 through 98 removed outlier: 3.887A pdb=" N ILEI2 77 " --> pdb=" O ALAI2 73 " (cutoff:3.500A) Processing helix chain 'I2' and resid 108 through 119 Processing helix chain 'I2' and resid 123 through 140 removed outlier: 6.166A pdb=" N VALI2 129 " --> pdb=" O ILEI2 125 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VALI2 140 " --> pdb=" O ILEI2 136 " (cutoff:3.500A) Processing helix chain 'I2' and resid 140 through 173 removed outlier: 3.527A pdb=" N GLYI2 144 " --> pdb=" O VALI2 140 " (cutoff:3.500A) Proline residue: I2 161 - end of helix Processing helix chain 'I2' and resid 177 through 231 removed outlier: 3.686A pdb=" N ASPI2 199 " --> pdb=" O TYRI2 195 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLYI2 200 " --> pdb=" O GLYI2 196 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N HISI2 231 " --> pdb=" O GLYI2 227 " (cutoff:3.500A) Processing helix chain 'I2' and resid 234 through 268 removed outlier: 3.732A pdb=" N ALAI2 238 " --> pdb=" O SERI2 234 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N SERI2 241 " --> pdb=" O SERI2 237 " (cutoff:3.500A) Proline residue: I2 256 - end of helix Processing helix chain 'I2' and resid 276 through 286 Processing helix chain 'I2' and resid 288 through 304 removed outlier: 3.830A pdb=" N METI2 292 " --> pdb=" O ASNI2 288 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALAI2 295 " --> pdb=" O VALI2 291 " (cutoff:3.500A) Processing helix chain 'I2' and resid 310 through 327 2937 hydrogen bonds defined for protein. 8775 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: 7.17 Time building geometry restraints manager: 4.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 10944 1.34 - 1.46: 5641 1.46 - 1.58: 18706 1.58 - 1.69: 0 1.69 - 1.81: 502 Bond restraints: 35793 Sorted by residual: bond pdb=" C PHEB2 74 " pdb=" N PROB2 75 " ideal model delta sigma weight residual 1.335 1.366 -0.031 1.38e-02 5.25e+03 5.02e+00 bond pdb=" C ILED1 191 " pdb=" N PROD1 192 " ideal model delta sigma weight residual 1.335 1.365 -0.029 1.36e-02 5.41e+03 4.63e+00 bond pdb=" C PHEA2 74 " pdb=" N PROA2 75 " ideal model delta sigma weight residual 1.335 1.361 -0.026 1.38e-02 5.25e+03 3.48e+00 bond pdb=" C PHEH2 74 " pdb=" N PROH2 75 " ideal model delta sigma weight residual 1.335 1.357 -0.022 1.30e-02 5.92e+03 2.79e+00 bond pdb=" CA ILEB1 191 " pdb=" C ILEB1 191 " ideal model delta sigma weight residual 1.523 1.537 -0.014 9.20e-03 1.18e+04 2.29e+00 ... (remaining 35788 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 47691 1.77 - 3.55: 734 3.55 - 5.32: 211 5.32 - 7.10: 29 7.10 - 8.87: 9 Bond angle restraints: 48674 Sorted by residual: angle pdb=" C ILEB1 189 " pdb=" N PHEB1 190 " pdb=" CA PHEB1 190 " ideal model delta sigma weight residual 122.67 114.83 7.84 1.59e+00 3.96e-01 2.43e+01 angle pdb=" N ILEE2 125 " pdb=" CA ILEE2 125 " pdb=" C ILEE2 125 " ideal model delta sigma weight residual 109.30 103.86 5.44 1.25e+00 6.40e-01 1.89e+01 angle pdb=" N VALH2 271 " pdb=" CA VALH2 271 " pdb=" C VALH2 271 " ideal model delta sigma weight residual 112.98 108.17 4.81 1.25e+00 6.40e-01 1.48e+01 angle pdb=" C ILED1 191 " pdb=" CA ILED1 191 " pdb=" CB ILED1 191 " ideal model delta sigma weight residual 113.70 110.39 3.31 9.50e-01 1.11e+00 1.21e+01 angle pdb=" N VALF2 291 " pdb=" CA VALF2 291 " pdb=" C VALF2 291 " ideal model delta sigma weight residual 113.00 109.13 3.87 1.30e+00 5.92e-01 8.84e+00 ... (remaining 48669 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.03: 18859 17.03 - 34.06: 1945 34.06 - 51.09: 362 51.09 - 68.12: 67 68.12 - 85.15: 18 Dihedral angle restraints: 21251 sinusoidal: 8026 harmonic: 13225 Sorted by residual: dihedral pdb=" CA ILEF2 125 " pdb=" C ILEF2 125 " pdb=" N GLYF2 126 " pdb=" CA GLYF2 126 " ideal model delta harmonic sigma weight residual -180.00 -146.26 -33.74 0 5.00e+00 4.00e-02 4.55e+01 dihedral pdb=" CA ILED2 125 " pdb=" C ILED2 125 " pdb=" N GLYD2 126 " pdb=" CA GLYD2 126 " ideal model delta harmonic sigma weight residual 180.00 -148.29 -31.71 0 5.00e+00 4.00e-02 4.02e+01 dihedral pdb=" CA ILEG2 125 " pdb=" C ILEG2 125 " pdb=" N GLYG2 126 " pdb=" CA GLYG2 126 " ideal model delta harmonic sigma weight residual -180.00 -149.48 -30.52 0 5.00e+00 4.00e-02 3.72e+01 ... (remaining 21248 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 4479 0.040 - 0.079: 1272 0.079 - 0.119: 316 0.119 - 0.158: 25 0.158 - 0.198: 2 Chirality restraints: 6094 Sorted by residual: chirality pdb=" CA PHEB1 190 " pdb=" N PHEB1 190 " pdb=" C PHEB1 190 " pdb=" CB PHEB1 190 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.79e-01 chirality pdb=" CA GLNB1 87 " pdb=" N GLNB1 87 " pdb=" C GLNB1 87 " pdb=" CB GLNB1 87 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.75e-01 chirality pdb=" CA ILEE2 125 " pdb=" N ILEE2 125 " pdb=" C ILEE2 125 " pdb=" CB ILEE2 125 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.20e-01 ... (remaining 6091 not shown) Planarity restraints: 5985 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THRH1 2 " -0.036 5.00e-02 4.00e+02 5.50e-02 4.84e+00 pdb=" N PROH1 3 " 0.095 5.00e-02 4.00e+02 pdb=" CA PROH1 3 " -0.028 5.00e-02 4.00e+02 pdb=" CD PROH1 3 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THRJ1 2 " 0.036 5.00e-02 4.00e+02 5.49e-02 4.82e+00 pdb=" N PROJ1 3 " -0.095 5.00e-02 4.00e+02 pdb=" CA PROJ1 3 " 0.028 5.00e-02 4.00e+02 pdb=" CD PROJ1 3 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLYE2 126 " -0.011 2.00e-02 2.50e+03 2.15e-02 4.62e+00 pdb=" C GLYE2 126 " 0.037 2.00e-02 2.50e+03 pdb=" O GLYE2 126 " -0.014 2.00e-02 2.50e+03 pdb=" N ILEE2 127 " -0.013 2.00e-02 2.50e+03 ... (remaining 5982 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 12279 2.86 - 3.37: 39688 3.37 - 3.88: 59795 3.88 - 4.39: 63787 4.39 - 4.90: 109910 Nonbonded interactions: 285459 Sorted by model distance: nonbonded pdb=" O ILED2 235 " pdb=" CB ALAD2 239 " model vdw 2.353 2.768 nonbonded pdb=" O ILEB2 235 " pdb=" CB ALAB2 239 " model vdw 2.354 2.768 nonbonded pdb=" O ILEG2 235 " pdb=" CB ALAG2 239 " model vdw 2.386 2.768 nonbonded pdb=" O ILEC2 235 " pdb=" CB ALAC2 239 " model vdw 2.388 2.768 nonbonded pdb=" O ILEA2 235 " pdb=" CB ALAA2 239 " model vdw 2.412 2.768 ... (remaining 285454 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 'A1' selection = chain 'B1' selection = chain 'C1' selection = chain 'D1' selection = chain 'E1' } ncs_group { reference = chain 'A2' selection = chain 'B2' selection = chain 'C2' selection = chain 'D2' selection = chain 'E2' selection = chain 'F2' selection = chain 'G2' selection = chain 'H2' selection = chain 'I2' } ncs_group { reference = chain 'G1' selection = chain 'H1' selection = chain 'I1' selection = chain 'J1' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 12.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.620 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 31.860 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 35793 Z= 0.135 Angle : 0.614 8.870 48674 Z= 0.331 Chirality : 0.038 0.198 6094 Planarity : 0.005 0.055 5985 Dihedral : 14.250 85.147 12719 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.30 % Favored : 94.66 % Rotamer: Outliers : 0.08 % Allowed : 6.57 % Favored : 93.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1.16 (0.13), residues: 4624 helix: 1.35 (0.09), residues: 3778 sheet: None (None), residues: 0 loop : -1.80 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGG2 206 TYR 0.017 0.001 TYRD2 195 PHE 0.032 0.001 PHEE1 190 TRP 0.008 0.001 TRPK1 165 HIS 0.006 0.001 HISA2 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.13 (35793) covalent geometry : angle 0.61439 / 0.33 (48674) hydrogen bonds : bond 0.09479 / 6.38 ( 2937) hydrogen bonds : angle 5.32090 / 3.82 ( 8775) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1053 residues out of total 3745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1050 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A1 60 MET cc_start: 0.8763 (mmm) cc_final: 0.8455 (mtm) REVERT: A1 61 MET cc_start: 0.8801 (mtp) cc_final: 0.8494 (mtm) REVERT: A1 138 MET cc_start: 0.8183 (mtm) cc_final: 0.7972 (mtp) REVERT: A1 140 ARG cc_start: 0.8364 (mtm110) cc_final: 0.7848 (tpm170) REVERT: A1 209 MET cc_start: 0.8244 (mtt) cc_final: 0.7890 (mtt) REVERT: B1 244 TYR cc_start: 0.8192 (m-80) cc_final: 0.6928 (t80) REVERT: C1 114 GLN cc_start: 0.8917 (tt0) cc_final: 0.8531 (tm-30) REVERT: C1 128 ASP cc_start: 0.7684 (p0) cc_final: 0.7223 (m-30) REVERT: C1 147 LEU cc_start: 0.9430 (tp) cc_final: 0.9142 (tp) REVERT: D1 113 TYR cc_start: 0.7805 (t80) cc_final: 0.7410 (t80) REVERT: D1 152 ARG cc_start: 0.8743 (tpt90) cc_final: 0.7666 (tmt170) REVERT: D1 211 MET cc_start: 0.8310 (mmm) cc_final: 0.7730 (tpp) REVERT: E1 87 GLN cc_start: 0.8741 (mt0) cc_final: 0.8413 (tp40) REVERT: E1 211 MET cc_start: 0.8781 (mmm) cc_final: 0.7690 (mmm) REVERT: F1 9 TRP cc_start: 0.8133 (m100) cc_final: 0.7899 (m-10) REVERT: F1 49 MET cc_start: 0.8633 (mtt) cc_final: 0.8400 (mmm) REVERT: F1 79 LEU cc_start: 0.8719 (mt) cc_final: 0.8478 (mm) REVERT: F1 121 ASN cc_start: 0.9086 (t0) cc_final: 0.8852 (t0) REVERT: F1 228 LEU cc_start: 0.8998 (mt) cc_final: 0.8792 (mm) REVERT: F1 233 MET cc_start: 0.9074 (mmt) cc_final: 0.8814 (mmm) REVERT: G1 45 ASN cc_start: 0.8413 (m110) cc_final: 0.7902 (p0) REVERT: H1 51 PHE cc_start: 0.8607 (t80) cc_final: 0.8283 (t80) REVERT: I1 1 MET cc_start: 0.8887 (ttm) cc_final: 0.8642 (ttm) REVERT: I1 2 THR cc_start: 0.8144 (t) cc_final: 0.7876 (p) REVERT: I1 59 PHE cc_start: 0.8435 (t80) cc_final: 0.8062 (t80) REVERT: J1 56 VAL cc_start: 0.8787 (t) cc_final: 0.8579 (p) REVERT: J1 86 TYR cc_start: 0.8837 (m-80) cc_final: 0.8607 (m-10) REVERT: K1 17 ARG cc_start: 0.9450 (tpm170) cc_final: 0.9233 (tpm170) REVERT: K1 71 MET cc_start: 0.8111 (mmp) cc_final: 0.7882 (tpp) REVERT: K1 73 ASN cc_start: 0.8404 (m110) cc_final: 0.8097 (p0) REVERT: K1 74 ASP cc_start: 0.6884 (t0) cc_final: 0.6481 (m-30) REVERT: K1 172 MET cc_start: 0.9328 (mtm) cc_final: 0.9113 (tpp) REVERT: K1 175 MET cc_start: 0.8985 (mtp) cc_final: 0.8424 (mtp) REVERT: A2 29 LEU cc_start: 0.9191 (tp) cc_final: 0.8934 (tp) REVERT: A2 32 LEU cc_start: 0.8997 (mt) cc_final: 0.8693 (pp) REVERT: A2 225 LEU cc_start: 0.9430 (mt) cc_final: 0.9220 (pp) REVERT: A2 226 VAL cc_start: 0.8683 (m) cc_final: 0.8372 (p) REVERT: B2 57 MET cc_start: 0.8434 (ttt) cc_final: 0.7661 (tpt) REVERT: B2 89 ASN cc_start: 0.7533 (m-40) cc_final: 0.7066 (m110) REVERT: B2 139 MET cc_start: 0.7952 (ptm) cc_final: 0.7123 (tmm) REVERT: B2 312 VAL cc_start: 0.9222 (m) cc_final: 0.8991 (p) REVERT: C2 139 MET cc_start: 0.7667 (ptm) cc_final: 0.6291 (tmm) REVERT: C2 182 LYS cc_start: 0.9064 (tmmt) cc_final: 0.8551 (tptt) REVERT: C2 190 GLN cc_start: 0.8946 (mt0) cc_final: 0.8075 (mm-40) REVERT: C2 191 GLU cc_start: 0.8872 (tm-30) cc_final: 0.8558 (tp30) REVERT: C2 231 HIS cc_start: 0.7906 (m90) cc_final: 0.7291 (m90) REVERT: C2 302 LEU cc_start: 0.8166 (tp) cc_final: 0.7573 (pp) REVERT: C2 308 MET cc_start: 0.9419 (mtp) cc_final: 0.9163 (ppp) REVERT: D2 191 GLU cc_start: 0.9070 (tm-30) cc_final: 0.8828 (tp30) REVERT: D2 217 VAL cc_start: 0.9058 (t) cc_final: 0.8789 (p) REVERT: D2 235 ILE cc_start: 0.8879 (tt) cc_final: 0.8616 (mm) REVERT: E2 28 ILE cc_start: 0.9054 (tp) cc_final: 0.8848 (pt) REVERT: E2 34 MET cc_start: 0.8815 (mtt) cc_final: 0.8578 (mtm) REVERT: E2 276 ASP cc_start: 0.8535 (m-30) cc_final: 0.8061 (t70) REVERT: E2 316 PHE cc_start: 0.9046 (m-80) cc_final: 0.8665 (m-10) REVERT: F2 34 MET cc_start: 0.8878 (mtt) cc_final: 0.8152 (ttm) REVERT: F2 51 ASN cc_start: 0.9200 (t0) cc_final: 0.8944 (t0) REVERT: F2 187 GLU cc_start: 0.9504 (mt-10) cc_final: 0.9107 (tm-30) REVERT: F2 240 GLU cc_start: 0.9191 (pp20) cc_final: 0.8915 (pm20) REVERT: G2 35 MET cc_start: 0.6244 (mtm) cc_final: 0.5999 (mmm) REVERT: G2 37 LEU cc_start: 0.8748 (mm) cc_final: 0.8384 (tt) REVERT: G2 101 HIS cc_start: 0.7936 (p-80) cc_final: 0.7454 (p-80) REVERT: G2 137 ASN cc_start: 0.8069 (t0) cc_final: 0.7457 (t0) REVERT: H2 35 MET cc_start: 0.7661 (mtm) cc_final: 0.7143 (mtp) REVERT: H2 37 LEU cc_start: 0.9136 (tp) cc_final: 0.8703 (tp) REVERT: H2 39 LEU cc_start: 0.8877 (mt) cc_final: 0.8591 (mt) REVERT: H2 139 MET cc_start: 0.8458 (ptm) cc_final: 0.8179 (ptm) REVERT: H2 208 ASP cc_start: 0.6852 (t70) cc_final: 0.6154 (t0) REVERT: H2 233 MET cc_start: 0.6247 (ptp) cc_final: 0.5121 (ppp) REVERT: I2 34 MET cc_start: 0.8861 (mtt) cc_final: 0.8358 (ttp) REVERT: I2 48 PHE cc_start: 0.8451 (m-80) cc_final: 0.8025 (m-80) REVERT: I2 89 ASN cc_start: 0.8957 (m-40) cc_final: 0.8075 (m110) REVERT: I2 143 LYS cc_start: 0.8949 (ptmt) cc_final: 0.8248 (ptmt) REVERT: I2 281 MET cc_start: 0.8398 (mtm) cc_final: 0.8127 (mpp) REVERT: I2 326 TRP cc_start: 0.6292 (t60) cc_final: 0.5877 (t60) outliers start: 3 outliers final: 0 residues processed: 1053 average time/residue: 0.2512 time to fit residues: 413.8160 Evaluate side-chains 667 residues out of total 3745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 667 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 432 optimal weight: 0.8980 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 0.9980 chunk 455 optimal weight: 0.9980 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 chunk 401 optimal weight: 0.8980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1 141 GLN A1 184 GLN ** A1 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1 76 ASN C1 141 GLN D1 86 ASN D1 184 GLN E1 43 GLN E1 141 GLN E1 184 GLN F1 141 ASN A2 51 ASN ** A2 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2 280 GLN B2 172 ASN ** B2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2 172 ASN C2 280 GLN ** C2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 172 ASN D2 280 GLN E2 172 ASN E2 219 ASN ** E2 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2 280 GLN F2 122 ASN ** F2 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F2 288 ASN G2 51 ASN G2 172 ASN G2 280 GLN ** G2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H2 66 GLN H2 172 ASN I2 51 ASN I2 89 ASN I2 172 ASN ** I2 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.055533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.044805 restraints weight = 226987.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.046100 restraints weight = 132788.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.047010 restraints weight = 86886.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.047654 restraints weight = 61545.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.048115 restraints weight = 46388.506| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 35793 Z= 0.173 Angle : 0.735 14.032 48674 Z= 0.367 Chirality : 0.043 0.318 6094 Planarity : 0.005 0.062 5985 Dihedral : 5.150 33.733 4847 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.36 % Favored : 94.59 % Rotamer: Outliers : 0.21 % Allowed : 5.07 % Favored : 94.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.25 (0.13), residues: 4624 helix: 1.45 (0.09), residues: 3772 sheet: None (None), residues: 0 loop : -1.91 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARGF2 85 TYR 0.013 0.001 TYRE1 109 PHE 0.030 0.002 PHEB1 187 TRP 0.018 0.001 TRPK1 47 HIS 0.016 0.002 HISA2 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.17 (35793) covalent geometry : angle 0.73545 / 0.37 (48674) hydrogen bonds : bond 0.04506 / 2.98 ( 2937) hydrogen bonds : angle 4.26287 / 3.05 ( 8775) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 797 residues out of total 3745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 789 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A1 60 MET cc_start: 0.8673 (mmm) cc_final: 0.7096 (mmm) REVERT: A1 111 ASP cc_start: 0.8621 (t70) cc_final: 0.8241 (t0) REVERT: A1 138 MET cc_start: 0.7694 (mtm) cc_final: 0.7378 (mtp) REVERT: A1 140 ARG cc_start: 0.8184 (mtm110) cc_final: 0.7721 (tpm170) REVERT: A1 211 MET cc_start: 0.8905 (mmm) cc_final: 0.8431 (mmp) REVERT: A1 236 MET cc_start: 0.8976 (mmm) cc_final: 0.8459 (mtm) REVERT: B1 211 MET cc_start: 0.7778 (mmm) cc_final: 0.6985 (tpp) REVERT: B1 244 TYR cc_start: 0.8091 (m-80) cc_final: 0.6974 (t80) REVERT: D1 113 TYR cc_start: 0.7282 (t80) cc_final: 0.6996 (t80) REVERT: D1 138 MET cc_start: 0.7925 (ttm) cc_final: 0.7506 (ttm) REVERT: D1 146 ASP cc_start: 0.7755 (p0) cc_final: 0.7536 (p0) REVERT: D1 152 ARG cc_start: 0.8533 (tpt90) cc_final: 0.7519 (tmt170) REVERT: D1 211 MET cc_start: 0.8216 (mmm) cc_final: 0.7827 (tpp) REVERT: E1 146 ASP cc_start: 0.7502 (p0) cc_final: 0.6810 (p0) REVERT: F1 9 TRP cc_start: 0.7952 (m100) cc_final: 0.7693 (m-10) REVERT: F1 233 MET cc_start: 0.8994 (mmt) cc_final: 0.8747 (mmm) REVERT: G1 2 THR cc_start: 0.8054 (p) cc_final: 0.7852 (p) REVERT: G1 8 MET cc_start: 0.8638 (tmm) cc_final: 0.8264 (tmm) REVERT: G1 45 ASN cc_start: 0.8322 (m110) cc_final: 0.7614 (p0) REVERT: K1 17 ARG cc_start: 0.9320 (tpm170) cc_final: 0.9046 (tpm170) REVERT: A2 139 MET cc_start: 0.7871 (tpp) cc_final: 0.7628 (tpp) REVERT: A2 233 MET cc_start: 0.7243 (ppp) cc_final: 0.6288 (ppp) REVERT: B2 57 MET cc_start: 0.8125 (ttt) cc_final: 0.7448 (tpt) REVERT: B2 67 ARG cc_start: 0.8724 (mmp-170) cc_final: 0.8495 (mmp-170) REVERT: B2 139 MET cc_start: 0.7479 (ptm) cc_final: 0.6811 (tmm) REVERT: B2 143 LYS cc_start: 0.9225 (ptmt) cc_final: 0.8907 (ttpp) REVERT: B2 225 LEU cc_start: 0.8933 (mt) cc_final: 0.8663 (pp) REVERT: B2 233 MET cc_start: 0.5364 (ppp) cc_final: 0.4703 (ppp) REVERT: C2 35 MET cc_start: 0.6551 (mtp) cc_final: 0.6316 (mtp) REVERT: C2 101 HIS cc_start: 0.8294 (p-80) cc_final: 0.7522 (p-80) REVERT: C2 139 MET cc_start: 0.7119 (ptm) cc_final: 0.6082 (tmm) REVERT: C2 190 GLN cc_start: 0.8890 (mt0) cc_final: 0.8507 (mt0) REVERT: C2 191 GLU cc_start: 0.8726 (tm-30) cc_final: 0.8259 (tp30) REVERT: C2 302 LEU cc_start: 0.8114 (tp) cc_final: 0.7644 (pp) REVERT: D2 57 MET cc_start: 0.9296 (mmm) cc_final: 0.9035 (mmm) REVERT: D2 139 MET cc_start: 0.8030 (tmm) cc_final: 0.7642 (tpt) REVERT: D2 230 GLN cc_start: 0.8078 (pt0) cc_final: 0.7127 (pt0) REVERT: D2 235 ILE cc_start: 0.8837 (tt) cc_final: 0.8599 (mm) REVERT: E2 28 ILE cc_start: 0.8950 (tp) cc_final: 0.8715 (pt) REVERT: E2 34 MET cc_start: 0.8485 (mtt) cc_final: 0.8064 (mtm) REVERT: E2 57 MET cc_start: 0.8706 (mtm) cc_final: 0.8363 (mtt) REVERT: E2 183 LYS cc_start: 0.9240 (pptt) cc_final: 0.8802 (pttp) REVERT: E2 233 MET cc_start: 0.4474 (ppp) cc_final: 0.3495 (ppp) REVERT: E2 292 MET cc_start: 0.7790 (mpp) cc_final: 0.7571 (mpp) REVERT: E2 316 PHE cc_start: 0.8740 (m-80) cc_final: 0.8273 (m-10) REVERT: F2 39 LEU cc_start: 0.8162 (mm) cc_final: 0.7906 (mm) REVERT: F2 190 GLN cc_start: 0.9196 (tt0) cc_final: 0.8967 (mm-40) REVERT: F2 191 GLU cc_start: 0.9098 (OUTLIER) cc_final: 0.7976 (pm20) REVERT: G2 37 LEU cc_start: 0.8489 (mm) cc_final: 0.8213 (tt) REVERT: G2 137 ASN cc_start: 0.8161 (t0) cc_final: 0.7843 (t0) REVERT: G2 143 LYS cc_start: 0.8570 (ptmt) cc_final: 0.8106 (ptmt) REVERT: G2 182 LYS cc_start: 0.9397 (tmmt) cc_final: 0.9169 (mmmt) REVERT: G2 198 MET cc_start: 0.8676 (mmm) cc_final: 0.8476 (mmm) REVERT: H2 37 LEU cc_start: 0.9139 (tp) cc_final: 0.8758 (tp) REVERT: H2 39 LEU cc_start: 0.8727 (mt) cc_final: 0.8373 (mt) REVERT: H2 96 ILE cc_start: 0.9117 (mm) cc_final: 0.8874 (tt) REVERT: H2 139 MET cc_start: 0.7768 (ptm) cc_final: 0.7164 (ptm) REVERT: H2 147 ARG cc_start: 0.8950 (tpt-90) cc_final: 0.8711 (tpp-160) REVERT: H2 165 MET cc_start: 0.8876 (tpt) cc_final: 0.8621 (mtt) REVERT: H2 233 MET cc_start: 0.4573 (ptp) cc_final: 0.3790 (ppp) REVERT: I2 34 MET cc_start: 0.8527 (mtt) cc_final: 0.8064 (ttp) REVERT: I2 48 PHE cc_start: 0.8475 (m-80) cc_final: 0.8052 (m-80) REVERT: I2 51 ASN cc_start: 0.9194 (OUTLIER) cc_final: 0.8980 (t160) REVERT: I2 89 ASN cc_start: 0.8801 (m110) cc_final: 0.8307 (m110) REVERT: I2 233 MET cc_start: 0.3213 (ptp) cc_final: 0.2550 (ptp) outliers start: 8 outliers final: 2 residues processed: 795 average time/residue: 0.2308 time to fit residues: 291.3697 Evaluate side-chains 618 residues out of total 3745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 614 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 424 optimal weight: 0.8980 chunk 177 optimal weight: 0.8980 chunk 318 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 179 optimal weight: 3.9990 chunk 365 optimal weight: 4.9990 chunk 268 optimal weight: 8.9990 chunk 99 optimal weight: 2.9990 chunk 238 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1 124 GLN A1 132 GLN ** C1 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1 43 GLN ** E1 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2 172 ASN B2 190 GLN ** B2 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2 254 GLN ** B2 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F2 122 ASN F2 284 GLN G2 190 GLN I2 20 GLN I2 137 ASN I2 254 GLN ** I2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.054123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.043538 restraints weight = 228733.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.044784 restraints weight = 134622.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.045656 restraints weight = 88590.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.046262 restraints weight = 63080.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.046724 restraints weight = 48070.080| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 35793 Z= 0.219 Angle : 0.787 13.331 48674 Z= 0.396 Chirality : 0.044 0.313 6094 Planarity : 0.006 0.186 5985 Dihedral : 5.302 32.868 4847 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.28 % Favored : 94.68 % Rotamer: Outliers : 0.08 % Allowed : 5.10 % Favored : 94.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.13), residues: 4624 helix: 1.20 (0.08), residues: 3812 sheet: None (None), residues: 0 loop : -1.99 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARGE2 85 TYR 0.013 0.001 TYRE1 109 PHE 0.040 0.002 PHEB1 187 TRP 0.014 0.001 TRPK1 165 HIS 0.006 0.002 HISH2 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.22 (35793) covalent geometry : angle 0.78739 / 0.40 (48674) hydrogen bonds : bond 0.04807 / 3.17 ( 2937) hydrogen bonds : angle 4.34507 / 3.13 ( 8775) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 733 residues out of total 3745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 730 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A1 60 MET cc_start: 0.8485 (mmm) cc_final: 0.8197 (mmm) REVERT: A1 140 ARG cc_start: 0.8593 (mtm110) cc_final: 0.7817 (tpm170) REVERT: A1 211 MET cc_start: 0.8928 (mmm) cc_final: 0.8714 (mmm) REVERT: B1 210 MET cc_start: 0.8624 (ptm) cc_final: 0.8303 (ptp) REVERT: B1 211 MET cc_start: 0.7851 (mmm) cc_final: 0.7198 (tpp) REVERT: B1 244 TYR cc_start: 0.7843 (m-80) cc_final: 0.7168 (t80) REVERT: C1 123 MET cc_start: 0.7966 (tpp) cc_final: 0.7599 (tpp) REVERT: D1 62 THR cc_start: 0.8143 (p) cc_final: 0.7940 (t) REVERT: D1 113 TYR cc_start: 0.7434 (t80) cc_final: 0.7188 (t80) REVERT: D1 152 ARG cc_start: 0.8442 (tpt90) cc_final: 0.7465 (tmt170) REVERT: D1 236 MET cc_start: 0.8905 (mmp) cc_final: 0.8700 (mmp) REVERT: E1 146 ASP cc_start: 0.7573 (p0) cc_final: 0.6919 (p0) REVERT: E1 211 MET cc_start: 0.8531 (mmm) cc_final: 0.7936 (mmm) REVERT: E1 236 MET cc_start: 0.8688 (mmt) cc_final: 0.8405 (mmt) REVERT: F1 9 TRP cc_start: 0.7955 (m100) cc_final: 0.7491 (m-10) REVERT: F1 228 LEU cc_start: 0.8991 (mm) cc_final: 0.8775 (mm) REVERT: F1 233 MET cc_start: 0.9159 (mmt) cc_final: 0.8825 (mmm) REVERT: G1 45 ASN cc_start: 0.8298 (m110) cc_final: 0.7592 (p0) REVERT: I1 59 PHE cc_start: 0.7776 (t80) cc_final: 0.7449 (t80) REVERT: J1 88 ILE cc_start: 0.8436 (mm) cc_final: 0.8006 (mt) REVERT: A2 139 MET cc_start: 0.7725 (tpp) cc_final: 0.7405 (tpp) REVERT: A2 231 HIS cc_start: 0.8096 (p90) cc_final: 0.7876 (p90) REVERT: A2 233 MET cc_start: 0.7667 (ppp) cc_final: 0.7152 (ppp) REVERT: A2 326 TRP cc_start: 0.3115 (t60) cc_final: 0.2572 (t60) REVERT: B2 30 LEU cc_start: 0.9200 (tp) cc_final: 0.8953 (tp) REVERT: B2 57 MET cc_start: 0.8031 (ttt) cc_final: 0.7404 (tpt) REVERT: B2 139 MET cc_start: 0.7764 (ptm) cc_final: 0.7152 (tmm) REVERT: B2 143 LYS cc_start: 0.9236 (ptmt) cc_final: 0.8973 (ttpp) REVERT: B2 203 LYS cc_start: 0.8802 (mtmm) cc_final: 0.8514 (mttt) REVERT: B2 308 MET cc_start: 0.8228 (mmm) cc_final: 0.7914 (mmm) REVERT: B2 312 VAL cc_start: 0.9015 (m) cc_final: 0.8804 (p) REVERT: C2 57 MET cc_start: 0.7960 (tpt) cc_final: 0.7614 (tpt) REVERT: C2 101 HIS cc_start: 0.8180 (p-80) cc_final: 0.7559 (p-80) REVERT: C2 139 MET cc_start: 0.7267 (ptm) cc_final: 0.6129 (tmm) REVERT: C2 190 GLN cc_start: 0.8899 (mt0) cc_final: 0.8126 (mm-40) REVERT: C2 191 GLU cc_start: 0.8719 (tm-30) cc_final: 0.8316 (tp30) REVERT: C2 230 GLN cc_start: 0.8250 (pt0) cc_final: 0.7840 (pt0) REVERT: C2 231 HIS cc_start: 0.6693 (m90) cc_final: 0.6233 (m90) REVERT: D2 139 MET cc_start: 0.7835 (tmm) cc_final: 0.7548 (tpt) REVERT: D2 235 ILE cc_start: 0.8888 (tt) cc_final: 0.8620 (mm) REVERT: E2 28 ILE cc_start: 0.8919 (tp) cc_final: 0.8691 (pt) REVERT: E2 34 MET cc_start: 0.8457 (mtt) cc_final: 0.7976 (mtm) REVERT: E2 57 MET cc_start: 0.8681 (mtm) cc_final: 0.8296 (mtt) REVERT: E2 139 MET cc_start: 0.8211 (tpp) cc_final: 0.7949 (tpp) REVERT: E2 182 LYS cc_start: 0.9001 (mmtt) cc_final: 0.8588 (mmmt) REVERT: E2 316 PHE cc_start: 0.8711 (m-80) cc_final: 0.8256 (m-10) REVERT: F2 35 MET cc_start: 0.6050 (mmm) cc_final: 0.5796 (mmm) REVERT: F2 39 LEU cc_start: 0.8199 (mm) cc_final: 0.7946 (mm) REVERT: F2 57 MET cc_start: 0.8266 (mmp) cc_final: 0.7956 (mmm) REVERT: F2 139 MET cc_start: 0.8715 (tpp) cc_final: 0.8511 (tpt) REVERT: F2 190 GLN cc_start: 0.9172 (tt0) cc_final: 0.8927 (mm-40) REVERT: F2 203 LYS cc_start: 0.9006 (tppt) cc_final: 0.8626 (tppt) REVERT: G2 37 LEU cc_start: 0.8486 (mm) cc_final: 0.8213 (mm) REVERT: G2 57 MET cc_start: 0.8598 (tpt) cc_final: 0.8341 (tpt) REVERT: G2 137 ASN cc_start: 0.8191 (t0) cc_final: 0.7547 (t0) REVERT: G2 143 LYS cc_start: 0.8585 (ptmt) cc_final: 0.8109 (ptmt) REVERT: G2 216 MET cc_start: 0.8087 (mmm) cc_final: 0.7675 (mmm) REVERT: G2 231 HIS cc_start: 0.6946 (p-80) cc_final: 0.6651 (p-80) REVERT: H2 34 MET cc_start: 0.7500 (ttt) cc_final: 0.7274 (ttt) REVERT: H2 139 MET cc_start: 0.7508 (ptm) cc_final: 0.7296 (ptm) REVERT: H2 143 LYS cc_start: 0.8708 (mmtt) cc_final: 0.8217 (mmtt) REVERT: H2 165 MET cc_start: 0.8885 (tpt) cc_final: 0.8668 (mtt) REVERT: H2 191 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8493 (mm-30) REVERT: H2 233 MET cc_start: 0.4848 (ptp) cc_final: 0.3814 (ppp) REVERT: I2 34 MET cc_start: 0.8517 (mtt) cc_final: 0.8295 (ttt) REVERT: I2 48 PHE cc_start: 0.8454 (m-80) cc_final: 0.7983 (m-80) REVERT: I2 51 ASN cc_start: 0.9016 (m110) cc_final: 0.8681 (t0) REVERT: I2 89 ASN cc_start: 0.8381 (m110) cc_final: 0.7962 (m110) REVERT: I2 233 MET cc_start: 0.2827 (ptp) cc_final: 0.2463 (ptp) outliers start: 3 outliers final: 1 residues processed: 732 average time/residue: 0.2232 time to fit residues: 262.6571 Evaluate side-chains 604 residues out of total 3745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 603 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 398 optimal weight: 8.9990 chunk 373 optimal weight: 1.9990 chunk 349 optimal weight: 1.9990 chunk 357 optimal weight: 0.8980 chunk 453 optimal weight: 1.9990 chunk 421 optimal weight: 0.6980 chunk 307 optimal weight: 8.9990 chunk 180 optimal weight: 0.8980 chunk 231 optimal weight: 0.6980 chunk 220 optimal weight: 1.9990 chunk 392 optimal weight: 10.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C1 184 GLN E1 43 GLN I1 43 GLN K1 122 GLN A2 51 ASN A2 231 HIS ** B2 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2 66 GLN ** E2 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G2 51 ASN G2 190 GLN ** G2 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H2 137 ASN ** I2 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I2 137 ASN I2 190 GLN ** I2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.054861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.044296 restraints weight = 225195.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.045584 restraints weight = 131650.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.046476 restraints weight = 86106.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.047109 restraints weight = 61046.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.047561 restraints weight = 46139.491| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 35793 Z= 0.161 Angle : 0.744 15.090 48674 Z= 0.370 Chirality : 0.042 0.220 6094 Planarity : 0.005 0.072 5985 Dihedral : 5.228 32.973 4847 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.49 % Favored : 94.46 % Rotamer: Outliers : 0.03 % Allowed : 4.03 % Favored : 95.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.04 (0.13), residues: 4624 helix: 1.27 (0.08), residues: 3814 sheet: None (None), residues: 0 loop : -2.01 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARGE2 85 TYR 0.011 0.001 TYRB1 109 PHE 0.036 0.002 PHEI1 59 TRP 0.013 0.001 TRPK1 165 HIS 0.008 0.002 HISE2 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (35793) covalent geometry : angle 0.74409 / 0.37 (48674) hydrogen bonds : bond 0.04425 / 2.92 ( 2937) hydrogen bonds : angle 4.27112 / 3.08 ( 8775) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 3745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 721 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A1 140 ARG cc_start: 0.8390 (mtm110) cc_final: 0.7724 (tpm170) REVERT: A1 211 MET cc_start: 0.8821 (mmm) cc_final: 0.8308 (mmp) REVERT: B1 211 MET cc_start: 0.7921 (mmm) cc_final: 0.7169 (tpp) REVERT: B1 244 TYR cc_start: 0.7721 (m-80) cc_final: 0.7032 (t80) REVERT: C1 123 MET cc_start: 0.7779 (tpp) cc_final: 0.7406 (tpp) REVERT: D1 113 TYR cc_start: 0.7317 (t80) cc_final: 0.7047 (t80) REVERT: D1 152 ARG cc_start: 0.8379 (tpt90) cc_final: 0.7375 (tmt170) REVERT: E1 146 ASP cc_start: 0.7658 (p0) cc_final: 0.6970 (p0) REVERT: E1 211 MET cc_start: 0.8481 (mmm) cc_final: 0.8211 (mmm) REVERT: F1 9 TRP cc_start: 0.7946 (m100) cc_final: 0.7422 (m-10) REVERT: F1 233 MET cc_start: 0.9117 (mmt) cc_final: 0.8883 (tpp) REVERT: G1 45 ASN cc_start: 0.8203 (m110) cc_final: 0.7649 (p0) REVERT: G1 69 MET cc_start: 0.8906 (mtp) cc_final: 0.8704 (mtp) REVERT: J1 88 ILE cc_start: 0.8326 (mm) cc_final: 0.8006 (mt) REVERT: K1 16 HIS cc_start: 0.8875 (t70) cc_final: 0.7765 (t-90) REVERT: K1 20 LYS cc_start: 0.9351 (mmpt) cc_final: 0.8726 (mmmm) REVERT: K1 175 MET cc_start: 0.8422 (mtp) cc_final: 0.8144 (mtp) REVERT: A2 139 MET cc_start: 0.7738 (tpp) cc_final: 0.7384 (tpp) REVERT: A2 187 GLU cc_start: 0.9274 (pt0) cc_final: 0.9054 (pp20) REVERT: A2 206 ARG cc_start: 0.8769 (ttp80) cc_final: 0.8478 (ttp80) REVERT: A2 233 MET cc_start: 0.7543 (ppp) cc_final: 0.6630 (ppp) REVERT: A2 326 TRP cc_start: 0.3257 (t60) cc_final: 0.2706 (t60) REVERT: B2 57 MET cc_start: 0.8072 (ttt) cc_final: 0.7404 (tpt) REVERT: B2 139 MET cc_start: 0.7683 (ptm) cc_final: 0.7209 (tmm) REVERT: B2 203 LYS cc_start: 0.8724 (mtmm) cc_final: 0.8490 (mttt) REVERT: B2 231 HIS cc_start: 0.7099 (p-80) cc_final: 0.6374 (p-80) REVERT: B2 312 VAL cc_start: 0.8989 (m) cc_final: 0.8753 (p) REVERT: C2 35 MET cc_start: 0.6658 (mtp) cc_final: 0.6376 (mmm) REVERT: C2 57 MET cc_start: 0.8016 (tpt) cc_final: 0.7707 (tpt) REVERT: C2 101 HIS cc_start: 0.8208 (p-80) cc_final: 0.7409 (p-80) REVERT: C2 183 LYS cc_start: 0.9341 (pptt) cc_final: 0.9038 (pptt) REVERT: C2 190 GLN cc_start: 0.8915 (mt0) cc_final: 0.8044 (mm-40) REVERT: C2 191 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8375 (tp30) REVERT: C2 230 GLN cc_start: 0.8332 (pt0) cc_final: 0.8109 (pt0) REVERT: C2 231 HIS cc_start: 0.6770 (m90) cc_final: 0.6095 (m90) REVERT: D2 34 MET cc_start: 0.8227 (mtt) cc_final: 0.7905 (mtt) REVERT: D2 139 MET cc_start: 0.7901 (tmm) cc_final: 0.7565 (tmm) REVERT: D2 235 ILE cc_start: 0.8915 (tt) cc_final: 0.8705 (mm) REVERT: D2 275 GLN cc_start: 0.8113 (mt0) cc_final: 0.7656 (mp10) REVERT: E2 28 ILE cc_start: 0.8934 (tp) cc_final: 0.8693 (pt) REVERT: E2 34 MET cc_start: 0.8362 (mtt) cc_final: 0.7846 (mtm) REVERT: E2 57 MET cc_start: 0.8677 (mtm) cc_final: 0.8248 (mtt) REVERT: E2 66 GLN cc_start: 0.8723 (mm110) cc_final: 0.8468 (mm-40) REVERT: E2 139 MET cc_start: 0.8171 (tpp) cc_final: 0.7838 (tpp) REVERT: E2 182 LYS cc_start: 0.9012 (mmtt) cc_final: 0.8635 (mmmt) REVERT: E2 233 MET cc_start: 0.4610 (ppp) cc_final: 0.3263 (ppp) REVERT: E2 302 LEU cc_start: 0.8268 (tp) cc_final: 0.7862 (mt) REVERT: E2 316 PHE cc_start: 0.8684 (m-80) cc_final: 0.8239 (m-10) REVERT: F2 57 MET cc_start: 0.8337 (mmp) cc_final: 0.7986 (mmm) REVERT: F2 139 MET cc_start: 0.8751 (tpp) cc_final: 0.8486 (tpt) REVERT: F2 203 LYS cc_start: 0.9029 (tppt) cc_final: 0.8811 (tppt) REVERT: G2 37 LEU cc_start: 0.8355 (mm) cc_final: 0.8077 (mm) REVERT: G2 57 MET cc_start: 0.8756 (tpt) cc_final: 0.8503 (tpt) REVERT: G2 137 ASN cc_start: 0.8166 (t0) cc_final: 0.7825 (t0) REVERT: G2 198 MET cc_start: 0.8822 (mmm) cc_final: 0.8521 (mmm) REVERT: G2 233 MET cc_start: 0.4994 (ppp) cc_final: 0.4509 (ppp) REVERT: G2 308 MET cc_start: 0.8790 (ppp) cc_final: 0.8137 (ppp) REVERT: H2 165 MET cc_start: 0.8914 (tpt) cc_final: 0.8704 (mtt) REVERT: H2 191 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8563 (mm-30) REVERT: I2 48 PHE cc_start: 0.8497 (m-80) cc_final: 0.8040 (m-80) REVERT: I2 89 ASN cc_start: 0.8517 (m110) cc_final: 0.8021 (m110) REVERT: I2 233 MET cc_start: 0.2398 (ptp) cc_final: -0.0082 (ptm) outliers start: 1 outliers final: 1 residues processed: 721 average time/residue: 0.2277 time to fit residues: 262.3151 Evaluate side-chains 592 residues out of total 3745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 591 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 376 optimal weight: 0.9980 chunk 413 optimal weight: 0.8980 chunk 191 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 211 optimal weight: 5.9990 chunk 380 optimal weight: 1.9990 chunk 435 optimal weight: 0.7980 chunk 159 optimal weight: 0.9980 chunk 115 optimal weight: 0.0370 chunk 195 optimal weight: 0.8980 chunk 218 optimal weight: 3.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B2 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2 190 GLN ** E2 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2 275 GLN F2 231 HIS ** F2 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H2 89 ASN H2 116 HIS I2 51 ASN I2 288 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.055632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.045046 restraints weight = 225653.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.046334 restraints weight = 132103.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.047234 restraints weight = 86581.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.047861 restraints weight = 61438.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.048329 restraints weight = 46721.084| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35793 Z= 0.150 Angle : 0.728 14.442 48674 Z= 0.361 Chirality : 0.042 0.222 6094 Planarity : 0.005 0.067 5985 Dihedral : 5.138 32.670 4847 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.32 % Favored : 94.64 % Rotamer: Outliers : 0.03 % Allowed : 2.67 % Favored : 97.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.12 (0.13), residues: 4624 helix: 1.30 (0.08), residues: 3824 sheet: None (None), residues: 0 loop : -1.87 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARGF1 174 TYR 0.019 0.001 TYRE2 195 PHE 0.027 0.002 PHEB2 114 TRP 0.022 0.001 TRPK1 168 HIS 0.019 0.002 HISH2 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.15 (35793) covalent geometry : angle 0.72787 / 0.36 (48674) hydrogen bonds : bond 0.04229 / 2.80 ( 2937) hydrogen bonds : angle 4.18321 / 3.01 ( 8775) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 719 residues out of total 3745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 718 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A1 140 ARG cc_start: 0.8477 (mtm110) cc_final: 0.7748 (tpm170) REVERT: A1 211 MET cc_start: 0.8815 (mmm) cc_final: 0.8340 (mmp) REVERT: B1 210 MET cc_start: 0.8411 (ptm) cc_final: 0.8025 (ptp) REVERT: B1 211 MET cc_start: 0.7626 (mmm) cc_final: 0.7211 (tpp) REVERT: B1 244 TYR cc_start: 0.7540 (m-80) cc_final: 0.7066 (t80) REVERT: C1 120 LYS cc_start: 0.9108 (ptpt) cc_final: 0.8855 (pttt) REVERT: C1 123 MET cc_start: 0.7864 (tpp) cc_final: 0.7566 (tpp) REVERT: D1 152 ARG cc_start: 0.8371 (tpt90) cc_final: 0.7439 (tmt170) REVERT: D1 210 MET cc_start: 0.8606 (ppp) cc_final: 0.7566 (ppp) REVERT: E1 146 ASP cc_start: 0.7463 (p0) cc_final: 0.6709 (p0) REVERT: E1 205 MET cc_start: 0.8435 (mmm) cc_final: 0.8216 (mmm) REVERT: F1 9 TRP cc_start: 0.7922 (m100) cc_final: 0.7472 (m-10) REVERT: F1 233 MET cc_start: 0.9161 (mmt) cc_final: 0.8850 (mmm) REVERT: G1 45 ASN cc_start: 0.8251 (m110) cc_final: 0.7562 (p0) REVERT: I1 86 TYR cc_start: 0.8467 (m-10) cc_final: 0.8205 (m-10) REVERT: J1 88 ILE cc_start: 0.8271 (mm) cc_final: 0.7978 (mt) REVERT: K1 68 ASP cc_start: 0.7914 (p0) cc_final: 0.7449 (m-30) REVERT: K1 141 GLN cc_start: 0.8383 (mp10) cc_final: 0.8073 (tp40) REVERT: K1 148 LYS cc_start: 0.7448 (tppt) cc_final: 0.7000 (tppt) REVERT: A2 139 MET cc_start: 0.7734 (tpp) cc_final: 0.7437 (tpp) REVERT: A2 187 GLU cc_start: 0.9236 (pt0) cc_final: 0.9020 (pp20) REVERT: A2 206 ARG cc_start: 0.8777 (ttp80) cc_final: 0.8509 (ttp80) REVERT: A2 233 MET cc_start: 0.7405 (ppp) cc_final: 0.6586 (ppp) REVERT: A2 326 TRP cc_start: 0.3275 (t60) cc_final: 0.2686 (t60) REVERT: B2 30 LEU cc_start: 0.9171 (tp) cc_final: 0.8913 (tp) REVERT: B2 57 MET cc_start: 0.8009 (ttt) cc_final: 0.7487 (tpt) REVERT: B2 139 MET cc_start: 0.7668 (ptm) cc_final: 0.7175 (tmm) REVERT: B2 187 GLU cc_start: 0.8748 (pt0) cc_final: 0.8448 (pp20) REVERT: B2 216 MET cc_start: 0.8417 (mmt) cc_final: 0.8190 (mmt) REVERT: B2 312 VAL cc_start: 0.8899 (m) cc_final: 0.8451 (p) REVERT: C2 57 MET cc_start: 0.7980 (tpt) cc_final: 0.7682 (tpt) REVERT: C2 101 HIS cc_start: 0.8150 (p-80) cc_final: 0.7219 (p-80) REVERT: C2 139 MET cc_start: 0.6943 (ptm) cc_final: 0.6008 (tmm) REVERT: C2 183 LYS cc_start: 0.9376 (pptt) cc_final: 0.9101 (pptt) REVERT: C2 190 GLN cc_start: 0.8892 (mt0) cc_final: 0.8539 (mt0) REVERT: C2 191 GLU cc_start: 0.8645 (tm-30) cc_final: 0.8277 (tp30) REVERT: C2 230 GLN cc_start: 0.8234 (pt0) cc_final: 0.7937 (pt0) REVERT: C2 231 HIS cc_start: 0.6446 (m90) cc_final: 0.5656 (m90) REVERT: D2 34 MET cc_start: 0.8182 (mtt) cc_final: 0.7875 (mtt) REVERT: D2 139 MET cc_start: 0.7876 (tmm) cc_final: 0.7658 (tmm) REVERT: D2 230 GLN cc_start: 0.8730 (tm-30) cc_final: 0.8496 (tm-30) REVERT: D2 233 MET cc_start: 0.2925 (ptm) cc_final: 0.2679 (ptm) REVERT: E2 28 ILE cc_start: 0.8873 (tp) cc_final: 0.8646 (pt) REVERT: E2 34 MET cc_start: 0.8366 (mtt) cc_final: 0.7905 (mtm) REVERT: E2 39 LEU cc_start: 0.8014 (mt) cc_final: 0.7747 (mt) REVERT: E2 57 MET cc_start: 0.8611 (mtm) cc_final: 0.8254 (mtt) REVERT: E2 66 GLN cc_start: 0.8628 (mm110) cc_final: 0.8390 (mm-40) REVERT: E2 139 MET cc_start: 0.8273 (tpp) cc_final: 0.7929 (tpp) REVERT: E2 182 LYS cc_start: 0.8992 (mmtt) cc_final: 0.8652 (mmmt) REVERT: E2 302 LEU cc_start: 0.8207 (tp) cc_final: 0.7713 (mt) REVERT: E2 316 PHE cc_start: 0.8618 (m-80) cc_final: 0.8196 (m-10) REVERT: F2 34 MET cc_start: 0.8676 (mtt) cc_final: 0.8117 (mmm) REVERT: F2 57 MET cc_start: 0.8338 (mmp) cc_final: 0.7981 (mmm) REVERT: F2 139 MET cc_start: 0.8695 (tpp) cc_final: 0.8381 (tpt) REVERT: F2 190 GLN cc_start: 0.9295 (tt0) cc_final: 0.8997 (tp40) REVERT: F2 203 LYS cc_start: 0.9012 (tppt) cc_final: 0.8804 (tppt) REVERT: G2 37 LEU cc_start: 0.8391 (mm) cc_final: 0.8139 (mm) REVERT: G2 57 MET cc_start: 0.8723 (tpt) cc_final: 0.8468 (tpt) REVERT: G2 137 ASN cc_start: 0.8050 (t0) cc_final: 0.7776 (t0) REVERT: G2 216 MET cc_start: 0.7985 (mmm) cc_final: 0.7762 (mmm) REVERT: G2 308 MET cc_start: 0.8674 (ppp) cc_final: 0.8302 (ppp) REVERT: H2 30 LEU cc_start: 0.9115 (tt) cc_final: 0.8864 (pp) REVERT: I2 34 MET cc_start: 0.8725 (mtt) cc_final: 0.8240 (ttp) REVERT: I2 48 PHE cc_start: 0.8358 (m-80) cc_final: 0.7975 (m-80) REVERT: I2 89 ASN cc_start: 0.8490 (m110) cc_final: 0.8093 (m110) REVERT: I2 143 LYS cc_start: 0.9045 (ptmm) cc_final: 0.8822 (ptmm) REVERT: I2 216 MET cc_start: 0.7966 (tmm) cc_final: 0.7716 (tmm) REVERT: I2 233 MET cc_start: 0.2320 (ptp) cc_final: 0.2095 (ptm) outliers start: 1 outliers final: 1 residues processed: 718 average time/residue: 0.2265 time to fit residues: 259.3618 Evaluate side-chains 579 residues out of total 3745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 578 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 92 optimal weight: 2.9990 chunk 75 optimal weight: 0.0670 chunk 87 optimal weight: 5.9990 chunk 140 optimal weight: 0.6980 chunk 299 optimal weight: 5.9990 chunk 297 optimal weight: 4.9990 chunk 141 optimal weight: 0.8980 chunk 215 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 347 optimal weight: 2.9990 chunk 191 optimal weight: 0.9980 overall best weight: 0.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1 184 GLN D1 233 GLN H1 39 GLN I1 39 GLN A2 66 GLN A2 172 ASN B2 230 GLN ** B2 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2 230 GLN ** F2 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G2 51 ASN H2 116 HIS ** H2 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.055028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.044472 restraints weight = 225090.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.045772 restraints weight = 131606.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.046671 restraints weight = 85926.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.047300 restraints weight = 60748.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.047759 restraints weight = 45960.123| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.4382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 35793 Z= 0.155 Angle : 0.738 11.525 48674 Z= 0.366 Chirality : 0.042 0.210 6094 Planarity : 0.005 0.066 5985 Dihedral : 5.119 32.930 4847 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.56 % Favored : 94.40 % Rotamer: Outliers : 0.08 % Allowed : 2.75 % Favored : 97.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.10 (0.13), residues: 4624 helix: 1.27 (0.08), residues: 3833 sheet: None (None), residues: 0 loop : -1.82 (0.22), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARGE2 85 TYR 0.010 0.001 TYRB1 109 PHE 0.033 0.002 PHEI1 59 TRP 0.014 0.001 TRPK1 165 HIS 0.016 0.002 HISH2 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.16 (35793) covalent geometry : angle 0.73848 / 0.37 (48674) hydrogen bonds : bond 0.04237 / 2.81 ( 2937) hydrogen bonds : angle 4.16633 / 3.00 ( 8775) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 708 residues out of total 3745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 705 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A1 140 ARG cc_start: 0.8602 (mtm110) cc_final: 0.7778 (tpm170) REVERT: A1 211 MET cc_start: 0.8833 (mmm) cc_final: 0.8285 (mmp) REVERT: B1 101 MET cc_start: 0.8783 (mmm) cc_final: 0.8492 (mmp) REVERT: B1 107 LYS cc_start: 0.8721 (pttt) cc_final: 0.8499 (pttm) REVERT: B1 211 MET cc_start: 0.7516 (mmm) cc_final: 0.7112 (tpp) REVERT: B1 244 TYR cc_start: 0.7513 (m-80) cc_final: 0.6980 (t80) REVERT: C1 123 MET cc_start: 0.7870 (tpp) cc_final: 0.7515 (tpp) REVERT: C1 211 MET cc_start: 0.8802 (mmt) cc_final: 0.8325 (mmm) REVERT: D1 152 ARG cc_start: 0.8383 (tpt90) cc_final: 0.7455 (tmt170) REVERT: D1 211 MET cc_start: 0.8249 (tpp) cc_final: 0.8045 (tpp) REVERT: E1 138 MET cc_start: 0.7321 (mmt) cc_final: 0.7003 (mmt) REVERT: E1 146 ASP cc_start: 0.7518 (p0) cc_final: 0.6831 (p0) REVERT: E1 236 MET cc_start: 0.8761 (mmt) cc_final: 0.8511 (mmt) REVERT: F1 9 TRP cc_start: 0.7937 (m100) cc_final: 0.7485 (m-10) REVERT: F1 75 MET cc_start: 0.8416 (mmp) cc_final: 0.7233 (ptm) REVERT: F1 233 MET cc_start: 0.9108 (mmt) cc_final: 0.8844 (mmm) REVERT: G1 45 ASN cc_start: 0.8262 (m110) cc_final: 0.7833 (p0) REVERT: J1 88 ILE cc_start: 0.8222 (mm) cc_final: 0.7968 (mt) REVERT: K1 19 GLU cc_start: 0.8826 (mp0) cc_final: 0.8560 (pm20) REVERT: K1 68 ASP cc_start: 0.7768 (p0) cc_final: 0.7401 (m-30) REVERT: A2 139 MET cc_start: 0.7760 (tpp) cc_final: 0.7425 (tpp) REVERT: A2 187 GLU cc_start: 0.9232 (pt0) cc_final: 0.9003 (pp20) REVERT: B2 30 LEU cc_start: 0.9190 (tp) cc_final: 0.8958 (tp) REVERT: B2 57 MET cc_start: 0.8107 (ttt) cc_final: 0.7485 (tpt) REVERT: B2 98 MET cc_start: 0.8095 (ppp) cc_final: 0.7885 (mmt) REVERT: B2 139 MET cc_start: 0.7581 (ptm) cc_final: 0.7197 (tmm) REVERT: B2 187 GLU cc_start: 0.8735 (pt0) cc_final: 0.8406 (pp20) REVERT: B2 312 VAL cc_start: 0.8809 (m) cc_final: 0.8603 (p) REVERT: C2 57 MET cc_start: 0.7888 (tpt) cc_final: 0.7630 (tpt) REVERT: C2 63 MET cc_start: 0.7907 (tpt) cc_final: 0.7628 (tpp) REVERT: C2 101 HIS cc_start: 0.8126 (p-80) cc_final: 0.7165 (p-80) REVERT: C2 183 LYS cc_start: 0.9347 (pptt) cc_final: 0.9126 (pptt) REVERT: C2 190 GLN cc_start: 0.8908 (mt0) cc_final: 0.8571 (mt0) REVERT: C2 191 GLU cc_start: 0.8619 (tm-30) cc_final: 0.8252 (tp30) REVERT: C2 230 GLN cc_start: 0.8265 (pt0) cc_final: 0.7980 (pt0) REVERT: C2 231 HIS cc_start: 0.6339 (m90) cc_final: 0.5598 (m90) REVERT: D2 34 MET cc_start: 0.8182 (mtt) cc_final: 0.7806 (mtt) REVERT: D2 275 GLN cc_start: 0.8117 (mt0) cc_final: 0.7663 (mp10) REVERT: E2 28 ILE cc_start: 0.8925 (tp) cc_final: 0.8712 (pt) REVERT: E2 34 MET cc_start: 0.8382 (mtt) cc_final: 0.7927 (mtm) REVERT: E2 39 LEU cc_start: 0.7947 (mt) cc_final: 0.7641 (mt) REVERT: E2 57 MET cc_start: 0.8552 (mtm) cc_final: 0.8243 (mtt) REVERT: E2 66 GLN cc_start: 0.8600 (mm110) cc_final: 0.8378 (mm-40) REVERT: E2 139 MET cc_start: 0.8265 (tpp) cc_final: 0.7932 (tpp) REVERT: E2 182 LYS cc_start: 0.9038 (mmtt) cc_final: 0.8622 (mmmt) REVERT: E2 316 PHE cc_start: 0.8586 (m-80) cc_final: 0.8155 (m-10) REVERT: F2 34 MET cc_start: 0.8707 (mtt) cc_final: 0.8230 (mmp) REVERT: F2 57 MET cc_start: 0.8336 (mmp) cc_final: 0.7962 (mmm) REVERT: F2 139 MET cc_start: 0.8589 (tpp) cc_final: 0.8248 (tpt) REVERT: F2 190 GLN cc_start: 0.9293 (tt0) cc_final: 0.9083 (tp40) REVERT: F2 304 MET cc_start: 0.6925 (tmm) cc_final: 0.6687 (tmm) REVERT: G2 37 LEU cc_start: 0.8388 (mm) cc_final: 0.8148 (mm) REVERT: G2 137 ASN cc_start: 0.8021 (t0) cc_final: 0.7725 (t0) REVERT: G2 198 MET cc_start: 0.8899 (mmm) cc_final: 0.8612 (mmm) REVERT: G2 216 MET cc_start: 0.7980 (mmm) cc_final: 0.7574 (mmm) REVERT: G2 230 GLN cc_start: 0.8048 (pp30) cc_final: 0.7577 (pp30) REVERT: G2 308 MET cc_start: 0.8669 (ppp) cc_final: 0.8378 (ppp) REVERT: I2 34 MET cc_start: 0.8762 (mtt) cc_final: 0.8484 (ttm) REVERT: I2 37 LEU cc_start: 0.7688 (tt) cc_final: 0.6528 (mp) REVERT: I2 48 PHE cc_start: 0.8335 (m-80) cc_final: 0.7833 (m-80) REVERT: I2 51 ASN cc_start: 0.8956 (m110) cc_final: 0.8740 (m-40) REVERT: I2 63 MET cc_start: 0.7739 (ptm) cc_final: 0.7219 (ttt) REVERT: I2 89 ASN cc_start: 0.8501 (m110) cc_final: 0.8160 (m110) REVERT: I2 143 LYS cc_start: 0.9020 (ptmm) cc_final: 0.8794 (ptmm) REVERT: I2 216 MET cc_start: 0.7943 (tmm) cc_final: 0.7695 (tmm) outliers start: 3 outliers final: 0 residues processed: 706 average time/residue: 0.2238 time to fit residues: 252.0080 Evaluate side-chains 583 residues out of total 3745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 583 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 308 optimal weight: 1.9990 chunk 389 optimal weight: 6.9990 chunk 224 optimal weight: 3.9990 chunk 301 optimal weight: 5.9990 chunk 278 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 383 optimal weight: 5.9990 chunk 431 optimal weight: 0.5980 chunk 17 optimal weight: 0.0060 chunk 306 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.0600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F1 61 ASN K1 141 GLN A2 51 ASN ** B2 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F2 284 GLN H2 116 HIS ** H2 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.055041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.044500 restraints weight = 226905.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.045778 restraints weight = 132622.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.046663 restraints weight = 86713.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.047295 restraints weight = 61568.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.047747 restraints weight = 46474.974| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.4573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 35793 Z= 0.159 Angle : 0.764 14.040 48674 Z= 0.376 Chirality : 0.042 0.208 6094 Planarity : 0.005 0.065 5985 Dihedral : 5.115 33.188 4847 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.38 % Favored : 94.57 % Rotamer: Outliers : 0.05 % Allowed : 2.00 % Favored : 97.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.11 (0.13), residues: 4624 helix: 1.28 (0.08), residues: 3826 sheet: None (None), residues: 0 loop : -1.81 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARGA2 85 TYR 0.022 0.001 TYRE1 109 PHE 0.035 0.002 PHEA2 204 TRP 0.013 0.001 TRPK1 165 HIS 0.017 0.002 HISH2 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 (35793) covalent geometry : angle 0.76437 / 0.38 (48674) hydrogen bonds : bond 0.04251 / 2.82 ( 2937) hydrogen bonds : angle 4.18913 / 3.01 ( 8775) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 3745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 699 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A1 123 MET cc_start: 0.8631 (ppp) cc_final: 0.7879 (ppp) REVERT: A1 140 ARG cc_start: 0.8675 (mtm110) cc_final: 0.7773 (tpm170) REVERT: A1 211 MET cc_start: 0.8876 (mmm) cc_final: 0.8324 (mmp) REVERT: B1 101 MET cc_start: 0.8753 (mmm) cc_final: 0.8499 (mmp) REVERT: B1 107 LYS cc_start: 0.8727 (pttt) cc_final: 0.8513 (pttm) REVERT: B1 211 MET cc_start: 0.7447 (mmm) cc_final: 0.7017 (tpp) REVERT: B1 244 TYR cc_start: 0.7692 (m-80) cc_final: 0.7007 (t80) REVERT: C1 123 MET cc_start: 0.7884 (tpp) cc_final: 0.7654 (tpp) REVERT: C1 211 MET cc_start: 0.8781 (mmt) cc_final: 0.8326 (mmm) REVERT: D1 152 ARG cc_start: 0.8365 (tpt90) cc_final: 0.7426 (tmt170) REVERT: E1 138 MET cc_start: 0.7455 (mmt) cc_final: 0.7155 (mmt) REVERT: E1 140 ARG cc_start: 0.8230 (tpp-160) cc_final: 0.8001 (tpp-160) REVERT: E1 146 ASP cc_start: 0.7867 (p0) cc_final: 0.7615 (p0) REVERT: E1 205 MET cc_start: 0.7893 (mmm) cc_final: 0.7662 (tpp) REVERT: F1 9 TRP cc_start: 0.7962 (m100) cc_final: 0.7503 (m-10) REVERT: F1 119 HIS cc_start: 0.8216 (p-80) cc_final: 0.7940 (p-80) REVERT: F1 233 MET cc_start: 0.9103 (mmt) cc_final: 0.8817 (mmm) REVERT: G1 45 ASN cc_start: 0.8094 (m110) cc_final: 0.7386 (p0) REVERT: H1 1 MET cc_start: 0.8489 (ttm) cc_final: 0.8082 (ttm) REVERT: I1 39 GLN cc_start: 0.7892 (mm-40) cc_final: 0.7572 (mm110) REVERT: K1 68 ASP cc_start: 0.7827 (p0) cc_final: 0.7472 (m-30) REVERT: K1 175 MET cc_start: 0.8555 (tpp) cc_final: 0.8329 (tpp) REVERT: A2 139 MET cc_start: 0.7877 (tpp) cc_final: 0.7491 (tpp) REVERT: A2 206 ARG cc_start: 0.8892 (ttp80) cc_final: 0.8411 (ttp80) REVERT: B2 30 LEU cc_start: 0.9181 (tp) cc_final: 0.8960 (tp) REVERT: B2 57 MET cc_start: 0.8168 (ttt) cc_final: 0.7496 (tpt) REVERT: B2 94 ARG cc_start: 0.8499 (tmm160) cc_final: 0.8295 (tmm160) REVERT: B2 139 MET cc_start: 0.7661 (ptm) cc_final: 0.7269 (tmm) REVERT: B2 187 GLU cc_start: 0.8814 (pt0) cc_final: 0.8474 (pp20) REVERT: B2 312 VAL cc_start: 0.8766 (m) cc_final: 0.8563 (p) REVERT: C2 57 MET cc_start: 0.7891 (tpt) cc_final: 0.7660 (tpt) REVERT: C2 63 MET cc_start: 0.7957 (tpt) cc_final: 0.7675 (tpp) REVERT: C2 101 HIS cc_start: 0.8183 (p-80) cc_final: 0.6984 (p-80) REVERT: C2 139 MET cc_start: 0.6474 (ppp) cc_final: 0.6015 (tmm) REVERT: C2 190 GLN cc_start: 0.8908 (mt0) cc_final: 0.8579 (mt0) REVERT: C2 191 GLU cc_start: 0.8644 (tm-30) cc_final: 0.8266 (tp30) REVERT: C2 231 HIS cc_start: 0.6464 (m90) cc_final: 0.5866 (m90) REVERT: D2 34 MET cc_start: 0.8159 (mtt) cc_final: 0.7832 (mtt) REVERT: D2 98 MET cc_start: 0.7961 (ptt) cc_final: 0.7677 (ptt) REVERT: D2 139 MET cc_start: 0.7853 (tmm) cc_final: 0.7420 (tmm) REVERT: D2 275 GLN cc_start: 0.7958 (mt0) cc_final: 0.7577 (mp10) REVERT: E2 28 ILE cc_start: 0.8944 (tp) cc_final: 0.8713 (pt) REVERT: E2 34 MET cc_start: 0.8419 (mtt) cc_final: 0.7939 (mtm) REVERT: E2 39 LEU cc_start: 0.7935 (mt) cc_final: 0.7653 (mt) REVERT: E2 57 MET cc_start: 0.8532 (mtm) cc_final: 0.8109 (mtt) REVERT: E2 139 MET cc_start: 0.8262 (tpp) cc_final: 0.7946 (tpp) REVERT: E2 182 LYS cc_start: 0.9009 (mmtt) cc_final: 0.8389 (mmmt) REVERT: E2 302 LEU cc_start: 0.8154 (tp) cc_final: 0.7732 (mt) REVERT: E2 316 PHE cc_start: 0.8544 (m-80) cc_final: 0.8069 (m-10) REVERT: F2 57 MET cc_start: 0.8357 (mmp) cc_final: 0.7983 (mmm) REVERT: F2 139 MET cc_start: 0.8649 (tpp) cc_final: 0.8286 (tpt) REVERT: F2 190 GLN cc_start: 0.9274 (tt0) cc_final: 0.9025 (tp40) REVERT: F2 304 MET cc_start: 0.6944 (tmm) cc_final: 0.6675 (tmm) REVERT: G2 37 LEU cc_start: 0.8294 (mm) cc_final: 0.8061 (mm) REVERT: G2 137 ASN cc_start: 0.8117 (t0) cc_final: 0.7787 (t0) REVERT: G2 216 MET cc_start: 0.8000 (mmm) cc_final: 0.7631 (mmm) REVERT: G2 308 MET cc_start: 0.8684 (ppp) cc_final: 0.8481 (ppp) REVERT: H2 30 LEU cc_start: 0.9112 (tt) cc_final: 0.8813 (pp) REVERT: I2 89 ASN cc_start: 0.8500 (m110) cc_final: 0.8140 (m110) REVERT: I2 233 MET cc_start: 0.1555 (ptm) cc_final: 0.0430 (ptm) outliers start: 2 outliers final: 1 residues processed: 699 average time/residue: 0.2238 time to fit residues: 249.8140 Evaluate side-chains 582 residues out of total 3745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 581 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 193 optimal weight: 6.9990 chunk 150 optimal weight: 0.8980 chunk 241 optimal weight: 4.9990 chunk 224 optimal weight: 5.9990 chunk 168 optimal weight: 0.2980 chunk 11 optimal weight: 0.6980 chunk 405 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F1 61 ASN ** B2 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2 275 GLN ** B2 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2 190 GLN E2 230 GLN F2 231 HIS G2 51 ASN H2 116 HIS ** H2 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.055524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.045000 restraints weight = 226460.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.046293 restraints weight = 132316.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.047183 restraints weight = 86295.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.047799 restraints weight = 61133.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.048260 restraints weight = 46472.871| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.4764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35793 Z= 0.151 Angle : 0.773 11.188 48674 Z= 0.381 Chirality : 0.042 0.277 6094 Planarity : 0.005 0.066 5985 Dihedral : 5.092 33.023 4847 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.28 % Favored : 94.68 % Rotamer: Outliers : 0.05 % Allowed : 1.42 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.13 (0.13), residues: 4624 helix: 1.30 (0.08), residues: 3829 sheet: None (None), residues: 0 loop : -1.82 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARGK1 173 TYR 0.012 0.001 TYRE1 109 PHE 0.030 0.002 PHEH1 59 TRP 0.020 0.001 TRPK1 168 HIS 0.016 0.002 HISH2 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (35793) covalent geometry : angle 0.77349 / 0.38 (48674) hydrogen bonds : bond 0.04220 / 2.79 ( 2937) hydrogen bonds : angle 4.20774 / 3.03 ( 8775) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 3745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 708 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A1 123 MET cc_start: 0.8715 (ppp) cc_final: 0.8371 (ppp) REVERT: A1 140 ARG cc_start: 0.8871 (mtm110) cc_final: 0.7781 (tpm170) REVERT: A1 211 MET cc_start: 0.8830 (mmm) cc_final: 0.8340 (mmp) REVERT: B1 101 MET cc_start: 0.8797 (mmm) cc_final: 0.8573 (mmp) REVERT: B1 107 LYS cc_start: 0.8685 (pttt) cc_final: 0.8466 (pttm) REVERT: B1 211 MET cc_start: 0.7514 (mmm) cc_final: 0.7028 (tpp) REVERT: B1 244 TYR cc_start: 0.7779 (m-80) cc_final: 0.7006 (t80) REVERT: C1 123 MET cc_start: 0.7851 (tpp) cc_final: 0.7552 (tpp) REVERT: C1 205 MET cc_start: 0.8289 (tpp) cc_final: 0.7966 (tpp) REVERT: C1 211 MET cc_start: 0.8813 (mmt) cc_final: 0.8347 (mmm) REVERT: D1 152 ARG cc_start: 0.8322 (tpt90) cc_final: 0.7392 (tmt170) REVERT: D1 211 MET cc_start: 0.8501 (tpp) cc_final: 0.8106 (tpp) REVERT: E1 57 ILE cc_start: 0.9010 (mm) cc_final: 0.8704 (tt) REVERT: E1 138 MET cc_start: 0.7290 (mmt) cc_final: 0.7051 (mmt) REVERT: E1 140 ARG cc_start: 0.8313 (tpp-160) cc_final: 0.8102 (tpp-160) REVERT: E1 146 ASP cc_start: 0.8034 (p0) cc_final: 0.7736 (p0) REVERT: F1 9 TRP cc_start: 0.8004 (m100) cc_final: 0.7449 (m-10) REVERT: F1 75 MET cc_start: 0.8428 (mmp) cc_final: 0.7317 (ptm) REVERT: F1 119 HIS cc_start: 0.8357 (p-80) cc_final: 0.8109 (p-80) REVERT: F1 185 MET cc_start: 0.8112 (tpt) cc_final: 0.7843 (tpt) REVERT: F1 233 MET cc_start: 0.9120 (mmt) cc_final: 0.8807 (mmm) REVERT: G1 45 ASN cc_start: 0.8042 (m110) cc_final: 0.7419 (p0) REVERT: K1 68 ASP cc_start: 0.7900 (p0) cc_final: 0.7365 (p0) REVERT: A2 139 MET cc_start: 0.7862 (tpp) cc_final: 0.7546 (tpp) REVERT: A2 187 GLU cc_start: 0.9329 (pt0) cc_final: 0.9122 (pp20) REVERT: A2 206 ARG cc_start: 0.8980 (ttp80) cc_final: 0.8518 (ttp80) REVERT: A2 304 MET cc_start: 0.7669 (ptp) cc_final: 0.7262 (mmm) REVERT: B2 30 LEU cc_start: 0.9181 (tp) cc_final: 0.8970 (tp) REVERT: B2 57 MET cc_start: 0.8198 (ttt) cc_final: 0.7533 (tpt) REVERT: B2 139 MET cc_start: 0.7764 (ptm) cc_final: 0.7322 (tmm) REVERT: B2 187 GLU cc_start: 0.8805 (pt0) cc_final: 0.8502 (pp20) REVERT: B2 312 VAL cc_start: 0.8750 (m) cc_final: 0.8549 (p) REVERT: C2 63 MET cc_start: 0.7989 (tpt) cc_final: 0.7733 (tpp) REVERT: C2 101 HIS cc_start: 0.8234 (p-80) cc_final: 0.7175 (p-80) REVERT: C2 139 MET cc_start: 0.6510 (ppp) cc_final: 0.5954 (tmm) REVERT: C2 190 GLN cc_start: 0.8948 (mt0) cc_final: 0.8624 (mt0) REVERT: C2 191 GLU cc_start: 0.8678 (tm-30) cc_final: 0.8314 (tp30) REVERT: C2 230 GLN cc_start: 0.8419 (pt0) cc_final: 0.8055 (pt0) REVERT: C2 231 HIS cc_start: 0.7288 (m90) cc_final: 0.6212 (m90) REVERT: C2 240 GLU cc_start: 0.8402 (pp20) cc_final: 0.8023 (pp20) REVERT: C2 304 MET cc_start: 0.7560 (mtm) cc_final: 0.7352 (mmp) REVERT: D2 34 MET cc_start: 0.8192 (mtt) cc_final: 0.7820 (mtt) REVERT: D2 98 MET cc_start: 0.8027 (ptt) cc_final: 0.7768 (ptt) REVERT: D2 275 GLN cc_start: 0.8206 (mt0) cc_final: 0.7752 (mp10) REVERT: E2 28 ILE cc_start: 0.8983 (tp) cc_final: 0.8746 (pt) REVERT: E2 34 MET cc_start: 0.8424 (mtt) cc_final: 0.7974 (mtm) REVERT: E2 39 LEU cc_start: 0.7882 (mt) cc_final: 0.7557 (mt) REVERT: E2 57 MET cc_start: 0.8551 (mtm) cc_final: 0.8130 (mtt) REVERT: E2 139 MET cc_start: 0.8287 (tpp) cc_final: 0.7934 (tpp) REVERT: E2 160 MET cc_start: 0.8784 (tmm) cc_final: 0.8569 (tmm) REVERT: E2 182 LYS cc_start: 0.9022 (mmtt) cc_final: 0.8410 (mmmt) REVERT: E2 233 MET cc_start: 0.4428 (ppp) cc_final: 0.4164 (ppp) REVERT: E2 302 LEU cc_start: 0.8147 (tp) cc_final: 0.7688 (mt) REVERT: E2 316 PHE cc_start: 0.8598 (m-80) cc_final: 0.8127 (m-10) REVERT: F2 34 MET cc_start: 0.8774 (mtt) cc_final: 0.8246 (mmp) REVERT: F2 57 MET cc_start: 0.8445 (mmp) cc_final: 0.8068 (mmm) REVERT: F2 139 MET cc_start: 0.8703 (tpp) cc_final: 0.8316 (tpt) REVERT: F2 190 GLN cc_start: 0.9270 (tt0) cc_final: 0.9041 (tp40) REVERT: F2 304 MET cc_start: 0.6988 (tmm) cc_final: 0.6726 (tmm) REVERT: G2 37 LEU cc_start: 0.8261 (mm) cc_final: 0.8022 (mm) REVERT: G2 198 MET cc_start: 0.8864 (mmm) cc_final: 0.8599 (mmm) REVERT: G2 216 MET cc_start: 0.8004 (mmm) cc_final: 0.7656 (mmm) REVERT: I2 34 MET cc_start: 0.8808 (mtt) cc_final: 0.8419 (ttp) REVERT: I2 37 LEU cc_start: 0.7822 (tt) cc_final: 0.6809 (mp) REVERT: I2 89 ASN cc_start: 0.8614 (m110) cc_final: 0.8223 (m110) outliers start: 2 outliers final: 0 residues processed: 708 average time/residue: 0.2163 time to fit residues: 243.8731 Evaluate side-chains 583 residues out of total 3745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 583 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 445 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 296 optimal weight: 10.0000 chunk 209 optimal weight: 0.7980 chunk 137 optimal weight: 0.8980 chunk 435 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 163 optimal weight: 0.9990 chunk 378 optimal weight: 2.9990 chunk 297 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G1 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2 284 GLN ** E2 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F2 231 HIS G2 101 HIS ** G2 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G2 280 GLN H2 116 HIS H2 284 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.055425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.044764 restraints weight = 226566.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.046094 restraints weight = 131611.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.047006 restraints weight = 85579.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.047647 restraints weight = 60380.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.048102 restraints weight = 45453.899| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.4872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 35793 Z= 0.156 Angle : 0.784 11.235 48674 Z= 0.385 Chirality : 0.043 0.258 6094 Planarity : 0.005 0.066 5985 Dihedral : 5.105 32.727 4847 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.30 % Favored : 94.66 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.14 (0.13), residues: 4624 helix: 1.34 (0.08), residues: 3784 sheet: None (None), residues: 0 loop : -1.84 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARGA2 85 TYR 0.018 0.001 TYRJ1 76 PHE 0.029 0.002 PHEI2 138 TRP 0.022 0.001 TRPK1 168 HIS 0.017 0.002 HISH2 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 (35793) covalent geometry : angle 0.78427 / 0.39 (48674) hydrogen bonds : bond 0.04224 / 2.80 ( 2937) hydrogen bonds : angle 4.22068 / 3.04 ( 8775) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 3745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 694 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A1 140 ARG cc_start: 0.8835 (mtm110) cc_final: 0.7802 (tpm170) REVERT: A1 211 MET cc_start: 0.8863 (mmm) cc_final: 0.8302 (mmp) REVERT: B1 101 MET cc_start: 0.8782 (mmm) cc_final: 0.8513 (mmp) REVERT: B1 107 LYS cc_start: 0.8735 (pttt) cc_final: 0.8505 (pttp) REVERT: B1 210 MET cc_start: 0.8205 (ptm) cc_final: 0.7797 (ptm) REVERT: B1 211 MET cc_start: 0.7459 (mmm) cc_final: 0.6971 (tpp) REVERT: B1 244 TYR cc_start: 0.7627 (m-80) cc_final: 0.7024 (t80) REVERT: C1 61 MET cc_start: 0.8552 (mpp) cc_final: 0.8189 (mmm) REVERT: C1 123 MET cc_start: 0.7867 (tpp) cc_final: 0.7648 (tpp) REVERT: C1 134 LEU cc_start: 0.8649 (tp) cc_final: 0.8365 (tp) REVERT: C1 138 MET cc_start: 0.7534 (mtm) cc_final: 0.7265 (mtm) REVERT: C1 211 MET cc_start: 0.8787 (mmt) cc_final: 0.8356 (mmm) REVERT: D1 61 MET cc_start: 0.8386 (mmp) cc_final: 0.8167 (mmm) REVERT: D1 128 ASP cc_start: 0.8088 (p0) cc_final: 0.7859 (p0) REVERT: D1 152 ARG cc_start: 0.8344 (tpt90) cc_final: 0.7431 (tmt170) REVERT: E1 138 MET cc_start: 0.7391 (mmt) cc_final: 0.7076 (mmt) REVERT: E1 146 ASP cc_start: 0.8035 (p0) cc_final: 0.7720 (p0) REVERT: E1 205 MET cc_start: 0.7787 (mmm) cc_final: 0.7329 (tpp) REVERT: E1 224 MET cc_start: 0.8220 (tpp) cc_final: 0.6974 (tpp) REVERT: F1 9 TRP cc_start: 0.7982 (m100) cc_final: 0.7440 (m-10) REVERT: F1 119 HIS cc_start: 0.8257 (p-80) cc_final: 0.7987 (p-80) REVERT: F1 233 MET cc_start: 0.9142 (mmt) cc_final: 0.8869 (mmm) REVERT: G1 2 THR cc_start: 0.8131 (p) cc_final: 0.7925 (p) REVERT: G1 45 ASN cc_start: 0.8041 (m110) cc_final: 0.7482 (p0) REVERT: K1 68 ASP cc_start: 0.7870 (p0) cc_final: 0.7380 (p0) REVERT: A2 139 MET cc_start: 0.7826 (tpp) cc_final: 0.7535 (tpp) REVERT: A2 147 ARG cc_start: 0.8359 (tpt170) cc_final: 0.7891 (tpm170) REVERT: A2 187 GLU cc_start: 0.9295 (pt0) cc_final: 0.9074 (pp20) REVERT: A2 206 ARG cc_start: 0.8975 (ttp80) cc_final: 0.8703 (ttp80) REVERT: A2 326 TRP cc_start: 0.3551 (t60) cc_final: 0.2828 (t60) REVERT: B2 30 LEU cc_start: 0.9174 (tp) cc_final: 0.8955 (tp) REVERT: B2 57 MET cc_start: 0.8122 (ttt) cc_final: 0.7468 (tpt) REVERT: B2 98 MET cc_start: 0.8095 (ppp) cc_final: 0.7857 (mmt) REVERT: B2 139 MET cc_start: 0.7719 (ptm) cc_final: 0.7260 (tmm) REVERT: B2 187 GLU cc_start: 0.8836 (pt0) cc_final: 0.8480 (pp20) REVERT: C2 57 MET cc_start: 0.7897 (tpt) cc_final: 0.7507 (tpt) REVERT: C2 63 MET cc_start: 0.7919 (tpt) cc_final: 0.7660 (tpp) REVERT: C2 101 HIS cc_start: 0.8148 (p-80) cc_final: 0.7011 (p-80) REVERT: C2 139 MET cc_start: 0.6495 (ppp) cc_final: 0.6028 (tmm) REVERT: C2 190 GLN cc_start: 0.8901 (mt0) cc_final: 0.8592 (mt0) REVERT: C2 191 GLU cc_start: 0.8644 (tm-30) cc_final: 0.8303 (tp30) REVERT: C2 230 GLN cc_start: 0.8422 (pt0) cc_final: 0.8042 (pt0) REVERT: C2 231 HIS cc_start: 0.7087 (m90) cc_final: 0.6214 (m90) REVERT: C2 240 GLU cc_start: 0.8376 (pp20) cc_final: 0.8018 (pp20) REVERT: C2 304 MET cc_start: 0.7528 (mtm) cc_final: 0.7320 (mmp) REVERT: D2 34 MET cc_start: 0.8138 (mtt) cc_final: 0.7757 (mtt) REVERT: D2 98 MET cc_start: 0.7796 (ptt) cc_final: 0.7440 (ptt) REVERT: D2 139 MET cc_start: 0.7929 (tmm) cc_final: 0.7340 (tpt) REVERT: D2 275 GLN cc_start: 0.7942 (mt0) cc_final: 0.7545 (mp10) REVERT: E2 28 ILE cc_start: 0.8950 (tp) cc_final: 0.8718 (pt) REVERT: E2 34 MET cc_start: 0.8442 (mtt) cc_final: 0.7978 (mtm) REVERT: E2 39 LEU cc_start: 0.7858 (mt) cc_final: 0.7555 (mt) REVERT: E2 57 MET cc_start: 0.8455 (mtm) cc_final: 0.8009 (mtp) REVERT: E2 139 MET cc_start: 0.8245 (tpp) cc_final: 0.7920 (tpp) REVERT: E2 182 LYS cc_start: 0.9059 (mmtt) cc_final: 0.8689 (mmmt) REVERT: E2 302 LEU cc_start: 0.8123 (tp) cc_final: 0.7764 (mt) REVERT: E2 316 PHE cc_start: 0.8570 (m-80) cc_final: 0.8109 (m-10) REVERT: F2 34 MET cc_start: 0.8763 (mtt) cc_final: 0.8255 (mmp) REVERT: F2 57 MET cc_start: 0.8399 (mmp) cc_final: 0.8033 (mmm) REVERT: F2 139 MET cc_start: 0.8635 (tpp) cc_final: 0.8256 (tpt) REVERT: F2 190 GLN cc_start: 0.9229 (tt0) cc_final: 0.8997 (tp40) REVERT: F2 304 MET cc_start: 0.6866 (tmm) cc_final: 0.6613 (tmm) REVERT: G2 37 LEU cc_start: 0.8249 (mm) cc_final: 0.8027 (mm) REVERT: G2 198 MET cc_start: 0.8863 (mmm) cc_final: 0.8567 (mmm) REVERT: G2 216 MET cc_start: 0.7934 (mmm) cc_final: 0.7585 (mmm) REVERT: G2 231 HIS cc_start: 0.7190 (p-80) cc_final: 0.6917 (p-80) REVERT: H2 30 LEU cc_start: 0.9110 (tt) cc_final: 0.8806 (pp) REVERT: I2 34 MET cc_start: 0.8721 (mtt) cc_final: 0.8393 (ttp) REVERT: I2 37 LEU cc_start: 0.7837 (tt) cc_final: 0.6846 (mp) REVERT: I2 63 MET cc_start: 0.7753 (ptm) cc_final: 0.7451 (ttt) REVERT: I2 89 ASN cc_start: 0.8575 (m110) cc_final: 0.8228 (m110) outliers start: 0 outliers final: 0 residues processed: 694 average time/residue: 0.2127 time to fit residues: 234.0285 Evaluate side-chains 578 residues out of total 3745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 578 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 102 optimal weight: 6.9990 chunk 53 optimal weight: 0.3980 chunk 200 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 377 optimal weight: 0.9990 chunk 223 optimal weight: 10.0000 chunk 399 optimal weight: 6.9990 chunk 364 optimal weight: 0.0570 chunk 108 optimal weight: 0.9990 chunk 376 optimal weight: 1.9990 chunk 213 optimal weight: 5.9990 overall best weight: 0.8904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I1 39 GLN K1 141 GLN K1 166 HIS ** B2 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2 288 ASN D2 89 ASN ** E2 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F2 231 HIS G2 51 ASN G2 101 HIS G2 230 GLN H2 116 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.055459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.044995 restraints weight = 226665.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.046262 restraints weight = 133512.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.047144 restraints weight = 87661.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.047772 restraints weight = 62346.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.048197 restraints weight = 47141.352| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.5035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 35793 Z= 0.160 Angle : 0.802 11.977 48674 Z= 0.394 Chirality : 0.043 0.260 6094 Planarity : 0.005 0.064 5985 Dihedral : 5.114 32.664 4847 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.23 % Favored : 94.72 % Rotamer: Outliers : 0.08 % Allowed : 0.45 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.12 (0.13), residues: 4624 helix: 1.33 (0.09), residues: 3778 sheet: None (None), residues: 0 loop : -1.84 (0.22), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARGA2 85 TYR 0.026 0.001 TYRE1 109 PHE 0.035 0.002 PHEB2 114 TRP 0.036 0.001 TRPK1 168 HIS 0.016 0.001 HISH2 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (35793) covalent geometry : angle 0.80213 / 0.39 (48674) hydrogen bonds : bond 0.04310 / 2.85 ( 2937) hydrogen bonds : angle 4.24476 / 3.07 ( 8775) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 3745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 697 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A1 114 GLN cc_start: 0.8456 (pp30) cc_final: 0.8010 (pp30) REVERT: A1 140 ARG cc_start: 0.8846 (mtm110) cc_final: 0.7767 (tpm170) REVERT: A1 211 MET cc_start: 0.8889 (mmm) cc_final: 0.8436 (mmp) REVERT: B1 101 MET cc_start: 0.8781 (mmm) cc_final: 0.8541 (mmp) REVERT: B1 107 LYS cc_start: 0.8686 (pttt) cc_final: 0.8464 (pttp) REVERT: B1 211 MET cc_start: 0.7498 (mmm) cc_final: 0.7035 (tpp) REVERT: B1 244 TYR cc_start: 0.7713 (m-80) cc_final: 0.7046 (t80) REVERT: C1 123 MET cc_start: 0.7881 (tpp) cc_final: 0.7672 (tpp) REVERT: D1 128 ASP cc_start: 0.8105 (p0) cc_final: 0.7902 (p0) REVERT: D1 152 ARG cc_start: 0.8326 (tpt90) cc_final: 0.7397 (tmt170) REVERT: E1 138 MET cc_start: 0.7389 (mmt) cc_final: 0.7029 (mmt) REVERT: E1 146 ASP cc_start: 0.8047 (p0) cc_final: 0.7741 (p0) REVERT: E1 205 MET cc_start: 0.7458 (mmm) cc_final: 0.6710 (tpp) REVERT: E1 224 MET cc_start: 0.8091 (tpp) cc_final: 0.7401 (tpp) REVERT: F1 9 TRP cc_start: 0.8028 (m100) cc_final: 0.7465 (m-10) REVERT: F1 119 HIS cc_start: 0.8330 (p-80) cc_final: 0.8098 (p-80) REVERT: F1 233 MET cc_start: 0.9142 (mmt) cc_final: 0.8864 (mmm) REVERT: G1 2 THR cc_start: 0.8094 (p) cc_final: 0.7891 (p) REVERT: G1 45 ASN cc_start: 0.8201 (m110) cc_final: 0.7564 (p0) REVERT: K1 68 ASP cc_start: 0.7940 (p0) cc_final: 0.7429 (p0) REVERT: K1 218 LYS cc_start: 0.8731 (ptpp) cc_final: 0.8530 (ptpp) REVERT: A2 139 MET cc_start: 0.7974 (tpp) cc_final: 0.7592 (tpp) REVERT: A2 147 ARG cc_start: 0.8389 (tpt170) cc_final: 0.7874 (tpm170) REVERT: A2 187 GLU cc_start: 0.9315 (pt0) cc_final: 0.9090 (pp20) REVERT: A2 326 TRP cc_start: 0.3395 (t60) cc_final: 0.2694 (t60) REVERT: B2 30 LEU cc_start: 0.9176 (tp) cc_final: 0.8955 (tp) REVERT: B2 57 MET cc_start: 0.8223 (ttt) cc_final: 0.7493 (tpt) REVERT: B2 139 MET cc_start: 0.7630 (ptm) cc_final: 0.7369 (tmm) REVERT: B2 187 GLU cc_start: 0.8826 (pt0) cc_final: 0.8520 (pp20) REVERT: B2 216 MET cc_start: 0.8397 (mmm) cc_final: 0.8186 (mmt) REVERT: C2 57 MET cc_start: 0.7992 (tpt) cc_final: 0.7607 (tpt) REVERT: C2 63 MET cc_start: 0.7947 (tpt) cc_final: 0.7705 (tpp) REVERT: C2 101 HIS cc_start: 0.8186 (p-80) cc_final: 0.6984 (p-80) REVERT: C2 139 MET cc_start: 0.6545 (ppp) cc_final: 0.5991 (tmm) REVERT: C2 190 GLN cc_start: 0.8900 (mt0) cc_final: 0.8598 (mt0) REVERT: C2 191 GLU cc_start: 0.8685 (tm-30) cc_final: 0.8326 (tp30) REVERT: C2 230 GLN cc_start: 0.8454 (pt0) cc_final: 0.7891 (pt0) REVERT: C2 231 HIS cc_start: 0.7109 (m90) cc_final: 0.6364 (m90) REVERT: C2 240 GLU cc_start: 0.8472 (pp20) cc_final: 0.8146 (pp20) REVERT: C2 288 ASN cc_start: 0.7654 (OUTLIER) cc_final: 0.7297 (t0) REVERT: D2 34 MET cc_start: 0.8224 (mtt) cc_final: 0.7861 (mtt) REVERT: D2 98 MET cc_start: 0.7946 (ptt) cc_final: 0.7657 (ptt) REVERT: D2 139 MET cc_start: 0.7781 (tmm) cc_final: 0.7456 (tmm) REVERT: D2 230 GLN cc_start: 0.8893 (tm-30) cc_final: 0.8630 (tm-30) REVERT: D2 275 GLN cc_start: 0.8030 (mt0) cc_final: 0.7646 (mp10) REVERT: E2 28 ILE cc_start: 0.9005 (tp) cc_final: 0.8771 (pt) REVERT: E2 34 MET cc_start: 0.8468 (mtt) cc_final: 0.7994 (mtm) REVERT: E2 39 LEU cc_start: 0.7889 (mt) cc_final: 0.7582 (mt) REVERT: E2 57 MET cc_start: 0.8508 (mtm) cc_final: 0.8056 (mtp) REVERT: E2 98 MET cc_start: 0.8398 (ptp) cc_final: 0.8178 (ptt) REVERT: E2 139 MET cc_start: 0.8116 (tpp) cc_final: 0.7844 (tpp) REVERT: E2 160 MET cc_start: 0.8768 (tmm) cc_final: 0.8554 (tmm) REVERT: E2 182 LYS cc_start: 0.8995 (mmtt) cc_final: 0.8727 (mmmt) REVERT: E2 316 PHE cc_start: 0.8629 (m-80) cc_final: 0.8118 (m-10) REVERT: F2 34 MET cc_start: 0.8765 (mtt) cc_final: 0.8284 (mmp) REVERT: F2 57 MET cc_start: 0.8454 (mmp) cc_final: 0.8087 (mmm) REVERT: F2 139 MET cc_start: 0.8680 (tpp) cc_final: 0.8355 (tpt) REVERT: F2 190 GLN cc_start: 0.9240 (tt0) cc_final: 0.9006 (tp40) REVERT: F2 191 GLU cc_start: 0.8682 (pm20) cc_final: 0.8391 (pm20) REVERT: F2 203 LYS cc_start: 0.8974 (tptp) cc_final: 0.8752 (tptt) REVERT: F2 304 MET cc_start: 0.6966 (tmm) cc_final: 0.6698 (tmm) REVERT: G2 37 LEU cc_start: 0.8183 (mm) cc_final: 0.7861 (tt) REVERT: G2 143 LYS cc_start: 0.7977 (ptmt) cc_final: 0.7508 (ptmt) REVERT: G2 198 MET cc_start: 0.8859 (mmm) cc_final: 0.8543 (mmm) REVERT: G2 216 MET cc_start: 0.7951 (mmm) cc_final: 0.7620 (mmm) REVERT: H2 30 LEU cc_start: 0.9090 (tt) cc_final: 0.8580 (pp) REVERT: H2 34 MET cc_start: 0.7288 (ttt) cc_final: 0.6354 (ptm) REVERT: I2 34 MET cc_start: 0.8763 (mtt) cc_final: 0.8458 (ttp) REVERT: I2 37 LEU cc_start: 0.7777 (tt) cc_final: 0.6830 (mp) REVERT: I2 89 ASN cc_start: 0.8647 (m110) cc_final: 0.8227 (m110) outliers start: 3 outliers final: 0 residues processed: 699 average time/residue: 0.2192 time to fit residues: 244.1235 Evaluate side-chains 577 residues out of total 3745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 576 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 32 optimal weight: 0.4980 chunk 67 optimal weight: 0.7980 chunk 142 optimal weight: 0.8980 chunk 415 optimal weight: 0.7980 chunk 441 optimal weight: 2.9990 chunk 344 optimal weight: 2.9990 chunk 297 optimal weight: 0.9990 chunk 274 optimal weight: 4.9990 chunk 328 optimal weight: 0.3980 chunk 256 optimal weight: 0.9990 chunk 278 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G1 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1 39 GLN ** A2 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2 89 ASN C2 288 ASN E2 66 GLN E2 190 GLN ** E2 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2 275 GLN F2 231 HIS G2 101 HIS H2 116 HIS I2 280 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.055724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.045118 restraints weight = 222792.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.046426 restraints weight = 129525.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.047345 restraints weight = 84394.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.047992 restraints weight = 59549.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.048451 restraints weight = 44766.272| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.5140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 35793 Z= 0.153 Angle : 0.802 11.492 48674 Z= 0.392 Chirality : 0.043 0.226 6094 Planarity : 0.005 0.075 5985 Dihedral : 5.087 32.572 4847 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.08 % Favored : 94.87 % Rotamer: Outliers : 0.03 % Allowed : 0.29 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.13 (0.13), residues: 4624 helix: 1.33 (0.09), residues: 3786 sheet: None (None), residues: 0 loop : -1.85 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARGK1 173 TYR 0.023 0.001 TYRJ1 76 PHE 0.035 0.002 PHEI2 138 TRP 0.037 0.001 TRPK1 168 HIS 0.016 0.001 HISH2 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (35793) covalent geometry : angle 0.80244 / 0.39 (48674) hydrogen bonds : bond 0.04238 / 2.80 ( 2937) hydrogen bonds : angle 4.24287 / 3.06 ( 8775) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6715.78 seconds wall clock time: 116 minutes 33.99 seconds (6993.99 seconds total)