Starting phenix.real_space_refine on Sat Mar 7 04:26:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6z2k_11042/03_2026/6z2k_11042_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6z2k_11042/03_2026/6z2k_11042.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6z2k_11042/03_2026/6z2k_11042_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6z2k_11042/03_2026/6z2k_11042_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6z2k_11042/03_2026/6z2k_11042.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6z2k_11042/03_2026/6z2k_11042.map" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 8 Type Number sf(0) Gaussians K 8 8.98 5 Zn 4 6.06 5 P 24 5.49 5 S 122 5.16 5 C 12224 2.51 5 N 3262 2.21 5 O 3622 1.98 5 H 18577 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37843 Number of models: 1 Model: "" Number of chains: 19 Chain: "C" Number of atoms: 5802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 5802 Classifications: {'peptide': 369} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 353} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "E" Number of atoms: 5787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 5787 Classifications: {'peptide': 368} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 352} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "K" Number of atoms: 5802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 5802 Classifications: {'peptide': 369} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 353} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "I" Number of atoms: 5802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 5802 Classifications: {'peptide': 369} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 353} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 1139 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 69, 1098 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Conformer: "B" Number of residues, atoms: 69, 1098 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} bond proxies already assigned to first conformer: 1060 Chain: "B" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1098 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "G" Number of atoms: 1139 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 69, 1098 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Conformer: "B" Number of residues, atoms: 69, 1098 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} bond proxies already assigned to first conformer: 1060 Chain: "H" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1098 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "F" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2505 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 8, 'TRANS': 148} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2505 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 8, 'TRANS': 148} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "L" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2505 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 8, 'TRANS': 148} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "J" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2505 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 8, 'TRANS': 148} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 39 Unusual residues: {' K': 2, ' ZN': 1, 'IHP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "K" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N ACYS A 121 " occ=0.50 ... (20 atoms not shown) pdb=" HG BCYS A 121 " occ=0.50 residue: pdb=" N ACYS G 121 " occ=0.50 ... (20 atoms not shown) pdb=" HG BCYS G 121 " occ=0.50 residue: pdb=" C1 IHP E 501 " occ=0.70 ... (34 atoms not shown) pdb=" P6 IHP E 501 " occ=0.70 residue: pdb=" C1 IHP F 901 " occ=0.70 ... (34 atoms not shown) pdb=" P6 IHP F 901 " occ=0.70 residue: pdb=" C1 IHP D 901 " occ=0.70 ... (34 atoms not shown) pdb=" P6 IHP D 901 " occ=0.70 residue: pdb=" C1 IHP J 901 " occ=0.70 ... (34 atoms not shown) pdb=" P6 IHP J 901 " occ=0.70 Time building chain proxies: 8.48, per 1000 atoms: 0.22 Number of scatterers: 37843 At special positions: 0 Unit cell: (137.16, 169.56, 113.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 4 29.99 K 8 19.00 S 122 16.00 P 24 15.00 O 3622 8.00 N 3262 7.00 C 12224 6.00 H 18577 1.00 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.80 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" ND1 HIS C 178 " pdb=" ZN E 502 " pdb="ZN ZN E 502 " - pdb=" ND1 HIS E 178 " pdb=" ZN I 501 " pdb="ZN ZN I 501 " - pdb=" ND1 HIS I 178 " pdb=" ZN K 501 " pdb="ZN ZN K 501 " - pdb=" ND1 HIS K 178 " 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4474 Finding SS restraints... Secondary structure from input PDB file: 101 helices and 8 sheets defined 53.7% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'C' and resid 16 through 21 removed outlier: 3.528A pdb=" N VAL C 19 " --> pdb=" O ASP C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 45 removed outlier: 4.153A pdb=" N ARG C 36 " --> pdb=" O PRO C 32 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU C 43 " --> pdb=" O HIS C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 51 removed outlier: 3.508A pdb=" N MET C 51 " --> pdb=" O TYR C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 65 Processing helix chain 'C' and resid 69 through 79 Processing helix chain 'C' and resid 87 through 94 removed outlier: 3.707A pdb=" N ARG C 93 " --> pdb=" O LYS C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 126 removed outlier: 3.510A pdb=" N SER C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 167 removed outlier: 3.591A pdb=" N GLU C 162 " --> pdb=" O LEU C 158 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS C 165 " --> pdb=" O LEU C 161 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TYR C 166 " --> pdb=" O GLU C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 186 Processing helix chain 'C' and resid 216 through 220 Processing helix chain 'C' and resid 233 through 252 Proline residue: C 243 - end of helix Processing helix chain 'C' and resid 277 through 291 removed outlier: 3.937A pdb=" N VAL C 285 " --> pdb=" O HIS C 281 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE C 291 " --> pdb=" O PHE C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 320 Processing helix chain 'C' and resid 333 through 337 Processing helix chain 'C' and resid 355 through 372 Processing helix chain 'E' and resid 16 through 21 removed outlier: 3.529A pdb=" N VAL E 19 " --> pdb=" O ASP E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 45 removed outlier: 4.153A pdb=" N ARG E 36 " --> pdb=" O PRO E 32 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU E 43 " --> pdb=" O HIS E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 51 removed outlier: 3.508A pdb=" N MET E 51 " --> pdb=" O TYR E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 65 Processing helix chain 'E' and resid 69 through 79 Processing helix chain 'E' and resid 87 through 94 removed outlier: 3.706A pdb=" N ARG E 93 " --> pdb=" O LYS E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 126 removed outlier: 3.509A pdb=" N SER E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 167 removed outlier: 3.591A pdb=" N GLU E 162 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS E 165 " --> pdb=" O LEU E 161 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TYR E 166 " --> pdb=" O GLU E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 186 Processing helix chain 'E' and resid 216 through 220 Processing helix chain 'E' and resid 233 through 252 Proline residue: E 243 - end of helix Processing helix chain 'E' and resid 277 through 291 removed outlier: 3.937A pdb=" N VAL E 285 " --> pdb=" O HIS E 281 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE E 291 " --> pdb=" O PHE E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 320 Processing helix chain 'E' and resid 333 through 337 Processing helix chain 'E' and resid 355 through 372 Processing helix chain 'K' and resid 16 through 21 removed outlier: 3.529A pdb=" N VAL K 19 " --> pdb=" O ASP K 16 " (cutoff:3.500A) Processing helix chain 'K' and resid 32 through 45 removed outlier: 4.152A pdb=" N ARG K 36 " --> pdb=" O PRO K 32 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU K 43 " --> pdb=" O HIS K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 47 through 51 removed outlier: 3.508A pdb=" N MET K 51 " --> pdb=" O TYR K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 65 Processing helix chain 'K' and resid 69 through 79 Processing helix chain 'K' and resid 87 through 94 removed outlier: 3.707A pdb=" N ARG K 93 " --> pdb=" O LYS K 89 " (cutoff:3.500A) Processing helix chain 'K' and resid 105 through 126 removed outlier: 3.510A pdb=" N SER K 117 " --> pdb=" O SER K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 154 through 167 removed outlier: 3.591A pdb=" N GLU K 162 " --> pdb=" O LEU K 158 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS K 165 " --> pdb=" O LEU K 161 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TYR K 166 " --> pdb=" O GLU K 162 " (cutoff:3.500A) Processing helix chain 'K' and resid 180 through 186 Processing helix chain 'K' and resid 216 through 220 Processing helix chain 'K' and resid 233 through 252 Proline residue: K 243 - end of helix Processing helix chain 'K' and resid 277 through 291 removed outlier: 3.937A pdb=" N VAL K 285 " --> pdb=" O HIS K 281 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE K 291 " --> pdb=" O PHE K 287 " (cutoff:3.500A) Processing helix chain 'K' and resid 304 through 320 Processing helix chain 'K' and resid 333 through 337 Processing helix chain 'K' and resid 355 through 372 Processing helix chain 'I' and resid 16 through 21 removed outlier: 3.529A pdb=" N VAL I 19 " --> pdb=" O ASP I 16 " (cutoff:3.500A) Processing helix chain 'I' and resid 32 through 45 removed outlier: 4.152A pdb=" N ARG I 36 " --> pdb=" O PRO I 32 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU I 43 " --> pdb=" O HIS I 39 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 51 removed outlier: 3.508A pdb=" N MET I 51 " --> pdb=" O TYR I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 65 Processing helix chain 'I' and resid 69 through 79 Processing helix chain 'I' and resid 87 through 94 removed outlier: 3.706A pdb=" N ARG I 93 " --> pdb=" O LYS I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 126 removed outlier: 3.511A pdb=" N SER I 117 " --> pdb=" O SER I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 154 through 167 removed outlier: 3.591A pdb=" N GLU I 162 " --> pdb=" O LEU I 158 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS I 165 " --> pdb=" O LEU I 161 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TYR I 166 " --> pdb=" O GLU I 162 " (cutoff:3.500A) Processing helix chain 'I' and resid 180 through 186 Processing helix chain 'I' and resid 216 through 220 Processing helix chain 'I' and resid 233 through 252 Proline residue: I 243 - end of helix Processing helix chain 'I' and resid 277 through 291 removed outlier: 3.937A pdb=" N VAL I 285 " --> pdb=" O HIS I 281 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE I 291 " --> pdb=" O PHE I 287 " (cutoff:3.500A) Processing helix chain 'I' and resid 304 through 320 Processing helix chain 'I' and resid 333 through 337 Processing helix chain 'I' and resid 355 through 372 Processing helix chain 'A' and resid 64 through 104 removed outlier: 4.275A pdb=" N ASP A 68 " --> pdb=" O ALA A 64 " (cutoff:3.500A) Proline residue: A 76 - end of helix removed outlier: 3.848A pdb=" N LYS A 88 " --> pdb=" O THR A 84 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR A 89 " --> pdb=" O VAL A 85 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LYS A 91 " --> pdb=" O ASN A 87 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N PHE A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE A 93 " --> pdb=" O TYR A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 126 removed outlier: 3.639A pdb=" N LYS A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 130 Processing helix chain 'B' and resid 63 through 105 removed outlier: 3.522A pdb=" N VAL B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) Proline residue: B 76 - end of helix removed outlier: 3.834A pdb=" N LYS B 88 " --> pdb=" O THR B 84 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR B 89 " --> pdb=" O VAL B 85 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N LYS B 91 " --> pdb=" O ASN B 87 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N PHE B 92 " --> pdb=" O LYS B 88 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE B 93 " --> pdb=" O TYR B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 126 removed outlier: 3.542A pdb=" N LYS B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 130 removed outlier: 3.737A pdb=" N SER B 130 " --> pdb=" O LEU B 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 127 through 130' Processing helix chain 'G' and resid 62 through 63 No H-bonds generated for 'chain 'G' and resid 62 through 63' Processing helix chain 'G' and resid 64 through 104 removed outlier: 4.245A pdb=" N ASP G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) Proline residue: G 76 - end of helix removed outlier: 3.858A pdb=" N LYS G 88 " --> pdb=" O THR G 84 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TYR G 89 " --> pdb=" O VAL G 85 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N LYS G 91 " --> pdb=" O ASN G 87 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N PHE G 92 " --> pdb=" O LYS G 88 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE G 93 " --> pdb=" O TYR G 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 126 removed outlier: 3.528A pdb=" N LYS G 126 " --> pdb=" O LEU G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 130 removed outlier: 3.503A pdb=" N SER G 130 " --> pdb=" O LEU G 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 127 through 130' Processing helix chain 'H' and resid 63 through 105 Proline residue: H 76 - end of helix removed outlier: 3.817A pdb=" N LYS H 88 " --> pdb=" O THR H 84 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR H 89 " --> pdb=" O VAL H 85 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N LYS H 91 " --> pdb=" O ASN H 87 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N PHE H 92 " --> pdb=" O LYS H 88 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE H 93 " --> pdb=" O TYR H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 109 through 126 removed outlier: 3.608A pdb=" N LYS H 126 " --> pdb=" O LEU H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 130 removed outlier: 3.811A pdb=" N SER H 130 " --> pdb=" O LEU H 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 127 through 130' Processing helix chain 'F' and resid 765 through 775 removed outlier: 3.551A pdb=" N VAL F 769 " --> pdb=" O LYS F 765 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLU F 770 " --> pdb=" O GLN F 766 " (cutoff:3.500A) Processing helix chain 'F' and resid 786 through 799 removed outlier: 4.003A pdb=" N LEU F 790 " --> pdb=" O THR F 786 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA F 791 " --> pdb=" O ASN F 787 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG F 799 " --> pdb=" O LEU F 795 " (cutoff:3.500A) Processing helix chain 'F' and resid 802 through 811 Processing helix chain 'F' and resid 822 through 829 Processing helix chain 'F' and resid 834 through 848 removed outlier: 3.650A pdb=" N TYR F 848 " --> pdb=" O GLY F 844 " (cutoff:3.500A) Processing helix chain 'F' and resid 853 through 859 Processing helix chain 'F' and resid 863 through 879 removed outlier: 4.468A pdb=" N LYS F 879 " --> pdb=" O LYS F 875 " (cutoff:3.500A) Processing helix chain 'D' and resid 765 through 775 removed outlier: 3.551A pdb=" N VAL D 769 " --> pdb=" O LYS D 765 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLU D 770 " --> pdb=" O GLN D 766 " (cutoff:3.500A) Processing helix chain 'D' and resid 786 through 799 removed outlier: 4.004A pdb=" N LEU D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA D 791 " --> pdb=" O ASN D 787 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG D 799 " --> pdb=" O LEU D 795 " (cutoff:3.500A) Processing helix chain 'D' and resid 802 through 811 Processing helix chain 'D' and resid 822 through 829 Processing helix chain 'D' and resid 834 through 848 removed outlier: 3.649A pdb=" N TYR D 848 " --> pdb=" O GLY D 844 " (cutoff:3.500A) Processing helix chain 'D' and resid 853 through 859 Processing helix chain 'D' and resid 863 through 879 removed outlier: 4.469A pdb=" N LYS D 879 " --> pdb=" O LYS D 875 " (cutoff:3.500A) Processing helix chain 'L' and resid 765 through 775 removed outlier: 3.551A pdb=" N VAL L 769 " --> pdb=" O LYS L 765 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLU L 770 " --> pdb=" O GLN L 766 " (cutoff:3.500A) Processing helix chain 'L' and resid 786 through 799 removed outlier: 4.003A pdb=" N LEU L 790 " --> pdb=" O THR L 786 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA L 791 " --> pdb=" O ASN L 787 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG L 799 " --> pdb=" O LEU L 795 " (cutoff:3.500A) Processing helix chain 'L' and resid 802 through 811 Processing helix chain 'L' and resid 822 through 829 Processing helix chain 'L' and resid 834 through 848 removed outlier: 3.649A pdb=" N TYR L 848 " --> pdb=" O GLY L 844 " (cutoff:3.500A) Processing helix chain 'L' and resid 853 through 859 Processing helix chain 'L' and resid 863 through 879 removed outlier: 4.469A pdb=" N LYS L 879 " --> pdb=" O LYS L 875 " (cutoff:3.500A) Processing helix chain 'J' and resid 765 through 775 removed outlier: 3.551A pdb=" N VAL J 769 " --> pdb=" O LYS J 765 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLU J 770 " --> pdb=" O GLN J 766 " (cutoff:3.500A) Processing helix chain 'J' and resid 786 through 799 removed outlier: 4.003A pdb=" N LEU J 790 " --> pdb=" O THR J 786 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA J 791 " --> pdb=" O ASN J 787 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG J 799 " --> pdb=" O LEU J 795 " (cutoff:3.500A) Processing helix chain 'J' and resid 802 through 811 Processing helix chain 'J' and resid 822 through 829 Processing helix chain 'J' and resid 834 through 848 removed outlier: 3.649A pdb=" N TYR J 848 " --> pdb=" O GLY J 844 " (cutoff:3.500A) Processing helix chain 'J' and resid 853 through 859 Processing helix chain 'J' and resid 863 through 879 removed outlier: 4.468A pdb=" N LYS J 879 " --> pdb=" O LYS J 875 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 193 through 195 removed outlier: 6.990A pdb=" N VAL C 257 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N LEU C 298 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU C 259 " --> pdb=" O LEU C 298 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ALA C 132 " --> pdb=" O MET C 297 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N CYS C 12 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 198 through 200 Processing sheet with id=AA3, first strand: chain 'E' and resid 193 through 195 removed outlier: 6.990A pdb=" N VAL E 257 " --> pdb=" O LEU E 296 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N LEU E 298 " --> pdb=" O VAL E 257 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LEU E 259 " --> pdb=" O LEU E 298 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ALA E 132 " --> pdb=" O MET E 297 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N CYS E 12 " --> pdb=" O VAL E 133 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N ILE E 53 " --> pdb=" O VAL F 752 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 198 through 200 Processing sheet with id=AA5, first strand: chain 'K' and resid 193 through 195 removed outlier: 6.991A pdb=" N VAL K 257 " --> pdb=" O LEU K 296 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N LEU K 298 " --> pdb=" O VAL K 257 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU K 259 " --> pdb=" O LEU K 298 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ALA K 132 " --> pdb=" O MET K 297 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N CYS K 12 " --> pdb=" O VAL K 133 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N ILE K 53 " --> pdb=" O VAL L 752 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 198 through 200 Processing sheet with id=AA7, first strand: chain 'I' and resid 193 through 195 removed outlier: 6.990A pdb=" N VAL I 257 " --> pdb=" O LEU I 296 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N LEU I 298 " --> pdb=" O VAL I 257 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU I 259 " --> pdb=" O LEU I 298 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ALA I 132 " --> pdb=" O MET I 297 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N CYS I 12 " --> pdb=" O VAL I 133 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ILE I 53 " --> pdb=" O VAL J 752 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 198 through 200 829 hydrogen bonds defined for protein. 2388 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: 10.89 Time building geometry restraints manager: 5.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 18523 1.03 - 1.23: 74 1.23 - 1.42: 8413 1.42 - 1.62: 11088 1.62 - 1.81: 194 Bond restraints: 38292 Sorted by residual: bond pdb=" O12 IHP F 901 " pdb=" P2 IHP F 901 " ideal model delta sigma weight residual 1.675 1.610 0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" O12 IHP J 901 " pdb=" P2 IHP J 901 " ideal model delta sigma weight residual 1.675 1.610 0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" O12 IHP E 501 " pdb=" P2 IHP E 501 " ideal model delta sigma weight residual 1.675 1.610 0.065 2.00e-02 2.50e+03 1.04e+01 bond pdb=" O12 IHP D 901 " pdb=" P2 IHP D 901 " ideal model delta sigma weight residual 1.675 1.611 0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" O15 IHP D 901 " pdb=" P5 IHP D 901 " ideal model delta sigma weight residual 1.675 1.617 0.058 2.00e-02 2.50e+03 8.28e+00 ... (remaining 38287 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 68157 2.61 - 5.23: 701 5.23 - 7.84: 87 7.84 - 10.45: 24 10.45 - 13.06: 16 Bond angle restraints: 68985 Sorted by residual: angle pdb=" C GLY D 785 " pdb=" N THR D 786 " pdb=" CA THR D 786 " ideal model delta sigma weight residual 121.33 129.53 -8.20 1.40e+00 5.10e-01 3.43e+01 angle pdb=" C GLY J 785 " pdb=" N THR J 786 " pdb=" CA THR J 786 " ideal model delta sigma weight residual 121.33 129.50 -8.17 1.40e+00 5.10e-01 3.40e+01 angle pdb=" C GLY F 785 " pdb=" N THR F 786 " pdb=" CA THR F 786 " ideal model delta sigma weight residual 121.33 129.49 -8.16 1.40e+00 5.10e-01 3.40e+01 angle pdb=" C GLY L 785 " pdb=" N THR L 786 " pdb=" CA THR L 786 " ideal model delta sigma weight residual 121.33 129.47 -8.14 1.40e+00 5.10e-01 3.38e+01 angle pdb=" CB LEU D 741 " pdb=" CG LEU D 741 " pdb=" HG LEU D 741 " ideal model delta sigma weight residual 109.00 95.94 13.06 3.00e+00 1.11e-01 1.90e+01 ... (remaining 68980 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.13: 17125 24.13 - 48.25: 868 48.25 - 72.38: 207 72.38 - 96.51: 23 96.51 - 120.63: 24 Dihedral angle restraints: 18247 sinusoidal: 9771 harmonic: 8476 Sorted by residual: dihedral pdb=" CA ASP J 745 " pdb=" C ASP J 745 " pdb=" N PRO J 746 " pdb=" CA PRO J 746 " ideal model delta harmonic sigma weight residual 180.00 116.60 63.40 0 5.00e+00 4.00e-02 1.61e+02 dihedral pdb=" CA ASP F 745 " pdb=" C ASP F 745 " pdb=" N PRO F 746 " pdb=" CA PRO F 746 " ideal model delta harmonic sigma weight residual 180.00 116.63 63.37 0 5.00e+00 4.00e-02 1.61e+02 dihedral pdb=" CA ASP D 745 " pdb=" C ASP D 745 " pdb=" N PRO D 746 " pdb=" CA PRO D 746 " ideal model delta harmonic sigma weight residual 180.00 116.68 63.32 0 5.00e+00 4.00e-02 1.60e+02 ... (remaining 18244 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.007: 2821 1.007 - 2.013: 4 2.013 - 3.020: 0 3.020 - 4.027: 0 4.027 - 5.033: 8 Chirality restraints: 2833 Sorted by residual: chirality pdb=" C2 IHP D 901 " pdb=" C1 IHP D 901 " pdb=" C3 IHP D 901 " pdb=" O12 IHP D 901 " both_signs ideal model delta sigma weight residual False -2.52 2.51 -5.03 2.00e-01 2.50e+01 6.33e+02 chirality pdb=" C2 IHP J 901 " pdb=" C1 IHP J 901 " pdb=" C3 IHP J 901 " pdb=" O12 IHP J 901 " both_signs ideal model delta sigma weight residual False -2.52 2.51 -5.03 2.00e-01 2.50e+01 6.33e+02 chirality pdb=" C2 IHP F 901 " pdb=" C1 IHP F 901 " pdb=" C3 IHP F 901 " pdb=" O12 IHP F 901 " both_signs ideal model delta sigma weight residual False -2.52 2.51 -5.03 2.00e-01 2.50e+01 6.33e+02 ... (remaining 2830 not shown) Planarity restraints: 5705 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 745 " 0.056 5.00e-02 4.00e+02 8.57e-02 1.18e+01 pdb=" N PRO D 746 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO D 746 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO D 746 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP L 745 " -0.056 5.00e-02 4.00e+02 8.55e-02 1.17e+01 pdb=" N PRO L 746 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO L 746 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO L 746 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP J 745 " 0.056 5.00e-02 4.00e+02 8.55e-02 1.17e+01 pdb=" N PRO J 746 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO J 746 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO J 746 " 0.047 5.00e-02 4.00e+02 ... (remaining 5702 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.27: 5295 2.27 - 2.98: 103752 2.98 - 3.70: 141138 3.70 - 4.42: 215340 4.42 - 5.14: 331723 Nonbonded interactions: 797248 Sorted by model distance: nonbonded pdb=" O ARG E 49 " pdb=" HE1 TRP F 753 " model vdw 1.547 2.450 nonbonded pdb=" OE2 GLU G 81 " pdb=" HH TYR H 89 " model vdw 1.573 2.450 nonbonded pdb=" O ALA C 309 " pdb=" HG1 THR C 313 " model vdw 1.595 2.450 nonbonded pdb=" O ALA K 309 " pdb=" HG1 THR K 313 " model vdw 1.595 2.450 nonbonded pdb=" O ALA I 309 " pdb=" HG1 THR I 313 " model vdw 1.595 2.450 ... (remaining 797243 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 62 through 70 or resid 72 through 76 or resid 78 through 1 \ 20 or resid 123 through 130)) selection = (chain 'B' and (resid 62 through 70 or resid 72 through 76 or resid 78 through 1 \ 20 or resid 123 through 130)) selection = (chain 'G' and (resid 62 through 70 or resid 72 through 76 or resid 78 through 1 \ 20 or resid 123 through 130)) selection = (chain 'H' and (resid 62 through 70 or resid 72 through 76 or resid 78 through 1 \ 20 or resid 123 through 130)) } ncs_group { reference = (chain 'C' and (resid 8 through 325 or (resid 327 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name OE1 or name OE2 or name HA \ or name HB2 or name HB3 or name HG2 or name HG3)) or resid 328 through 376 or r \ esid 503)) selection = (chain 'E' and (resid 8 through 376 or resid 503)) selection = (chain 'I' and (resid 8 through 325 or (resid 327 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name OE1 or name OE2 or name HA \ or name HB2 or name HB3 or name HG2 or name HG3)) or resid 328 through 376 or r \ esid 503)) selection = (chain 'K' and (resid 8 through 325 or (resid 327 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name OE1 or name OE2 or name HA \ or name HB2 or name HB3 or name HG2 or name HG3)) or resid 328 through 376 or r \ esid 503)) } ncs_group { reference = (chain 'D' and resid 720 through 879) selection = (chain 'F' and resid 720 through 879) selection = (chain 'J' and resid 720 through 879) selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 4.200 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: 0.230 Extract box with map and model: 0.590 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 50.210 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.090 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:1.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6357 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 : 0.012 0.879 19722 Z= 0.997 Angle : 0.994 12.261 26696 Z= 0.541 Chirality : 0.270 5.033 2833 Planarity : 0.005 0.086 3435 Dihedral : 16.147 120.634 7414 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.96 % Favored : 90.83 % Rotamer: Outliers : 0.15 % Allowed : 1.08 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.18 % 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: -3.76 (0.14), residues: 2355 helix: -2.01 (0.12), residues: 1130 sheet: -2.67 (0.34), residues: 200 loop : -2.95 (0.16), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 270 TYR 0.017 0.002 TYR E 303 PHE 0.022 0.002 PHE A 129 TRP 0.007 0.001 TRP J 753 HIS 0.008 0.002 HIS F 796 Details of bonding type rmsd covalent geometry : bond 0.00612 (19715) covalent geometry : angle 0.99385 (26696) hydrogen bonds : bond 0.24219 ( 829) hydrogen bonds : angle 7.97345 ( 2388) metal coordination : bond 0.27038 ( 4) Misc. bond : bond 0.76465 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Evaluate side-chains 688 residues out of total 2063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 687 time to evaluate : 0.942 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 18 ASP cc_start: 0.8695 (t0) cc_final: 0.8190 (t0) REVERT: C 47 LEU cc_start: 0.8784 (mt) cc_final: 0.8331 (mt) REVERT: C 110 CYS cc_start: 0.9467 (m) cc_final: 0.9243 (m) REVERT: C 242 LYS cc_start: 0.9266 (mttt) cc_final: 0.9056 (mtpp) REVERT: C 263 SER cc_start: 0.8471 (t) cc_final: 0.8163 (p) REVERT: C 284 CYS cc_start: 0.9011 (m) cc_final: 0.8507 (m) REVERT: E 18 ASP cc_start: 0.8691 (t0) cc_final: 0.8218 (t0) REVERT: E 47 LEU cc_start: 0.8870 (mt) cc_final: 0.8415 (mt) REVERT: E 110 CYS cc_start: 0.9410 (m) cc_final: 0.9176 (m) REVERT: E 242 LYS cc_start: 0.9267 (mttt) cc_final: 0.9047 (mtpp) REVERT: E 263 SER cc_start: 0.8542 (t) cc_final: 0.8321 (p) REVERT: E 367 PHE cc_start: 0.9355 (m-80) cc_final: 0.8760 (m-10) REVERT: K 18 ASP cc_start: 0.8595 (t0) cc_final: 0.8105 (t0) REVERT: K 47 LEU cc_start: 0.8617 (mt) cc_final: 0.8176 (mt) REVERT: K 110 CYS cc_start: 0.9483 (m) cc_final: 0.9265 (m) REVERT: K 242 LYS cc_start: 0.9239 (mttt) cc_final: 0.8926 (mtpp) REVERT: K 263 SER cc_start: 0.8572 (t) cc_final: 0.8367 (p) REVERT: K 367 PHE cc_start: 0.9366 (m-80) cc_final: 0.8762 (m-10) REVERT: I 18 ASP cc_start: 0.8624 (t0) cc_final: 0.8085 (t0) REVERT: I 47 LEU cc_start: 0.8969 (mt) cc_final: 0.8562 (mt) REVERT: I 110 CYS cc_start: 0.9419 (m) cc_final: 0.9194 (m) REVERT: I 242 LYS cc_start: 0.9328 (mttt) cc_final: 0.9076 (mtpp) REVERT: I 284 CYS cc_start: 0.9000 (m) cc_final: 0.8501 (m) REVERT: A 99 ASN cc_start: 0.8882 (m-40) cc_final: 0.8632 (t0) REVERT: B 65 ILE cc_start: 0.9018 (mm) cc_final: 0.8634 (tt) REVERT: H 65 ILE cc_start: 0.8997 (mm) cc_final: 0.8762 (tt) REVERT: F 757 GLU cc_start: 0.8978 (pt0) cc_final: 0.8685 (pp20) REVERT: F 801 ASP cc_start: 0.7790 (t70) cc_final: 0.6905 (m-30) REVERT: D 757 GLU cc_start: 0.9049 (pt0) cc_final: 0.8777 (pp20) REVERT: D 801 ASP cc_start: 0.8122 (t70) cc_final: 0.7684 (m-30) REVERT: D 874 TYR cc_start: 0.8672 (t80) cc_final: 0.8110 (t80) REVERT: L 757 GLU cc_start: 0.8790 (pt0) cc_final: 0.8580 (pp20) REVERT: L 801 ASP cc_start: 0.8179 (t70) cc_final: 0.7465 (m-30) REVERT: J 757 GLU cc_start: 0.8877 (pt0) cc_final: 0.8674 (pp20) REVERT: J 801 ASP cc_start: 0.8021 (t70) cc_final: 0.7467 (m-30) outliers start: 1 outliers final: 0 residues processed: 688 average time/residue: 0.3800 time to fit residues: 379.2822 Evaluate side-chains 477 residues out of total 2063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 477 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 0.6980 chunk 227 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 6.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 44 ASN C 281 HIS E 44 ASN K 44 ASN I 44 ASN F 766 GLN ** F 793 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 766 GLN ** D 793 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 766 GLN ** L 793 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 766 GLN ** J 793 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.108945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.085406 restraints weight = 345890.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.091044 restraints weight = 175352.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.095099 restraints weight = 105947.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.097934 restraints weight = 70909.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.099894 restraints weight = 51030.257| |-----------------------------------------------------------------------------| r_work (final): 0.4160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4159 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4159 r_free = 0.4159 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4154 r_free = 0.4154 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6509 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 19722 Z= 0.183 Angle : 0.826 17.688 26696 Z= 0.415 Chirality : 0.053 1.285 2833 Planarity : 0.006 0.084 3435 Dihedral : 8.134 59.445 2792 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.44 % Favored : 91.39 % Rotamer: Outliers : 0.15 % Allowed : 2.56 % Favored : 97.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.74 (0.15), residues: 2355 helix: -0.98 (0.14), residues: 1174 sheet: -2.58 (0.35), residues: 206 loop : -2.63 (0.17), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 365 TYR 0.016 0.001 TYR I 303 PHE 0.022 0.002 PHE F 870 TRP 0.005 0.001 TRP L 753 HIS 0.004 0.001 HIS I 167 Details of bonding type rmsd covalent geometry : bond 0.00366 (19715) covalent geometry : angle 0.82564 (26696) hydrogen bonds : bond 0.06984 ( 829) hydrogen bonds : angle 5.62909 ( 2388) metal coordination : bond 0.00151 ( 4) Misc. bond : bond 0.01054 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Evaluate side-chains 572 residues out of total 2063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 571 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 18 ASP cc_start: 0.8689 (t0) cc_final: 0.8227 (t0) REVERT: C 172 TYR cc_start: 0.8364 (t80) cc_final: 0.7987 (t80) REVERT: C 263 SER cc_start: 0.8365 (t) cc_final: 0.7915 (p) REVERT: C 296 LEU cc_start: 0.8944 (tp) cc_final: 0.8713 (tp) REVERT: E 18 ASP cc_start: 0.8801 (t0) cc_final: 0.8334 (t0) REVERT: E 172 TYR cc_start: 0.8341 (t80) cc_final: 0.8136 (t80) REVERT: E 263 SER cc_start: 0.8512 (t) cc_final: 0.8156 (p) REVERT: E 296 LEU cc_start: 0.8919 (tp) cc_final: 0.8673 (tp) REVERT: K 18 ASP cc_start: 0.8632 (t0) cc_final: 0.8220 (t0) REVERT: K 296 LEU cc_start: 0.8913 (tp) cc_final: 0.8637 (tp) REVERT: I 18 ASP cc_start: 0.8689 (t0) cc_final: 0.8198 (t0) REVERT: I 172 TYR cc_start: 0.8180 (t80) cc_final: 0.7807 (t80) REVERT: I 242 LYS cc_start: 0.9365 (mttt) cc_final: 0.9118 (mtpp) REVERT: I 296 LEU cc_start: 0.8996 (tp) cc_final: 0.8757 (tp) REVERT: I 315 GLU cc_start: 0.8857 (tt0) cc_final: 0.8449 (tt0) REVERT: A 99 ASN cc_start: 0.8959 (m-40) cc_final: 0.8447 (t0) REVERT: G 99 ASN cc_start: 0.8871 (m-40) cc_final: 0.8429 (t0) REVERT: H 65 ILE cc_start: 0.9067 (mm) cc_final: 0.8818 (tt) REVERT: F 757 GLU cc_start: 0.8872 (pt0) cc_final: 0.8638 (pp20) REVERT: F 801 ASP cc_start: 0.8042 (t70) cc_final: 0.7185 (m-30) REVERT: F 835 MET cc_start: 0.7821 (pmm) cc_final: 0.7472 (tpp) REVERT: F 868 VAL cc_start: 0.9377 (p) cc_final: 0.9160 (m) REVERT: D 801 ASP cc_start: 0.8340 (t70) cc_final: 0.7802 (m-30) REVERT: D 841 PHE cc_start: 0.7876 (t80) cc_final: 0.7242 (t80) REVERT: D 874 TYR cc_start: 0.8377 (t80) cc_final: 0.7915 (t80) REVERT: L 801 ASP cc_start: 0.8244 (t70) cc_final: 0.7690 (m-30) REVERT: J 801 ASP cc_start: 0.8195 (t70) cc_final: 0.7563 (m-30) outliers start: 1 outliers final: 0 residues processed: 571 average time/residue: 0.3574 time to fit residues: 301.0235 Evaluate side-chains 442 residues out of total 2063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 442 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 190 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 185 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 222 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 169 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 281 HIS K 281 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.102874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.079727 restraints weight = 341086.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.084885 restraints weight = 170697.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.088677 restraints weight = 103411.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.091342 restraints weight = 69722.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.093243 restraints weight = 50829.693| |-----------------------------------------------------------------------------| r_work (final): 0.4066 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4066 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4066 r_free = 0.4066 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4065 r_free = 0.4065 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4065 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6669 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 19722 Z= 0.270 Angle : 0.842 14.861 26696 Z= 0.430 Chirality : 0.055 1.125 2833 Planarity : 0.006 0.080 3435 Dihedral : 7.859 59.605 2792 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.59 % Favored : 90.23 % Rotamer: Outliers : 0.10 % Allowed : 2.31 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.63 (0.16), residues: 2355 helix: -0.83 (0.14), residues: 1171 sheet: -2.75 (0.35), residues: 208 loop : -2.60 (0.18), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 229 TYR 0.014 0.002 TYR H 89 PHE 0.017 0.002 PHE A 129 TRP 0.008 0.001 TRP F 753 HIS 0.006 0.001 HIS K 39 Details of bonding type rmsd covalent geometry : bond 0.00528 (19715) covalent geometry : angle 0.84164 (26696) hydrogen bonds : bond 0.06224 ( 829) hydrogen bonds : angle 5.62756 ( 2388) metal coordination : bond 0.00215 ( 4) Misc. bond : bond 0.01777 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Evaluate side-chains 518 residues out of total 2063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 517 time to evaluate : 0.775 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 18 ASP cc_start: 0.8835 (t0) cc_final: 0.8388 (t0) REVERT: C 163 LEU cc_start: 0.9671 (mm) cc_final: 0.9460 (mm) REVERT: C 172 TYR cc_start: 0.8538 (t80) cc_final: 0.8299 (t80) REVERT: C 175 ILE cc_start: 0.7145 (mt) cc_final: 0.6902 (tp) REVERT: C 263 SER cc_start: 0.8550 (t) cc_final: 0.7993 (p) REVERT: C 296 LEU cc_start: 0.9126 (tp) cc_final: 0.8872 (tp) REVERT: E 18 ASP cc_start: 0.8844 (t0) cc_final: 0.8423 (t0) REVERT: E 172 TYR cc_start: 0.8578 (t80) cc_final: 0.8352 (t80) REVERT: E 296 LEU cc_start: 0.9041 (tp) cc_final: 0.8829 (tp) REVERT: K 18 ASP cc_start: 0.8794 (t0) cc_final: 0.8337 (t0) REVERT: K 163 LEU cc_start: 0.9650 (mm) cc_final: 0.9443 (mm) REVERT: K 296 LEU cc_start: 0.9139 (tp) cc_final: 0.8899 (tp) REVERT: I 18 ASP cc_start: 0.8821 (t0) cc_final: 0.8349 (t0) REVERT: I 242 LYS cc_start: 0.9408 (mttt) cc_final: 0.9196 (mmtt) REVERT: I 259 LEU cc_start: 0.8286 (tp) cc_final: 0.8061 (tp) REVERT: I 287 PHE cc_start: 0.9002 (t80) cc_final: 0.8619 (t80) REVERT: I 296 LEU cc_start: 0.9067 (tp) cc_final: 0.8863 (tp) REVERT: A 99 ASN cc_start: 0.9020 (m-40) cc_final: 0.8512 (t0) REVERT: G 99 ASN cc_start: 0.9000 (m-40) cc_final: 0.8565 (t0) REVERT: F 835 MET cc_start: 0.7918 (pmm) cc_final: 0.7459 (tpp) REVERT: D 841 PHE cc_start: 0.7836 (t80) cc_final: 0.7415 (t80) REVERT: D 874 TYR cc_start: 0.8383 (t80) cc_final: 0.7840 (t80) REVERT: L 841 PHE cc_start: 0.7857 (t80) cc_final: 0.7601 (t80) REVERT: J 841 PHE cc_start: 0.7834 (t80) cc_final: 0.7554 (t80) REVERT: J 876 LYS cc_start: 0.8513 (mttt) cc_final: 0.8000 (tptt) outliers start: 1 outliers final: 0 residues processed: 518 average time/residue: 0.3315 time to fit residues: 256.6774 Evaluate side-chains 417 residues out of total 2063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 417 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 209 optimal weight: 1.9990 chunk 216 optimal weight: 0.6980 chunk 170 optimal weight: 3.9990 chunk 166 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 186 optimal weight: 0.0170 chunk 23 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 181 optimal weight: 0.2980 overall best weight: 0.8020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 ASN E 40 ASN K 40 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.104497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.080175 restraints weight = 329328.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.085313 restraints weight = 170659.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.089157 restraints weight = 106057.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.091869 restraints weight = 72523.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.093821 restraints weight = 53317.728| |-----------------------------------------------------------------------------| r_work (final): 0.4071 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4072 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4072 r_free = 0.4072 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4072 r_free = 0.4072 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 42 | |-----------------------------------------------------------------------------| r_final: 0.4072 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.4337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 19722 Z= 0.154 Angle : 0.722 16.425 26696 Z= 0.368 Chirality : 0.046 0.805 2833 Planarity : 0.005 0.079 3435 Dihedral : 7.238 57.677 2792 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.91 % Favored : 90.92 % Rotamer: Outliers : 0.05 % Allowed : 1.23 % Favored : 98.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.17 (0.16), residues: 2355 helix: -0.38 (0.14), residues: 1174 sheet: -2.53 (0.36), residues: 206 loop : -2.49 (0.18), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 229 TYR 0.016 0.001 TYR C 358 PHE 0.023 0.002 PHE E 334 TRP 0.004 0.001 TRP I 135 HIS 0.006 0.001 HIS F 796 Details of bonding type rmsd covalent geometry : bond 0.00313 (19715) covalent geometry : angle 0.72218 (26696) hydrogen bonds : bond 0.05460 ( 829) hydrogen bonds : angle 5.15180 ( 2388) metal coordination : bond 0.00058 ( 4) Misc. bond : bond 0.00540 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Evaluate side-chains 511 residues out of total 2063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 511 time to evaluate : 1.086 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 18 ASP cc_start: 0.8836 (t0) cc_final: 0.8408 (t0) REVERT: C 263 SER cc_start: 0.8500 (t) cc_final: 0.7915 (p) REVERT: C 296 LEU cc_start: 0.8992 (tp) cc_final: 0.8744 (tp) REVERT: E 18 ASP cc_start: 0.8863 (t0) cc_final: 0.8459 (t0) REVERT: K 18 ASP cc_start: 0.8802 (t0) cc_final: 0.8341 (t0) REVERT: K 172 TYR cc_start: 0.8375 (t80) cc_final: 0.7872 (t80) REVERT: K 242 LYS cc_start: 0.9356 (mtpt) cc_final: 0.9021 (mtpp) REVERT: K 367 PHE cc_start: 0.9285 (m-80) cc_final: 0.8634 (m-10) REVERT: I 18 ASP cc_start: 0.8851 (t0) cc_final: 0.8395 (t0) REVERT: I 51 MET cc_start: 0.9087 (pmm) cc_final: 0.8809 (pmm) REVERT: I 160 ILE cc_start: 0.9578 (mt) cc_final: 0.8991 (tp) REVERT: I 172 TYR cc_start: 0.8317 (t80) cc_final: 0.7892 (t80) REVERT: I 259 LEU cc_start: 0.8183 (tp) cc_final: 0.7836 (tp) REVERT: I 315 GLU cc_start: 0.8736 (tt0) cc_final: 0.8120 (tt0) REVERT: A 99 ASN cc_start: 0.9038 (m-40) cc_final: 0.8513 (t0) REVERT: G 99 ASN cc_start: 0.8979 (m-40) cc_final: 0.8456 (t0) REVERT: G 101 ARG cc_start: 0.8432 (tpt-90) cc_final: 0.8200 (tpt-90) REVERT: F 757 GLU cc_start: 0.8979 (pt0) cc_final: 0.8755 (pp20) REVERT: F 835 MET cc_start: 0.7918 (pmm) cc_final: 0.7421 (tpp) REVERT: F 867 CYS cc_start: 0.9521 (t) cc_final: 0.8840 (m) REVERT: D 841 PHE cc_start: 0.7808 (t80) cc_final: 0.7356 (t80) REVERT: D 874 TYR cc_start: 0.8448 (t80) cc_final: 0.7860 (t80) REVERT: L 841 PHE cc_start: 0.7845 (t80) cc_final: 0.7616 (t80) REVERT: J 839 LYS cc_start: 0.8833 (tptt) cc_final: 0.8470 (mmmt) REVERT: J 841 PHE cc_start: 0.7904 (t80) cc_final: 0.7565 (t80) outliers start: 0 outliers final: 0 residues processed: 511 average time/residue: 0.3482 time to fit residues: 267.0791 Evaluate side-chains 418 residues out of total 2063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 418 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 125 optimal weight: 5.9990 chunk 204 optimal weight: 0.8980 chunk 146 optimal weight: 2.9990 chunk 222 optimal weight: 0.3980 chunk 86 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 217 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 88 optimal weight: 4.9990 chunk 26 optimal weight: 8.9990 chunk 192 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 796 HIS D 796 HIS L 796 HIS J 796 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.100811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.076493 restraints weight = 381722.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.081630 restraints weight = 191963.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.085354 restraints weight = 117793.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.088059 restraints weight = 80432.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.089984 restraints weight = 59277.518| |-----------------------------------------------------------------------------| r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4007 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4007 r_free = 0.4007 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 42 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4007 r_free = 0.4007 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 42 | |-----------------------------------------------------------------------------| r_final: 0.4007 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6738 moved from start: 0.4917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19722 Z= 0.174 Angle : 0.682 8.524 26696 Z= 0.358 Chirality : 0.042 0.420 2833 Planarity : 0.005 0.076 3435 Dihedral : 6.977 54.525 2792 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.55 % Favored : 90.28 % Rotamer: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.16), residues: 2355 helix: -0.19 (0.15), residues: 1170 sheet: -2.50 (0.37), residues: 208 loop : -2.44 (0.18), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 722 TYR 0.028 0.001 TYR I 166 PHE 0.018 0.002 PHE F 870 TRP 0.013 0.001 TRP I 135 HIS 0.007 0.001 HIS J 796 Details of bonding type rmsd covalent geometry : bond 0.00344 (19715) covalent geometry : angle 0.68232 (26696) hydrogen bonds : bond 0.04950 ( 829) hydrogen bonds : angle 5.00630 ( 2388) metal coordination : bond 0.00013 ( 4) Misc. bond : bond 0.00279 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Evaluate side-chains 501 residues out of total 2063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 501 time to evaluate : 0.795 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 18 ASP cc_start: 0.8862 (t0) cc_final: 0.8428 (t0) REVERT: C 172 TYR cc_start: 0.8429 (t80) cc_final: 0.8053 (t80) REVERT: C 175 ILE cc_start: 0.7513 (mt) cc_final: 0.7311 (tp) REVERT: C 226 TYR cc_start: 0.7295 (t80) cc_final: 0.7078 (t80) REVERT: C 242 LYS cc_start: 0.9438 (mttt) cc_final: 0.9033 (mmmt) REVERT: C 259 LEU cc_start: 0.8433 (tp) cc_final: 0.8003 (tt) REVERT: C 263 SER cc_start: 0.8634 (t) cc_final: 0.8084 (p) REVERT: C 287 PHE cc_start: 0.8845 (t80) cc_final: 0.8487 (t80) REVERT: E 18 ASP cc_start: 0.8921 (t0) cc_final: 0.8514 (t0) REVERT: E 242 LYS cc_start: 0.9568 (pttm) cc_final: 0.9366 (ptpt) REVERT: K 18 ASP cc_start: 0.8856 (t0) cc_final: 0.8417 (t0) REVERT: K 242 LYS cc_start: 0.9366 (mtpt) cc_final: 0.9064 (mmtt) REVERT: K 259 LEU cc_start: 0.8433 (tp) cc_final: 0.8210 (tt) REVERT: K 366 LEU cc_start: 0.9509 (tp) cc_final: 0.9243 (tp) REVERT: I 18 ASP cc_start: 0.8858 (t0) cc_final: 0.8391 (t0) REVERT: I 51 MET cc_start: 0.9046 (pmm) cc_final: 0.8833 (pmm) REVERT: I 242 LYS cc_start: 0.9490 (mtpt) cc_final: 0.9262 (mtpp) REVERT: A 99 ASN cc_start: 0.9036 (m-40) cc_final: 0.8555 (t0) REVERT: B 65 ILE cc_start: 0.9065 (mm) cc_final: 0.8759 (tt) REVERT: G 99 ASN cc_start: 0.9073 (m-40) cc_final: 0.8531 (t0) REVERT: F 835 MET cc_start: 0.7889 (pmm) cc_final: 0.7414 (tpp) REVERT: F 867 CYS cc_start: 0.9574 (t) cc_final: 0.8934 (m) REVERT: D 807 ASN cc_start: 0.8584 (m110) cc_final: 0.8123 (t0) REVERT: D 841 PHE cc_start: 0.7868 (t80) cc_final: 0.7442 (t80) REVERT: L 807 ASN cc_start: 0.8589 (m110) cc_final: 0.8085 (t0) REVERT: L 841 PHE cc_start: 0.7891 (t80) cc_final: 0.7337 (t80) REVERT: J 841 PHE cc_start: 0.7955 (t80) cc_final: 0.7554 (t80) outliers start: 0 outliers final: 0 residues processed: 501 average time/residue: 0.3103 time to fit residues: 237.4355 Evaluate side-chains 413 residues out of total 2063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 413 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 133 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 209 optimal weight: 3.9990 chunk 206 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 chunk 85 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 178 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.094603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.073349 restraints weight = 349594.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.077588 restraints weight = 182523.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.080643 restraints weight = 114483.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.082801 restraints weight = 80099.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.084424 restraints weight = 60570.468| |-----------------------------------------------------------------------------| r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3906 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3906 r_free = 0.3906 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 42 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3906 r_free = 0.3906 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 42 | |-----------------------------------------------------------------------------| r_final: 0.3906 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.5710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.146 19722 Z= 0.291 Angle : 0.784 17.757 26696 Z= 0.421 Chirality : 0.043 0.444 2833 Planarity : 0.006 0.071 3435 Dihedral : 7.179 54.919 2792 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.75 % Favored : 87.08 % Rotamer: Outliers : 0.05 % Allowed : 2.51 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: -2.49 (0.16), residues: 2355 helix: -0.73 (0.14), residues: 1191 sheet: -2.69 (0.38), residues: 208 loop : -2.54 (0.18), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 49 TYR 0.014 0.002 TYR E 152 PHE 0.028 0.003 PHE C 367 TRP 0.013 0.002 TRP D 753 HIS 0.012 0.002 HIS D 796 Details of bonding type rmsd covalent geometry : bond 0.00559 (19715) covalent geometry : angle 0.78423 (26696) hydrogen bonds : bond 0.05314 ( 829) hydrogen bonds : angle 5.38729 ( 2388) metal coordination : bond 0.00058 ( 4) Misc. bond : bond 0.01293 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Evaluate side-chains 480 residues out of total 2063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 479 time to evaluate : 1.081 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 259 LEU cc_start: 0.8474 (tp) cc_final: 0.8237 (tt) REVERT: C 263 SER cc_start: 0.8764 (t) cc_final: 0.8323 (p) REVERT: E 172 TYR cc_start: 0.8481 (t80) cc_final: 0.8079 (t80) REVERT: E 242 LYS cc_start: 0.9577 (pttm) cc_final: 0.9345 (mtmm) REVERT: E 245 MET cc_start: 0.9152 (tpp) cc_final: 0.8872 (tpp) REVERT: E 248 VAL cc_start: 0.9527 (t) cc_final: 0.9316 (p) REVERT: E 259 LEU cc_start: 0.8703 (tp) cc_final: 0.8428 (tt) REVERT: K 18 ASP cc_start: 0.8972 (t0) cc_final: 0.8534 (t0) REVERT: K 172 TYR cc_start: 0.8502 (t80) cc_final: 0.8298 (t80) REVERT: K 242 LYS cc_start: 0.9502 (mtpt) cc_final: 0.8984 (mtpp) REVERT: K 287 PHE cc_start: 0.8986 (t80) cc_final: 0.8708 (t80) REVERT: K 296 LEU cc_start: 0.9084 (tp) cc_final: 0.8868 (tp) REVERT: I 242 LYS cc_start: 0.9514 (mtpt) cc_final: 0.9237 (mmmt) REVERT: I 372 MET cc_start: 0.8960 (tpp) cc_final: 0.8696 (tpp) REVERT: A 99 ASN cc_start: 0.9125 (m-40) cc_final: 0.8599 (t0) REVERT: B 65 ILE cc_start: 0.9066 (mm) cc_final: 0.8837 (tt) REVERT: B 67 MET cc_start: 0.9331 (mmt) cc_final: 0.9101 (mmm) REVERT: G 99 ASN cc_start: 0.9079 (m-40) cc_final: 0.8552 (t0) REVERT: H 67 MET cc_start: 0.9126 (mmm) cc_final: 0.8754 (mmm) REVERT: F 835 MET cc_start: 0.7879 (pmm) cc_final: 0.7465 (tpp) REVERT: D 807 ASN cc_start: 0.8731 (m110) cc_final: 0.8281 (t0) REVERT: D 841 PHE cc_start: 0.8046 (t80) cc_final: 0.7634 (t80) REVERT: L 807 ASN cc_start: 0.8746 (m110) cc_final: 0.8272 (t0) REVERT: L 841 PHE cc_start: 0.7830 (t80) cc_final: 0.7480 (t80) REVERT: J 807 ASN cc_start: 0.8662 (m110) cc_final: 0.8237 (t0) REVERT: J 841 PHE cc_start: 0.8152 (t80) cc_final: 0.7737 (t80) outliers start: 1 outliers final: 1 residues processed: 479 average time/residue: 0.3495 time to fit residues: 252.3874 Evaluate side-chains 401 residues out of total 2063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 400 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 219 optimal weight: 0.5980 chunk 149 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 226 optimal weight: 0.9990 chunk 175 optimal weight: 0.0070 chunk 32 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 overall best weight: 1.3002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.097385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.075115 restraints weight = 344332.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.079900 restraints weight = 172164.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.083328 restraints weight = 104561.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.085753 restraints weight = 71011.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.087448 restraints weight = 52241.768| |-----------------------------------------------------------------------------| r_work (final): 0.3962 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3962 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3962 r_free = 0.3962 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 42 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3963 r_free = 0.3963 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 42 | |-----------------------------------------------------------------------------| r_final: 0.3963 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.6007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 19722 Z= 0.169 Angle : 0.666 9.673 26696 Z= 0.355 Chirality : 0.040 0.205 2833 Planarity : 0.005 0.073 3435 Dihedral : 7.072 58.715 2792 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.85 % Favored : 90.15 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: -2.11 (0.17), residues: 2355 helix: -0.34 (0.14), residues: 1167 sheet: -2.63 (0.37), residues: 208 loop : -2.39 (0.18), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 49 TYR 0.021 0.002 TYR K 24 PHE 0.031 0.002 PHE B 129 TRP 0.010 0.001 TRP J 753 HIS 0.024 0.002 HIS D 796 Details of bonding type rmsd covalent geometry : bond 0.00339 (19715) covalent geometry : angle 0.66589 (26696) hydrogen bonds : bond 0.04718 ( 829) hydrogen bonds : angle 5.01364 ( 2388) metal coordination : bond 0.00020 ( 4) Misc. bond : bond 0.00263 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Evaluate side-chains 487 residues out of total 2063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 487 time to evaluate : 0.973 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 18 ASP cc_start: 0.9001 (t0) cc_final: 0.8624 (t70) REVERT: C 172 TYR cc_start: 0.8494 (t80) cc_final: 0.8238 (t80) REVERT: C 259 LEU cc_start: 0.8439 (tp) cc_final: 0.8214 (tt) REVERT: C 263 SER cc_start: 0.8654 (t) cc_final: 0.8189 (p) REVERT: C 296 LEU cc_start: 0.8938 (tp) cc_final: 0.8720 (tp) REVERT: E 18 ASP cc_start: 0.9037 (t0) cc_final: 0.8676 (t70) REVERT: E 172 TYR cc_start: 0.8553 (t80) cc_final: 0.7985 (t80) REVERT: E 185 GLU cc_start: 0.9587 (mt-10) cc_final: 0.9376 (mt-10) REVERT: E 259 LEU cc_start: 0.8480 (tp) cc_final: 0.8226 (tt) REVERT: E 284 CYS cc_start: 0.9360 (m) cc_final: 0.8496 (m) REVERT: K 18 ASP cc_start: 0.8958 (t0) cc_final: 0.8514 (t70) REVERT: K 172 TYR cc_start: 0.8504 (t80) cc_final: 0.8262 (t80) REVERT: K 175 ILE cc_start: 0.7857 (mt) cc_final: 0.7623 (tp) REVERT: K 242 LYS cc_start: 0.9459 (mtpt) cc_final: 0.8937 (mtpp) REVERT: K 287 PHE cc_start: 0.8933 (t80) cc_final: 0.8625 (t80) REVERT: I 18 ASP cc_start: 0.9011 (t0) cc_final: 0.8627 (t70) REVERT: I 221 TYR cc_start: 0.8332 (m-80) cc_final: 0.7874 (m-80) REVERT: I 242 LYS cc_start: 0.9453 (mtpt) cc_final: 0.9162 (mmmt) REVERT: I 372 MET cc_start: 0.8901 (tpp) cc_final: 0.8223 (tmm) REVERT: A 99 ASN cc_start: 0.9118 (m-40) cc_final: 0.8507 (t0) REVERT: B 65 ILE cc_start: 0.9069 (mm) cc_final: 0.8812 (tt) REVERT: G 99 ASN cc_start: 0.9080 (m-40) cc_final: 0.8503 (t0) REVERT: F 835 MET cc_start: 0.7783 (pmm) cc_final: 0.7375 (tmm) REVERT: F 867 CYS cc_start: 0.9573 (t) cc_final: 0.8943 (m) REVERT: D 807 ASN cc_start: 0.8657 (m110) cc_final: 0.8167 (t0) REVERT: D 841 PHE cc_start: 0.8028 (t80) cc_final: 0.7618 (t80) REVERT: L 807 ASN cc_start: 0.8641 (m110) cc_final: 0.8180 (t0) REVERT: L 841 PHE cc_start: 0.7827 (t80) cc_final: 0.7500 (t80) REVERT: J 807 ASN cc_start: 0.8526 (m110) cc_final: 0.8097 (t0) REVERT: J 841 PHE cc_start: 0.8198 (t80) cc_final: 0.7811 (t80) outliers start: 0 outliers final: 0 residues processed: 487 average time/residue: 0.3221 time to fit residues: 240.3376 Evaluate side-chains 415 residues out of total 2063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 415 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 127 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 184 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 162 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 793 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.094904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.073351 restraints weight = 353425.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.077880 restraints weight = 175965.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.081115 restraints weight = 106965.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.083384 restraints weight = 72899.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.085037 restraints weight = 54068.215| |-----------------------------------------------------------------------------| r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3923 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3923 r_free = 0.3923 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 42 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3923 r_free = 0.3923 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 42 | |-----------------------------------------------------------------------------| r_final: 0.3923 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.6404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.272 19722 Z= 0.264 Angle : 0.784 36.056 26696 Z= 0.399 Chirality : 0.045 0.728 2833 Planarity : 0.005 0.072 3435 Dihedral : 7.374 59.260 2792 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.20 % Favored : 87.80 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.46 (0.16), residues: 2355 helix: -0.67 (0.14), residues: 1194 sheet: -2.84 (0.36), residues: 203 loop : -2.54 (0.18), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 101 TYR 0.046 0.002 TYR I 24 PHE 0.037 0.002 PHE I 103 TRP 0.011 0.002 TRP J 753 HIS 0.024 0.002 HIS F 796 Details of bonding type rmsd covalent geometry : bond 0.00544 (19715) covalent geometry : angle 0.78366 (26696) hydrogen bonds : bond 0.04922 ( 829) hydrogen bonds : angle 5.22009 ( 2388) metal coordination : bond 0.00040 ( 4) Misc. bond : bond 0.02271 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Evaluate side-chains 484 residues out of total 2063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 484 time to evaluate : 1.080 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 18 ASP cc_start: 0.9038 (t0) cc_final: 0.8695 (t70) REVERT: C 117 SER cc_start: 0.8849 (m) cc_final: 0.8572 (p) REVERT: C 172 TYR cc_start: 0.8440 (t80) cc_final: 0.8204 (t80) REVERT: C 259 LEU cc_start: 0.8515 (tp) cc_final: 0.8291 (tt) REVERT: C 263 SER cc_start: 0.8843 (t) cc_final: 0.8405 (p) REVERT: C 296 LEU cc_start: 0.9005 (tp) cc_final: 0.8773 (tp) REVERT: E 172 TYR cc_start: 0.8407 (t80) cc_final: 0.8184 (t80) REVERT: E 284 CYS cc_start: 0.9295 (m) cc_final: 0.8479 (m) REVERT: K 18 ASP cc_start: 0.9022 (t0) cc_final: 0.8623 (t70) REVERT: K 242 LYS cc_start: 0.9491 (mtpt) cc_final: 0.9002 (mtpp) REVERT: K 287 PHE cc_start: 0.8988 (t80) cc_final: 0.8741 (t80) REVERT: K 296 LEU cc_start: 0.8980 (tp) cc_final: 0.8767 (tp) REVERT: I 372 MET cc_start: 0.8979 (tpp) cc_final: 0.8741 (tpp) REVERT: A 99 ASN cc_start: 0.9152 (m-40) cc_final: 0.8498 (t0) REVERT: B 65 ILE cc_start: 0.9052 (mm) cc_final: 0.8832 (tt) REVERT: G 99 ASN cc_start: 0.9112 (m-40) cc_final: 0.8512 (t0) REVERT: H 67 MET cc_start: 0.9135 (mmm) cc_final: 0.8704 (mmm) REVERT: F 757 GLU cc_start: 0.8963 (pt0) cc_final: 0.8710 (pp20) REVERT: F 807 ASN cc_start: 0.8777 (m110) cc_final: 0.8339 (t0) REVERT: F 835 MET cc_start: 0.7743 (pmm) cc_final: 0.7350 (tmm) REVERT: D 807 ASN cc_start: 0.8700 (m110) cc_final: 0.8286 (t0) REVERT: D 841 PHE cc_start: 0.8074 (t80) cc_final: 0.7650 (t80) REVERT: L 807 ASN cc_start: 0.8736 (m110) cc_final: 0.8307 (t0) REVERT: L 841 PHE cc_start: 0.7795 (t80) cc_final: 0.7436 (t80) REVERT: J 807 ASN cc_start: 0.8661 (m110) cc_final: 0.8252 (t0) REVERT: J 841 PHE cc_start: 0.8141 (t80) cc_final: 0.7694 (t80) REVERT: J 847 ILE cc_start: 0.7627 (mt) cc_final: 0.7419 (tp) outliers start: 0 outliers final: 0 residues processed: 484 average time/residue: 0.3202 time to fit residues: 239.8151 Evaluate side-chains 403 residues out of total 2063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 403 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 55 optimal weight: 0.7980 chunk 151 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 793 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 793 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 793 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.096165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.074299 restraints weight = 352487.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.078890 restraints weight = 179191.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.082155 restraints weight = 110383.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.084508 restraints weight = 75938.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.086176 restraints weight = 56400.881| |-----------------------------------------------------------------------------| r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3940 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3940 r_free = 0.3940 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 42 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3940 r_free = 0.3940 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 42 | |-----------------------------------------------------------------------------| r_final: 0.3940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.6556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19722 Z= 0.153 Angle : 0.675 10.390 26696 Z= 0.359 Chirality : 0.041 0.248 2833 Planarity : 0.005 0.073 3435 Dihedral : 7.236 58.421 2792 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.94 % Favored : 90.06 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: -2.12 (0.16), residues: 2355 helix: -0.34 (0.14), residues: 1180 sheet: -2.60 (0.37), residues: 203 loop : -2.45 (0.18), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 49 TYR 0.063 0.002 TYR F 874 PHE 0.060 0.002 PHE F 870 TRP 0.011 0.001 TRP J 753 HIS 0.020 0.002 HIS D 796 Details of bonding type rmsd covalent geometry : bond 0.00315 (19715) covalent geometry : angle 0.67537 (26696) hydrogen bonds : bond 0.04724 ( 829) hydrogen bonds : angle 4.91740 ( 2388) metal coordination : bond 0.00018 ( 4) Misc. bond : bond 0.00305 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Evaluate side-chains 492 residues out of total 2063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 492 time to evaluate : 1.004 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 18 ASP cc_start: 0.9046 (t0) cc_final: 0.8707 (t70) REVERT: C 221 TYR cc_start: 0.8158 (m-80) cc_final: 0.7903 (m-80) REVERT: C 241 PHE cc_start: 0.9058 (t80) cc_final: 0.8821 (t80) REVERT: C 259 LEU cc_start: 0.8446 (tp) cc_final: 0.8216 (tt) REVERT: C 263 SER cc_start: 0.8719 (t) cc_final: 0.8244 (p) REVERT: C 296 LEU cc_start: 0.8950 (tp) cc_final: 0.8713 (tp) REVERT: E 18 ASP cc_start: 0.9086 (t0) cc_final: 0.8774 (t70) REVERT: K 18 ASP cc_start: 0.8999 (t0) cc_final: 0.8596 (t70) REVERT: K 242 LYS cc_start: 0.9453 (mtpt) cc_final: 0.8947 (mtpp) REVERT: K 287 PHE cc_start: 0.8969 (t80) cc_final: 0.8711 (t80) REVERT: K 296 LEU cc_start: 0.8968 (tp) cc_final: 0.8731 (tp) REVERT: I 18 ASP cc_start: 0.9046 (t0) cc_final: 0.8712 (t70) REVERT: I 39 HIS cc_start: 0.9248 (t70) cc_final: 0.8925 (t70) REVERT: I 372 MET cc_start: 0.9031 (tpp) cc_final: 0.8804 (tpp) REVERT: A 99 ASN cc_start: 0.9138 (m-40) cc_final: 0.8462 (t0) REVERT: B 65 ILE cc_start: 0.9011 (mm) cc_final: 0.8786 (tt) REVERT: B 116 GLU cc_start: 0.9281 (tp30) cc_final: 0.9079 (tp30) REVERT: G 99 ASN cc_start: 0.9100 (m-40) cc_final: 0.8456 (t0) REVERT: F 807 ASN cc_start: 0.8829 (m110) cc_final: 0.8356 (t0) REVERT: F 835 MET cc_start: 0.7801 (pmm) cc_final: 0.7364 (tmm) REVERT: F 867 CYS cc_start: 0.9614 (t) cc_final: 0.8936 (m) REVERT: D 807 ASN cc_start: 0.8650 (m110) cc_final: 0.8211 (t0) REVERT: D 841 PHE cc_start: 0.7988 (t80) cc_final: 0.7596 (t80) REVERT: D 868 VAL cc_start: 0.9524 (m) cc_final: 0.9031 (m) REVERT: L 807 ASN cc_start: 0.8703 (m110) cc_final: 0.8220 (t0) REVERT: L 841 PHE cc_start: 0.7921 (t80) cc_final: 0.7517 (t80) REVERT: J 807 ASN cc_start: 0.8594 (m110) cc_final: 0.8095 (t0) REVERT: J 841 PHE cc_start: 0.7962 (t80) cc_final: 0.7483 (t80) outliers start: 0 outliers final: 0 residues processed: 492 average time/residue: 0.3006 time to fit residues: 229.3502 Evaluate side-chains 413 residues out of total 2063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 413 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 125 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 86 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 157 optimal weight: 0.0270 chunk 138 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 81 optimal weight: 0.4980 chunk 6 optimal weight: 0.9990 overall best weight: 0.8642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 83 GLN ** F 793 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 793 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 793 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.096263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.074676 restraints weight = 334787.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.079191 restraints weight = 172128.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.082453 restraints weight = 106585.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.084762 restraints weight = 73496.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.086461 restraints weight = 54790.110| |-----------------------------------------------------------------------------| r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3949 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3949 r_free = 0.3949 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 42 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3949 r_free = 0.3949 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 42 | |-----------------------------------------------------------------------------| r_final: 0.3949 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 moved from start: 0.6688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19722 Z= 0.141 Angle : 0.667 21.053 26696 Z= 0.347 Chirality : 0.043 0.595 2833 Planarity : 0.005 0.074 3435 Dihedral : 7.084 54.605 2792 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.23 % Favored : 89.77 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: -1.89 (0.17), residues: 2355 helix: -0.13 (0.15), residues: 1173 sheet: -2.50 (0.37), residues: 203 loop : -2.36 (0.19), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 49 TYR 0.056 0.002 TYR K 24 PHE 0.050 0.002 PHE K 103 TRP 0.011 0.001 TRP F 753 HIS 0.019 0.001 HIS F 796 Details of bonding type rmsd covalent geometry : bond 0.00291 (19715) covalent geometry : angle 0.66668 (26696) hydrogen bonds : bond 0.04531 ( 829) hydrogen bonds : angle 4.77316 ( 2388) metal coordination : bond 0.00011 ( 4) Misc. bond : bond 0.00162 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Evaluate side-chains 490 residues out of total 2063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 490 time to evaluate : 1.066 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 18 ASP cc_start: 0.8994 (t0) cc_final: 0.8652 (t70) REVERT: C 221 TYR cc_start: 0.8228 (m-80) cc_final: 0.7969 (m-80) REVERT: C 241 PHE cc_start: 0.8974 (t80) cc_final: 0.8731 (t80) REVERT: C 248 VAL cc_start: 0.9610 (t) cc_final: 0.9286 (p) REVERT: C 263 SER cc_start: 0.8728 (t) cc_final: 0.8224 (p) REVERT: C 296 LEU cc_start: 0.8906 (tp) cc_final: 0.8644 (tp) REVERT: E 18 ASP cc_start: 0.9072 (t0) cc_final: 0.8764 (t70) REVERT: E 296 LEU cc_start: 0.8909 (tp) cc_final: 0.8700 (tp) REVERT: K 18 ASP cc_start: 0.8973 (t0) cc_final: 0.8563 (t70) REVERT: K 242 LYS cc_start: 0.9462 (mtpt) cc_final: 0.8955 (mtpp) REVERT: K 287 PHE cc_start: 0.8923 (t80) cc_final: 0.8638 (t80) REVERT: K 296 LEU cc_start: 0.8905 (tp) cc_final: 0.8672 (tp) REVERT: I 18 ASP cc_start: 0.9005 (t0) cc_final: 0.8671 (t70) REVERT: I 39 HIS cc_start: 0.9251 (t70) cc_final: 0.8919 (t70) REVERT: I 372 MET cc_start: 0.9017 (tpp) cc_final: 0.8801 (tpp) REVERT: A 99 ASN cc_start: 0.9126 (m-40) cc_final: 0.8450 (t0) REVERT: B 65 ILE cc_start: 0.9078 (mm) cc_final: 0.8778 (tt) REVERT: G 99 ASN cc_start: 0.9087 (m-40) cc_final: 0.8439 (t0) REVERT: G 108 VAL cc_start: 0.8222 (t) cc_final: 0.8010 (p) REVERT: F 807 ASN cc_start: 0.8742 (m110) cc_final: 0.8350 (t0) REVERT: F 835 MET cc_start: 0.7729 (pmm) cc_final: 0.7339 (tmm) REVERT: F 867 CYS cc_start: 0.9621 (t) cc_final: 0.8985 (m) REVERT: D 807 ASN cc_start: 0.8662 (m110) cc_final: 0.8232 (t0) REVERT: D 841 PHE cc_start: 0.8060 (t80) cc_final: 0.7682 (t80) REVERT: D 868 VAL cc_start: 0.9494 (m) cc_final: 0.9027 (m) REVERT: L 777 CYS cc_start: 0.7423 (t) cc_final: 0.7070 (t) REVERT: L 807 ASN cc_start: 0.8721 (m110) cc_final: 0.8284 (t0) REVERT: L 841 PHE cc_start: 0.7983 (t80) cc_final: 0.7582 (t80) REVERT: J 807 ASN cc_start: 0.8620 (m110) cc_final: 0.8146 (t0) REVERT: J 841 PHE cc_start: 0.7969 (t80) cc_final: 0.7421 (t80) outliers start: 0 outliers final: 0 residues processed: 490 average time/residue: 0.3015 time to fit residues: 229.3107 Evaluate side-chains 419 residues out of total 2063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 419 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 160 optimal weight: 0.0980 chunk 216 optimal weight: 1.9990 chunk 213 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 204 optimal weight: 0.9990 chunk 118 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** F 793 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 793 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 793 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 793 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.095890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.074346 restraints weight = 342769.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.078837 restraints weight = 174402.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.082043 restraints weight = 107831.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.084361 restraints weight = 74382.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.086006 restraints weight = 55441.634| |-----------------------------------------------------------------------------| r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3937 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3937 r_free = 0.3937 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 42 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3937 r_free = 0.3937 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 42 | |-----------------------------------------------------------------------------| r_final: 0.3937 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.6834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.234 19722 Z= 0.173 Angle : 0.684 15.791 26696 Z= 0.355 Chirality : 0.040 0.237 2833 Planarity : 0.005 0.073 3435 Dihedral : 7.078 57.041 2792 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.17), residues: 2355 helix: -0.14 (0.15), residues: 1179 sheet: -2.52 (0.37), residues: 203 loop : -2.35 (0.19), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 49 TYR 0.037 0.002 TYR J 874 PHE 0.039 0.002 PHE K 103 TRP 0.013 0.001 TRP F 753 HIS 0.019 0.001 HIS D 796 Details of bonding type rmsd covalent geometry : bond 0.00364 (19715) covalent geometry : angle 0.68447 (26696) hydrogen bonds : bond 0.04416 ( 829) hydrogen bonds : angle 4.76675 ( 2388) metal coordination : bond 0.00021 ( 4) Misc. bond : bond 0.01563 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8182.69 seconds wall clock time: 140 minutes 0.49 seconds (8400.49 seconds total)