Starting phenix.real_space_refine on Fri Aug 7 03:13:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oqd_70746/08_2026/9oqd_70746.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oqd_70746/08_2026/9oqd_70746.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9oqd_70746/08_2026/9oqd_70746.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oqd_70746/08_2026/9oqd_70746.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9oqd_70746/08_2026/9oqd_70746.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oqd_70746/08_2026/9oqd_70746.map" } resolution = 3.36 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= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 99 5.16 5 C 11796 2.51 5 N 3012 2.21 5 O 3618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18531 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1662 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 12, 'TRANS': 200} Chain breaks: 1 Chain: "B" Number of atoms: 1560 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 203, 1551 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 13, 'TRANS': 189} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 203, 1551 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 13, 'TRANS': 189} Chain breaks: 2 bond proxies already assigned to first conformer: 1581 Chain: "C" Number of atoms: 2821 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 365, 2796 Classifications: {'peptide': 365} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 348} Conformer: "B" Number of residues, atoms: 365, 2796 Classifications: {'peptide': 365} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 348} bond proxies already assigned to first conformer: 2830 Chain: "D" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1662 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 12, 'TRANS': 200} Chain breaks: 1 Chain: "E" Number of atoms: 1560 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 203, 1551 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 13, 'TRANS': 189} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 203, 1551 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 13, 'TRANS': 189} Chain breaks: 2 bond proxies already assigned to first conformer: 1581 Chain: "F" Number of atoms: 2821 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 365, 2796 Classifications: {'peptide': 365} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 348} Conformer: "B" Number of residues, atoms: 365, 2796 Classifications: {'peptide': 365} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 348} bond proxies already assigned to first conformer: 2830 Chain: "G" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1662 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 12, 'TRANS': 200} Chain breaks: 1 Chain: "H" Number of atoms: 1560 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 203, 1551 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 13, 'TRANS': 189} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 203, 1551 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 13, 'TRANS': 189} Chain breaks: 2 bond proxies already assigned to first conformer: 1581 Chain: "I" Number of atoms: 2821 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 365, 2796 Classifications: {'peptide': 365} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 348} Conformer: "B" Number of residues, atoms: 365, 2796 Classifications: {'peptide': 365} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 348} bond proxies already assigned to first conformer: 2830 Chain: "C" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 190 Unusual residues: {'DAO': 2, 'FO4': 2, 'NAG': 1, 'PEX': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "F" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 134 Unusual residues: {'DAO': 2, 'FO4': 1, 'NAG': 1, 'PEX': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "I" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 78 Unusual residues: {'DAO': 2, 'NAG': 1, 'PEX': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N AASN C 57 " occ=0.54 ... (14 atoms not shown) pdb=" ND2BASN C 57 " occ=0.46 residue: pdb=" N APHE C 110 " occ=0.45 ... (20 atoms not shown) pdb=" CZ BPHE C 110 " occ=0.55 residue: pdb=" N AASN F 57 " occ=0.54 ... (14 atoms not shown) pdb=" ND2BASN F 57 " occ=0.46 residue: pdb=" N APHE F 110 " occ=0.45 ... (20 atoms not shown) pdb=" CZ BPHE F 110 " occ=0.55 residue: pdb=" N AASN I 57 " occ=0.54 ... (14 atoms not shown) pdb=" ND2BASN I 57 " occ=0.46 residue: pdb=" N APHE I 110 " occ=0.45 ... (20 atoms not shown) pdb=" CZ BPHE I 110 " occ=0.55 Time building chain proxies: 5.39, per 1000 atoms: 0.29 Number of scatterers: 18531 At special positions: 0 Unit cell: (141.349, 143.507, 160.771, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 99 16.00 P 6 15.00 O 3618 8.00 N 3012 7.00 C 11796 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 28 " - pdb=" SG CYS A 98 " distance=2.04 Simple disulfide: pdb=" SG CYS A 144 " - pdb=" SG CYS A 204 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 147 " - pdb=" SG CYS B 202 " distance=2.04 Simple disulfide: pdb=" SG CYS D 28 " - pdb=" SG CYS D 98 " distance=2.04 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 204 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 202 " distance=2.04 Simple disulfide: pdb=" SG CYS G 28 " - pdb=" SG CYS G 98 " distance=2.04 Simple disulfide: pdb=" SG CYS G 144 " - pdb=" SG CYS G 204 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 202 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.35 Conformation dependent library (CDL) restraints added in 1.2 seconds 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4404 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 39 sheets defined 2.8% alpha, 43.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'B' and resid 193 through 198 removed outlier: 3.916A pdb=" N SER B 197 " --> pdb=" O SER B 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 12 removed outlier: 4.430A pdb=" N MET C 12 " --> pdb=" O GLU C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 131 Processing helix chain 'D' and resid 192 through 197 Processing helix chain 'E' and resid 193 through 198 removed outlier: 3.916A pdb=" N SER E 197 " --> pdb=" O SER E 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 12 removed outlier: 4.430A pdb=" N MET F 12 " --> pdb=" O GLU F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 131 Processing helix chain 'G' and resid 192 through 197 Processing helix chain 'H' and resid 193 through 198 removed outlier: 3.917A pdb=" N SER H 197 " --> pdb=" O SER H 193 " (cutoff:3.500A) Processing helix chain 'I' and resid 7 through 12 removed outlier: 4.430A pdb=" N MET I 12 " --> pdb=" O GLU I 8 " (cutoff:3.500A) Processing helix chain 'I' and resid 128 through 131 Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 18 removed outlier: 6.337A pdb=" N VAL A 16 " --> pdb=" O GLU A 115 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU A 43 " --> pdb=" O TYR A 59 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N TYR A 59 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TRP A 45 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 29 Processing sheet with id=AA3, first strand: chain 'A' and resid 124 through 128 removed outlier: 5.959A pdb=" N TYR A 183 " --> pdb=" O ASN A 148 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 155 through 160 Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 6 Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.383A pdb=" N GLU B 10 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N MET B 34 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N VAL B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N TRP B 36 " --> pdb=" O ILE B 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 127 through 130 removed outlier: 5.387A pdb=" N CYS B 147 " --> pdb=" O SER B 186 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N SER B 186 " --> pdb=" O CYS B 147 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 158 through 160 Processing sheet with id=AA9, first strand: chain 'C' and resid 52 through 54 removed outlier: 6.181A pdb=" N ALA C 270 " --> pdb=" O SER C 325 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HIS C 244 " --> pdb=" O SER C 271 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ALA C 186 " --> pdb=" O ALA C 175 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ALA C 175 " --> pdb=" O ALA C 186 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N PHE C 188 " --> pdb=" O ARG C 173 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ARG C 173 " --> pdb=" O PHE C 188 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N TYR C 190 " --> pdb=" O GLY C 171 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLY C 171 " --> pdb=" O TYR C 190 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N GLN C 192 " --> pdb=" O SER C 169 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N SER C 169 " --> pdb=" O GLN C 192 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N ASP C 163 " --> pdb=" O VAL C 197 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL C 197 " --> pdb=" O ASP C 163 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 52 through 54 removed outlier: 6.181A pdb=" N ALA C 270 " --> pdb=" O SER C 325 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ARG C 355 " --> pdb=" O PHE C 48 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASP C 49 " --> pdb=" O ALA C 93 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ALA C 93 " --> pdb=" O ASP C 49 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU C 104 " --> pdb=" O VAL C 112 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL C 112 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE C 106 " --> pdb=" O APHE C 110 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N APHE C 110 " --> pdb=" O ILE C 106 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASP C 111 " --> pdb=" O ALA C 172 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ALA C 172 " --> pdb=" O ASP C 111 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N PHE C 113 " --> pdb=" O VAL C 170 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL C 170 " --> pdb=" O PHE C 113 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N THR C 115 " --> pdb=" O TRP C 168 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N TRP C 168 " --> pdb=" O THR C 115 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N GLY C 117 " --> pdb=" O PHE C 166 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N PHE C 166 " --> pdb=" O GLY C 117 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N THR C 119 " --> pdb=" O THR C 164 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N THR C 164 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY C 121 " --> pdb=" O THR C 162 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N ASP C 163 " --> pdb=" O VAL C 197 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL C 197 " --> pdb=" O ASP C 163 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 59 through 62 Processing sheet with id=AB3, first strand: chain 'C' and resid 151 through 152 removed outlier: 6.882A pdb=" N VAL C 133 " --> pdb=" O VAL C 316 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL C 316 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 237 through 238 Processing sheet with id=AB5, first strand: chain 'D' and resid 15 through 18 removed outlier: 6.337A pdb=" N VAL D 16 " --> pdb=" O GLU D 115 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU D 43 " --> pdb=" O TYR D 59 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N TYR D 59 " --> pdb=" O LEU D 43 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TRP D 45 " --> pdb=" O LEU D 57 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 24 through 29 Processing sheet with id=AB7, first strand: chain 'D' and resid 124 through 128 removed outlier: 5.960A pdb=" N TYR D 183 " --> pdb=" O ASN D 148 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 155 through 160 Processing sheet with id=AB9, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AC1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.383A pdb=" N GLU E 10 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N MET E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N VAL E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 127 through 130 removed outlier: 5.387A pdb=" N CYS E 147 " --> pdb=" O SER E 186 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N SER E 186 " --> pdb=" O CYS E 147 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 158 through 160 Processing sheet with id=AC4, first strand: chain 'F' and resid 52 through 54 removed outlier: 6.181A pdb=" N ALA F 270 " --> pdb=" O SER F 325 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HIS F 244 " --> pdb=" O SER F 271 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ALA F 186 " --> pdb=" O ALA F 175 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ALA F 175 " --> pdb=" O ALA F 186 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N PHE F 188 " --> pdb=" O ARG F 173 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ARG F 173 " --> pdb=" O PHE F 188 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N TYR F 190 " --> pdb=" O GLY F 171 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLY F 171 " --> pdb=" O TYR F 190 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N GLN F 192 " --> pdb=" O SER F 169 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N SER F 169 " --> pdb=" O GLN F 192 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N ASP F 163 " --> pdb=" O VAL F 197 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL F 197 " --> pdb=" O ASP F 163 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 52 through 54 removed outlier: 6.181A pdb=" N ALA F 270 " --> pdb=" O SER F 325 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ARG F 355 " --> pdb=" O PHE F 48 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASP F 49 " --> pdb=" O ALA F 93 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ALA F 93 " --> pdb=" O ASP F 49 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU F 104 " --> pdb=" O VAL F 112 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL F 112 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE F 106 " --> pdb=" O APHE F 110 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N APHE F 110 " --> pdb=" O ILE F 106 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASP F 111 " --> pdb=" O ALA F 172 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ALA F 172 " --> pdb=" O ASP F 111 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N PHE F 113 " --> pdb=" O VAL F 170 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL F 170 " --> pdb=" O PHE F 113 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N THR F 115 " --> pdb=" O TRP F 168 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N TRP F 168 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N GLY F 117 " --> pdb=" O PHE F 166 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N PHE F 166 " --> pdb=" O GLY F 117 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N THR F 119 " --> pdb=" O THR F 164 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N THR F 164 " --> pdb=" O THR F 119 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY F 121 " --> pdb=" O THR F 162 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N ASP F 163 " --> pdb=" O VAL F 197 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL F 197 " --> pdb=" O ASP F 163 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 59 through 62 Processing sheet with id=AC7, first strand: chain 'F' and resid 151 through 152 removed outlier: 6.882A pdb=" N VAL F 133 " --> pdb=" O VAL F 316 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL F 316 " --> pdb=" O VAL F 133 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 237 through 238 Processing sheet with id=AC9, first strand: chain 'G' and resid 15 through 18 removed outlier: 6.337A pdb=" N VAL G 16 " --> pdb=" O GLU G 115 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU G 43 " --> pdb=" O TYR G 59 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N TYR G 59 " --> pdb=" O LEU G 43 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TRP G 45 " --> pdb=" O LEU G 57 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 24 through 29 Processing sheet with id=AD2, first strand: chain 'G' and resid 124 through 128 removed outlier: 5.959A pdb=" N TYR G 183 " --> pdb=" O ASN G 148 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 155 through 160 Processing sheet with id=AD4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AD5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.383A pdb=" N GLU H 10 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 127 through 130 removed outlier: 5.387A pdb=" N CYS H 147 " --> pdb=" O SER H 186 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N SER H 186 " --> pdb=" O CYS H 147 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 158 through 160 Processing sheet with id=AD8, first strand: chain 'I' and resid 52 through 54 removed outlier: 6.181A pdb=" N ALA I 270 " --> pdb=" O SER I 325 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N HIS I 244 " --> pdb=" O SER I 271 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ALA I 186 " --> pdb=" O ALA I 175 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ALA I 175 " --> pdb=" O ALA I 186 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N PHE I 188 " --> pdb=" O ARG I 173 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ARG I 173 " --> pdb=" O PHE I 188 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N TYR I 190 " --> pdb=" O GLY I 171 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLY I 171 " --> pdb=" O TYR I 190 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N GLN I 192 " --> pdb=" O SER I 169 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N SER I 169 " --> pdb=" O GLN I 192 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N ASP I 163 " --> pdb=" O VAL I 197 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL I 197 " --> pdb=" O ASP I 163 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 52 through 54 removed outlier: 6.181A pdb=" N ALA I 270 " --> pdb=" O SER I 325 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ARG I 355 " --> pdb=" O PHE I 48 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASP I 49 " --> pdb=" O ALA I 93 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ALA I 93 " --> pdb=" O ASP I 49 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU I 104 " --> pdb=" O VAL I 112 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL I 112 " --> pdb=" O LEU I 104 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE I 106 " --> pdb=" O APHE I 110 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N APHE I 110 " --> pdb=" O ILE I 106 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASP I 111 " --> pdb=" O ALA I 172 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ALA I 172 " --> pdb=" O ASP I 111 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N PHE I 113 " --> pdb=" O VAL I 170 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL I 170 " --> pdb=" O PHE I 113 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N THR I 115 " --> pdb=" O TRP I 168 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N TRP I 168 " --> pdb=" O THR I 115 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N GLY I 117 " --> pdb=" O PHE I 166 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N PHE I 166 " --> pdb=" O GLY I 117 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N THR I 119 " --> pdb=" O THR I 164 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N THR I 164 " --> pdb=" O THR I 119 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY I 121 " --> pdb=" O THR I 162 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N ASP I 163 " --> pdb=" O VAL I 197 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL I 197 " --> pdb=" O ASP I 163 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 59 through 62 Processing sheet with id=AE2, first strand: chain 'I' and resid 151 through 152 removed outlier: 6.882A pdb=" N VAL I 133 " --> pdb=" O VAL I 316 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL I 316 " --> pdb=" O VAL I 133 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 237 through 238 681 hydrogen bonds defined for protein. 1728 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: 3.26 Time building geometry restraints manager: 1.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3018 1.31 - 1.44: 5166 1.44 - 1.56: 10581 1.56 - 1.69: 48 1.69 - 1.82: 150 Bond restraints: 18963 Sorted by residual: bond pdb=" C1 FO4 F 405 " pdb=" C2 FO4 F 405 " ideal model delta sigma weight residual 1.328 1.558 -0.230 2.00e-02 2.50e+03 1.33e+02 bond pdb=" C1 FO4 C 404 " pdb=" C2 FO4 C 404 " ideal model delta sigma weight residual 1.328 1.558 -0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C1 FO4 C 406 " pdb=" C2 FO4 C 406 " ideal model delta sigma weight residual 1.328 1.558 -0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C31 FO4 C 406 " pdb=" C32 FO4 C 406 " ideal model delta sigma weight residual 1.333 1.555 -0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" C31 FO4 C 404 " pdb=" C32 FO4 C 404 " ideal model delta sigma weight residual 1.333 1.555 -0.222 2.00e-02 2.50e+03 1.23e+02 ... (remaining 18958 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.67: 25576 3.67 - 7.34: 149 7.34 - 11.01: 6 11.01 - 14.69: 9 14.69 - 18.36: 6 Bond angle restraints: 25746 Sorted by residual: angle pdb=" C30 FO4 C 406 " pdb=" C31 FO4 C 406 " pdb=" C32 FO4 C 406 " ideal model delta sigma weight residual 126.80 108.44 18.36 3.00e+00 1.11e-01 3.74e+01 angle pdb=" C30 FO4 C 404 " pdb=" C31 FO4 C 404 " pdb=" C32 FO4 C 404 " ideal model delta sigma weight residual 126.80 108.45 18.35 3.00e+00 1.11e-01 3.74e+01 angle pdb=" C30 FO4 F 405 " pdb=" C31 FO4 F 405 " pdb=" C32 FO4 F 405 " ideal model delta sigma weight residual 126.80 108.48 18.32 3.00e+00 1.11e-01 3.73e+01 angle pdb=" C FO4 C 406 " pdb=" C1 FO4 C 406 " pdb=" C2 FO4 C 406 " ideal model delta sigma weight residual 125.43 108.63 16.80 3.00e+00 1.11e-01 3.14e+01 angle pdb=" C FO4 F 405 " pdb=" C1 FO4 F 405 " pdb=" C2 FO4 F 405 " ideal model delta sigma weight residual 125.43 108.64 16.79 3.00e+00 1.11e-01 3.13e+01 ... (remaining 25741 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.39: 10986 26.39 - 52.78: 360 52.78 - 79.17: 63 79.17 - 105.56: 33 105.56 - 131.95: 12 Dihedral angle restraints: 11454 sinusoidal: 4599 harmonic: 6855 Sorted by residual: dihedral pdb=" CB CYS G 28 " pdb=" SG CYS G 28 " pdb=" SG CYS G 98 " pdb=" CB CYS G 98 " ideal model delta sinusoidal sigma weight residual 93.00 155.97 -62.97 1 1.00e+01 1.00e-02 5.24e+01 dihedral pdb=" CB CYS D 28 " pdb=" SG CYS D 28 " pdb=" SG CYS D 98 " pdb=" CB CYS D 98 " ideal model delta sinusoidal sigma weight residual 93.00 155.97 -62.97 1 1.00e+01 1.00e-02 5.24e+01 dihedral pdb=" CB CYS A 28 " pdb=" SG CYS A 28 " pdb=" SG CYS A 98 " pdb=" CB CYS A 98 " ideal model delta sinusoidal sigma weight residual 93.00 155.96 -62.96 1 1.00e+01 1.00e-02 5.24e+01 ... (remaining 11451 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1410 0.042 - 0.085: 893 0.085 - 0.127: 491 0.127 - 0.170: 77 0.170 - 0.212: 6 Chirality restraints: 2877 Sorted by residual: chirality pdb=" CA PRO B 154 " pdb=" N PRO B 154 " pdb=" C PRO B 154 " pdb=" CB PRO B 154 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA PRO E 154 " pdb=" N PRO E 154 " pdb=" C PRO E 154 " pdb=" CB PRO E 154 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA PRO H 154 " pdb=" N PRO H 154 " pdb=" C PRO H 154 " pdb=" CB PRO H 154 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 2874 not shown) Planarity restraints: 3255 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C30 FO4 C 406 " 0.111 2.00e-02 2.50e+03 3.36e-01 1.13e+03 pdb=" C31 FO4 C 406 " -0.398 2.00e-02 2.50e+03 pdb=" C32 FO4 C 406 " 0.490 2.00e-02 2.50e+03 pdb=" C33 FO4 C 406 " -0.203 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C30 FO4 C 404 " 0.111 2.00e-02 2.50e+03 3.36e-01 1.13e+03 pdb=" C31 FO4 C 404 " -0.398 2.00e-02 2.50e+03 pdb=" C32 FO4 C 404 " 0.490 2.00e-02 2.50e+03 pdb=" C33 FO4 C 404 " -0.202 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C30 FO4 F 405 " -0.111 2.00e-02 2.50e+03 3.36e-01 1.13e+03 pdb=" C31 FO4 F 405 " 0.398 2.00e-02 2.50e+03 pdb=" C32 FO4 F 405 " -0.489 2.00e-02 2.50e+03 pdb=" C33 FO4 F 405 " 0.202 2.00e-02 2.50e+03 ... (remaining 3252 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 643 2.70 - 3.25: 17996 3.25 - 3.80: 28087 3.80 - 4.35: 37615 4.35 - 4.90: 64059 Nonbonded interactions: 148400 Sorted by model distance: nonbonded pdb=" O FO4 F 405 " pdb=" O2 FO4 F 405 " model vdw 2.150 3.040 nonbonded pdb=" O FO4 C 404 " pdb=" O2 FO4 C 404 " model vdw 2.150 3.040 nonbonded pdb=" O FO4 C 406 " pdb=" O2 FO4 C 406 " model vdw 2.150 3.040 nonbonded pdb=" OG1 THR H 160 " pdb=" OG SER H 203 " model vdw 2.207 3.040 nonbonded pdb=" OG1 THR E 160 " pdb=" OG SER E 203 " model vdw 2.207 3.040 ... (remaining 148395 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' } ncs_group { reference = (chain 'B' and (resid 1 through 104 or resid 106 through 219)) selection = (chain 'E' and (resid 1 through 104 or resid 106 through 219)) selection = (chain 'H' and (resid 1 through 104 or resid 106 through 219)) } ncs_group { reference = (chain 'C' and (resid 1 through 56 or resid 58 through 109 or resid 111 through \ 226 or resid 228 through 365)) selection = (chain 'F' and (resid 1 through 56 or resid 58 through 109 or resid 111 through \ 226 or resid 228 through 365)) selection = (chain 'I' and (resid 1 through 56 or resid 58 through 109 or resid 111 through \ 226 or resid 228 through 365)) } 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=0.16 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 18.110 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 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 : 0.011 0.230 18975 Z= 0.765 Angle : 1.099 18.358 25770 Z= 0.673 Chirality : 0.064 0.212 2877 Planarity : 0.014 0.336 3255 Dihedral : 15.411 131.945 7014 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 0.45 % Allowed : 1.99 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.17), residues: 2331 helix: 0.14 (1.44), residues: 18 sheet: -0.10 (0.16), residues: 1065 loop : -1.31 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 60 TYR 0.016 0.003 TYR C 43 PHE 0.013 0.002 PHE E 153 TRP 0.021 0.003 TRP C 246 HIS 0.008 0.002 HIS D 101 Details of bonding type rmsd/Z covalent geometry : bond 0.01150 / 0.77 (18963) covalent geometry : angle 1.09924 / 0.67 (25746) SS BOND : bond 0.00552 / 0.40 ( 12) SS BOND : angle 1.26410 / 0.94 ( 24) hydrogen bonds : bond 0.11485 / 8.16 ( 636) hydrogen bonds : angle 6.34799 / 4.35 ( 1728) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 196 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TYR cc_start: 0.7181 (OUTLIER) cc_final: 0.6352 (t80) REVERT: B 51 ILE cc_start: 0.9007 (tt) cc_final: 0.8731 (tt) REVERT: D 104 TYR cc_start: 0.6921 (OUTLIER) cc_final: 0.6291 (t80) REVERT: G 104 TYR cc_start: 0.7032 (OUTLIER) cc_final: 0.6201 (t80) outliers start: 6 outliers final: 0 residues processed: 202 average time/residue: 0.1444 time to fit residues: 43.1604 Evaluate side-chains 126 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 123 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 TYR Chi-restraints excluded: chain D residue 104 TYR Chi-restraints excluded: chain G residue 104 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 216 optimal weight: 0.3980 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 0.0980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 48 GLN ** A 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 GLN D 48 GLN ** D 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN ** F 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 48 GLN G 176 GLN ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN H 39 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.082222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.053740 restraints weight = 192070.372| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 5.35 r_work: 0.2791 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2802 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2802 r_free = 0.2802 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2802 r_free = 0.2802 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2802 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18975 Z= 0.132 Angle : 0.652 9.648 25770 Z= 0.331 Chirality : 0.046 0.235 2877 Planarity : 0.004 0.043 3255 Dihedral : 14.476 163.356 2916 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 0.80 % Allowed : 5.93 % Favored : 93.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.17), residues: 2331 helix: -0.24 (1.30), residues: 18 sheet: -0.07 (0.16), residues: 1059 loop : -1.12 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 221 TYR 0.016 0.002 TYR F 43 PHE 0.016 0.001 PHE H 153 TRP 0.024 0.001 TRP E 161 HIS 0.004 0.001 HIS C 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (18963) covalent geometry : angle 0.65190 / 0.33 (25746) SS BOND : bond 0.00403 / 0.25 ( 12) SS BOND : angle 0.90851 / 0.58 ( 24) hydrogen bonds : bond 0.03406 / 2.29 ( 636) hydrogen bonds : angle 5.57938 / 3.80 ( 1728) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 157 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TYR cc_start: 0.7671 (OUTLIER) cc_final: 0.6963 (t80) REVERT: B 31 ASP cc_start: 0.8908 (m-30) cc_final: 0.8619 (m-30) REVERT: B 34 MET cc_start: 0.8935 (mmm) cc_final: 0.8663 (mmm) REVERT: B 51 ILE cc_start: 0.9488 (tt) cc_final: 0.9286 (tt) REVERT: B 184 MET cc_start: 0.8300 (tpp) cc_final: 0.7662 (tmm) REVERT: C 290 LYS cc_start: 0.9622 (mmmt) cc_final: 0.9411 (mtmm) REVERT: D 104 TYR cc_start: 0.7365 (OUTLIER) cc_final: 0.6547 (t80) REVERT: E 3 GLN cc_start: 0.8265 (pm20) cc_final: 0.8024 (pm20) REVERT: E 31 ASP cc_start: 0.8920 (m-30) cc_final: 0.8597 (m-30) REVERT: E 184 MET cc_start: 0.8085 (tpp) cc_final: 0.7202 (tmm) REVERT: F 290 LYS cc_start: 0.9575 (mmmt) cc_final: 0.9346 (mtmm) REVERT: G 104 TYR cc_start: 0.7643 (OUTLIER) cc_final: 0.6783 (t80) REVERT: G 113 LYS cc_start: 0.8970 (ptmt) cc_final: 0.8684 (ptmm) REVERT: G 177 ASP cc_start: 0.8965 (t0) cc_final: 0.8584 (t0) REVERT: H 184 MET cc_start: 0.8021 (tpp) cc_final: 0.7319 (tmm) REVERT: I 290 LYS cc_start: 0.9566 (mmmt) cc_final: 0.9293 (mtmm) outliers start: 10 outliers final: 5 residues processed: 160 average time/residue: 0.1318 time to fit residues: 31.5999 Evaluate side-chains 141 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 133 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 TYR Chi-restraints excluded: chain A residue 158 TRP Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 104 TYR Chi-restraints excluded: chain D residue 158 TRP Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 104 TYR Chi-restraints excluded: chain H residue 46 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 48 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 120 optimal weight: 0.0980 chunk 204 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 226 optimal weight: 3.9990 chunk 225 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 6 GLN D 48 GLN E 39 GLN ** F 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 48 GLN H 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.080118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.051148 restraints weight = 185197.063| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 5.22 r_work: 0.2692 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2702 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2702 r_free = 0.2702 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2702 r_free = 0.2702 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2702 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 18975 Z= 0.192 Angle : 0.638 9.284 25770 Z= 0.326 Chirality : 0.045 0.236 2877 Planarity : 0.005 0.047 3255 Dihedral : 13.407 150.305 2916 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.00 % Allowed : 7.57 % Favored : 91.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.18), residues: 2331 helix: -0.28 (0.91), residues: 42 sheet: -0.18 (0.16), residues: 1068 loop : -1.07 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 50 TYR 0.019 0.002 TYR C 43 PHE 0.014 0.001 PHE H 153 TRP 0.019 0.001 TRP A 173 HIS 0.005 0.001 HIS C 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.19 (18963) covalent geometry : angle 0.63762 / 0.33 (25746) SS BOND : bond 0.00323 / 0.21 ( 12) SS BOND : angle 0.94691 / 0.58 ( 24) hydrogen bonds : bond 0.03473 / 2.29 ( 636) hydrogen bonds : angle 5.45562 / 3.69 ( 1728) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 TYR cc_start: 0.8054 (OUTLIER) cc_final: 0.7311 (t80) REVERT: B 3 GLN cc_start: 0.8252 (pm20) cc_final: 0.8047 (pm20) REVERT: B 31 ASP cc_start: 0.9003 (m-30) cc_final: 0.8643 (m-30) REVERT: B 184 MET cc_start: 0.8222 (tpp) cc_final: 0.7428 (tmm) REVERT: D 104 TYR cc_start: 0.7830 (OUTLIER) cc_final: 0.6995 (t80) REVERT: E 31 ASP cc_start: 0.9043 (m-30) cc_final: 0.8600 (m-30) REVERT: E 184 MET cc_start: 0.8074 (tpp) cc_final: 0.7145 (tmm) REVERT: F 290 LYS cc_start: 0.9552 (mmmt) cc_final: 0.9328 (mtmm) REVERT: F 323 MET cc_start: 0.9341 (mtm) cc_final: 0.9125 (mtm) REVERT: G 104 TYR cc_start: 0.7935 (OUTLIER) cc_final: 0.7189 (t80) REVERT: G 113 LYS cc_start: 0.9021 (ptmt) cc_final: 0.8784 (ptmm) REVERT: H 184 MET cc_start: 0.8086 (tpp) cc_final: 0.7400 (tmm) REVERT: I 82 GLU cc_start: 0.8637 (tm-30) cc_final: 0.8339 (tm-30) REVERT: I 290 LYS cc_start: 0.9574 (mmmt) cc_final: 0.9306 (mtmm) outliers start: 14 outliers final: 7 residues processed: 147 average time/residue: 0.1288 time to fit residues: 28.9065 Evaluate side-chains 131 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 104 TYR Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 104 TYR Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 104 TYR Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain I residue 318 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 224 optimal weight: 1.9990 chunk 203 optimal weight: 3.9990 chunk 109 optimal weight: 0.0170 chunk 227 optimal weight: 0.9990 chunk 138 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 92 optimal weight: 9.9990 chunk 41 optimal weight: 0.9990 chunk 211 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 overall best weight: 0.9624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 6 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 GLN ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.081502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.052070 restraints weight = 212124.753| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 5.53 r_work: 0.2695 rms_B_bonded: 5.06 restraints_weight: 2.0000 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2703 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2703 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18975 Z= 0.143 Angle : 0.607 9.549 25770 Z= 0.311 Chirality : 0.044 0.219 2877 Planarity : 0.004 0.049 3255 Dihedral : 12.829 148.002 2916 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.25 % Allowed : 8.92 % Favored : 89.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.17), residues: 2331 helix: -0.40 (0.90), residues: 42 sheet: -0.25 (0.16), residues: 1086 loop : -1.03 (0.18), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 29 TYR 0.017 0.002 TYR C 43 PHE 0.014 0.001 PHE E 153 TRP 0.014 0.001 TRP I 246 HIS 0.003 0.001 HIS H 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (18963) covalent geometry : angle 0.60642 / 0.31 (25746) SS BOND : bond 0.00270 / 0.17 ( 12) SS BOND : angle 0.77975 / 0.48 ( 24) hydrogen bonds : bond 0.03155 / 2.09 ( 636) hydrogen bonds : angle 5.33111 / 3.60 ( 1728) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 0.691 Fit side-chains revert: symmetry clash REVERT: A 87 ARG cc_start: 0.8799 (ptp-110) cc_final: 0.8552 (ptp90) REVERT: A 104 TYR cc_start: 0.7961 (OUTLIER) cc_final: 0.7115 (t80) REVERT: B 31 ASP cc_start: 0.8960 (m-30) cc_final: 0.8687 (m-30) REVERT: B 81 MET cc_start: 0.8434 (ttm) cc_final: 0.8228 (ttm) REVERT: B 184 MET cc_start: 0.8226 (tpp) cc_final: 0.7412 (tmm) REVERT: D 104 TYR cc_start: 0.7771 (OUTLIER) cc_final: 0.6856 (t80) REVERT: E 3 GLN cc_start: 0.8337 (pm20) cc_final: 0.8098 (pm20) REVERT: E 31 ASP cc_start: 0.9016 (m-30) cc_final: 0.8585 (m-30) REVERT: E 184 MET cc_start: 0.8213 (tpp) cc_final: 0.7278 (tmm) REVERT: G 85 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8410 (mm) REVERT: G 104 TYR cc_start: 0.7924 (OUTLIER) cc_final: 0.7019 (t80) REVERT: G 113 LYS cc_start: 0.9057 (ptmt) cc_final: 0.8764 (ptmm) REVERT: H 184 MET cc_start: 0.8102 (tpp) cc_final: 0.7617 (tmm) REVERT: I 82 GLU cc_start: 0.8749 (tm-30) cc_final: 0.8455 (tm-30) REVERT: I 290 LYS cc_start: 0.9573 (mmmt) cc_final: 0.9345 (mtmm) outliers start: 19 outliers final: 9 residues processed: 147 average time/residue: 0.1351 time to fit residues: 30.0004 Evaluate side-chains 134 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 104 TYR Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 104 TYR Chi-restraints excluded: chain F residue 263 ILE Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 85 ILE Chi-restraints excluded: chain G residue 104 TYR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 93 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 46 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 17 optimal weight: 9.9990 chunk 2 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 186 optimal weight: 0.9990 chunk 204 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 214 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** 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 = 0.3608 r_free = 0.3608 target = 0.080656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.052166 restraints weight = 179031.563| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 5.19 r_work: 0.2756 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2765 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2765 r_free = 0.2765 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2765 r_free = 0.2765 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2765 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18975 Z= 0.142 Angle : 0.603 9.724 25770 Z= 0.310 Chirality : 0.044 0.240 2877 Planarity : 0.004 0.052 3255 Dihedral : 12.546 152.292 2916 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.49 % Allowed : 9.42 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.17), residues: 2331 helix: -0.37 (0.90), residues: 42 sheet: -0.20 (0.16), residues: 1065 loop : -1.07 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 85 TYR 0.017 0.002 TYR C 43 PHE 0.013 0.001 PHE E 153 TRP 0.013 0.001 TRP I 246 HIS 0.003 0.001 HIS H 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (18963) covalent geometry : angle 0.60275 / 0.31 (25746) SS BOND : bond 0.00269 / 0.17 ( 12) SS BOND : angle 0.79284 / 0.48 ( 24) hydrogen bonds : bond 0.03108 / 2.06 ( 636) hydrogen bonds : angle 5.25344 / 3.55 ( 1728) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.618 Fit side-chains revert: symmetry clash REVERT: A 85 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8512 (mm) REVERT: A 87 ARG cc_start: 0.8765 (ptp-110) cc_final: 0.8469 (ptp90) REVERT: A 104 TYR cc_start: 0.8115 (OUTLIER) cc_final: 0.7229 (t80) REVERT: B 31 ASP cc_start: 0.8920 (m-30) cc_final: 0.8649 (m-30) REVERT: B 184 MET cc_start: 0.8197 (tpp) cc_final: 0.7428 (tmm) REVERT: D 104 TYR cc_start: 0.7795 (OUTLIER) cc_final: 0.6813 (t80) REVERT: D 113 LYS cc_start: 0.9062 (ptpp) cc_final: 0.8792 (ptmm) REVERT: E 31 ASP cc_start: 0.9024 (m-30) cc_final: 0.8442 (m-30) REVERT: E 184 MET cc_start: 0.8211 (tpp) cc_final: 0.7244 (tmm) REVERT: G 113 LYS cc_start: 0.9039 (ptmt) cc_final: 0.8753 (ptmm) REVERT: H 184 MET cc_start: 0.8111 (tpp) cc_final: 0.7786 (mmm) REVERT: I 82 GLU cc_start: 0.8722 (tm-30) cc_final: 0.8436 (tm-30) REVERT: I 290 LYS cc_start: 0.9587 (mmmt) cc_final: 0.9351 (mtmm) outliers start: 24 outliers final: 11 residues processed: 146 average time/residue: 0.1281 time to fit residues: 29.1375 Evaluate side-chains 136 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 104 TYR Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 104 TYR Chi-restraints excluded: chain F residue 263 ILE Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 104 TYR Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain I residue 263 ILE Chi-restraints excluded: chain I residue 299 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 10 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 115 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 0 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 200 optimal weight: 0.9990 chunk 120 optimal weight: 0.0170 chunk 18 optimal weight: 0.4980 chunk 67 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 overall best weight: 0.6020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 39 GLN ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** 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 = 0.3594 r_free = 0.3594 target = 0.081130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.052085 restraints weight = 205422.468| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 5.53 r_work: 0.2716 rms_B_bonded: 5.05 restraints_weight: 2.0000 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2721 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2721 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18975 Z= 0.114 Angle : 0.578 10.187 25770 Z= 0.299 Chirality : 0.044 0.231 2877 Planarity : 0.004 0.054 3255 Dihedral : 12.258 157.405 2916 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.25 % Allowed : 9.97 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.17), residues: 2331 helix: -2.02 (0.95), residues: 24 sheet: -0.17 (0.16), residues: 1062 loop : -1.02 (0.18), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 85 TYR 0.016 0.001 TYR B 152 PHE 0.013 0.001 PHE E 153 TRP 0.014 0.001 TRP F 246 HIS 0.003 0.001 HIS H 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (18963) covalent geometry : angle 0.57811 / 0.30 (25746) SS BOND : bond 0.00382 / 0.23 ( 12) SS BOND : angle 0.69493 / 0.43 ( 24) hydrogen bonds : bond 0.02952 / 1.97 ( 636) hydrogen bonds : angle 5.16915 / 3.49 ( 1728) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 0.499 Fit side-chains revert: symmetry clash REVERT: A 85 ILE cc_start: 0.8697 (OUTLIER) cc_final: 0.8406 (mm) REVERT: A 87 ARG cc_start: 0.8703 (ptp-110) cc_final: 0.8417 (ptp90) REVERT: A 104 TYR cc_start: 0.7982 (OUTLIER) cc_final: 0.7214 (t80) REVERT: A 185 MET cc_start: 0.8212 (tpp) cc_final: 0.7933 (tpp) REVERT: B 31 ASP cc_start: 0.8941 (m-30) cc_final: 0.8695 (m-30) REVERT: B 184 MET cc_start: 0.8162 (tpp) cc_final: 0.7403 (tmm) REVERT: D 104 TYR cc_start: 0.7698 (OUTLIER) cc_final: 0.6650 (t80) REVERT: D 113 LYS cc_start: 0.9005 (ptpp) cc_final: 0.8764 (ptmm) REVERT: D 185 MET cc_start: 0.8643 (tpp) cc_final: 0.8430 (tpp) REVERT: E 31 ASP cc_start: 0.9005 (m-30) cc_final: 0.8569 (m-30) REVERT: E 184 MET cc_start: 0.8217 (tpp) cc_final: 0.7266 (tmm) REVERT: G 113 LYS cc_start: 0.9008 (ptmt) cc_final: 0.8730 (ptmm) REVERT: H 184 MET cc_start: 0.8056 (tpp) cc_final: 0.7559 (mmm) REVERT: I 82 GLU cc_start: 0.8752 (tm-30) cc_final: 0.8468 (tm-30) outliers start: 19 outliers final: 8 residues processed: 148 average time/residue: 0.1481 time to fit residues: 32.9278 Evaluate side-chains 134 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 104 TYR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 104 TYR Chi-restraints excluded: chain F residue 263 ILE Chi-restraints excluded: chain G residue 104 TYR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 93 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 198 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 210 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 177 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 189 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** 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 = 0.3571 r_free = 0.3571 target = 0.079999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.050831 restraints weight = 207473.164| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 5.47 r_work: 0.2675 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2684 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2684 r_free = 0.2684 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2684 r_free = 0.2684 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2684 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18975 Z= 0.177 Angle : 0.607 9.348 25770 Z= 0.315 Chirality : 0.044 0.210 2877 Planarity : 0.004 0.057 3255 Dihedral : 12.260 164.373 2916 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.29 % Favored : 94.63 % Rotamer: Outliers : 1.54 % Allowed : 10.06 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.17), residues: 2331 helix: -0.26 (0.92), residues: 42 sheet: -0.18 (0.16), residues: 1068 loop : -1.04 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 85 TYR 0.020 0.002 TYR F 43 PHE 0.013 0.001 PHE H 153 TRP 0.012 0.001 TRP D 173 HIS 0.002 0.001 HIS B 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 (18963) covalent geometry : angle 0.60642 / 0.31 (25746) SS BOND : bond 0.00331 / 0.20 ( 12) SS BOND : angle 0.99400 / 0.62 ( 24) hydrogen bonds : bond 0.03191 / 2.12 ( 636) hydrogen bonds : angle 5.23108 / 3.53 ( 1728) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.687 Fit side-chains revert: symmetry clash REVERT: A 85 ILE cc_start: 0.8664 (OUTLIER) cc_final: 0.8393 (mm) REVERT: A 87 ARG cc_start: 0.8784 (ptp-110) cc_final: 0.8482 (ptp90) REVERT: A 104 TYR cc_start: 0.8247 (OUTLIER) cc_final: 0.7414 (t80) REVERT: B 31 ASP cc_start: 0.8986 (m-30) cc_final: 0.8692 (m-30) REVERT: B 184 MET cc_start: 0.8228 (tpp) cc_final: 0.7444 (tmm) REVERT: D 104 TYR cc_start: 0.8109 (OUTLIER) cc_final: 0.7121 (t80) REVERT: E 31 ASP cc_start: 0.9057 (m-30) cc_final: 0.8556 (m-30) REVERT: E 184 MET cc_start: 0.8223 (tpp) cc_final: 0.7264 (tmm) REVERT: G 113 LYS cc_start: 0.9039 (ptmt) cc_final: 0.8779 (ptmm) REVERT: H 184 MET cc_start: 0.8120 (tpp) cc_final: 0.7773 (mmm) outliers start: 25 outliers final: 18 residues processed: 138 average time/residue: 0.1270 time to fit residues: 27.6215 Evaluate side-chains 142 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 104 TYR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 104 TYR Chi-restraints excluded: chain F residue 263 ILE Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 104 TYR Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain I residue 263 ILE Chi-restraints excluded: chain I residue 271 SER Chi-restraints excluded: chain I residue 299 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 176 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 197 optimal weight: 0.0030 chunk 130 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 180 optimal weight: 0.9990 chunk 187 optimal weight: 6.9990 chunk 67 optimal weight: 0.6980 chunk 207 optimal weight: 3.9990 chunk 100 optimal weight: 0.0000 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 52 GLN ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** 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 = 0.3587 r_free = 0.3587 target = 0.080840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.051725 restraints weight = 230101.115| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 5.65 r_work: 0.2706 rms_B_bonded: 5.10 restraints_weight: 2.0000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2713 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2713 r_free = 0.2713 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2713 r_free = 0.2713 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2713 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 18975 Z= 0.110 Angle : 0.577 8.390 25770 Z= 0.301 Chirality : 0.043 0.194 2877 Planarity : 0.004 0.053 3255 Dihedral : 12.096 169.305 2916 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.72 % Favored : 95.19 % Rotamer: Outliers : 1.10 % Allowed : 10.76 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.17), residues: 2331 helix: -1.94 (0.98), residues: 24 sheet: -0.16 (0.16), residues: 1068 loop : -1.04 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 85 TYR 0.015 0.001 TYR B 152 PHE 0.013 0.001 PHE H 153 TRP 0.014 0.001 TRP F 246 HIS 0.003 0.001 HIS B 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (18963) covalent geometry : angle 0.57666 / 0.30 (25746) SS BOND : bond 0.00246 / 0.15 ( 12) SS BOND : angle 0.74361 / 0.48 ( 24) hydrogen bonds : bond 0.02930 / 1.95 ( 636) hydrogen bonds : angle 5.13400 / 3.46 ( 1728) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.702 Fit side-chains revert: symmetry clash REVERT: A 85 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8413 (mm) REVERT: A 87 ARG cc_start: 0.8687 (ptp-110) cc_final: 0.8424 (ptp90) REVERT: A 104 TYR cc_start: 0.8065 (OUTLIER) cc_final: 0.7217 (t80) REVERT: A 185 MET cc_start: 0.8278 (tpp) cc_final: 0.8039 (tpp) REVERT: B 31 ASP cc_start: 0.8940 (m-30) cc_final: 0.8691 (m-30) REVERT: B 184 MET cc_start: 0.8176 (tpp) cc_final: 0.7399 (tmm) REVERT: D 104 TYR cc_start: 0.7893 (OUTLIER) cc_final: 0.6834 (t80) REVERT: D 113 LYS cc_start: 0.8980 (ptpp) cc_final: 0.8759 (ptmm) REVERT: D 185 MET cc_start: 0.8589 (tpp) cc_final: 0.8381 (tpp) REVERT: E 31 ASP cc_start: 0.9020 (m-30) cc_final: 0.8567 (m-30) REVERT: E 184 MET cc_start: 0.8229 (tpp) cc_final: 0.7262 (tmm) REVERT: G 113 LYS cc_start: 0.8990 (ptmt) cc_final: 0.8751 (ptmm) REVERT: H 184 MET cc_start: 0.8065 (tpp) cc_final: 0.7594 (mmm) REVERT: I 82 GLU cc_start: 0.8743 (tm-30) cc_final: 0.8456 (tm-30) outliers start: 16 outliers final: 11 residues processed: 140 average time/residue: 0.1306 time to fit residues: 28.3986 Evaluate side-chains 136 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 104 TYR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 104 TYR Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 104 TYR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 93 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 16 optimal weight: 0.9990 chunk 102 optimal weight: 0.0570 chunk 156 optimal weight: 0.5980 chunk 228 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 overall best weight: 0.7304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** 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 = 0.3592 r_free = 0.3592 target = 0.080896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.051976 restraints weight = 192836.493| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 5.35 r_work: 0.2711 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2720 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2720 r_free = 0.2720 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2720 r_free = 0.2720 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2720 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18975 Z= 0.126 Angle : 0.586 9.834 25770 Z= 0.305 Chirality : 0.043 0.192 2877 Planarity : 0.004 0.055 3255 Dihedral : 12.013 179.612 2916 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.77 % Favored : 95.15 % Rotamer: Outliers : 1.00 % Allowed : 11.21 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.17), residues: 2331 helix: -1.93 (0.99), residues: 24 sheet: -0.13 (0.16), residues: 1074 loop : -1.02 (0.18), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 85 TYR 0.015 0.001 TYR F 43 PHE 0.013 0.001 PHE H 153 TRP 0.014 0.001 TRP D 158 HIS 0.003 0.001 HIS B 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (18963) covalent geometry : angle 0.58617 / 0.31 (25746) SS BOND : bond 0.00235 / 0.14 ( 12) SS BOND : angle 0.78265 / 0.49 ( 24) hydrogen bonds : bond 0.02944 / 1.96 ( 636) hydrogen bonds : angle 5.11671 / 3.45 ( 1728) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8407 (mm) REVERT: A 87 ARG cc_start: 0.8674 (ptp-110) cc_final: 0.8412 (ptp90) REVERT: A 104 TYR cc_start: 0.8109 (OUTLIER) cc_final: 0.7259 (t80) REVERT: A 185 MET cc_start: 0.8161 (tpp) cc_final: 0.7900 (tpp) REVERT: B 31 ASP cc_start: 0.8919 (m-30) cc_final: 0.8653 (m-30) REVERT: B 184 MET cc_start: 0.8211 (tpp) cc_final: 0.7429 (tmm) REVERT: D 104 TYR cc_start: 0.7924 (OUTLIER) cc_final: 0.6856 (t80) REVERT: D 113 LYS cc_start: 0.8978 (ptpp) cc_final: 0.8735 (ptmm) REVERT: E 31 ASP cc_start: 0.8963 (m-30) cc_final: 0.8535 (m-30) REVERT: E 184 MET cc_start: 0.8192 (tpp) cc_final: 0.7153 (tmm) REVERT: G 113 LYS cc_start: 0.8987 (ptmt) cc_final: 0.8750 (ptmm) outliers start: 14 outliers final: 10 residues processed: 133 average time/residue: 0.1186 time to fit residues: 24.8953 Evaluate side-chains 131 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 104 TYR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 104 TYR Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 104 TYR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain I residue 299 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 217 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 92 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 172 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 26 optimal weight: 0.0670 chunk 35 optimal weight: 2.9990 overall best weight: 1.5324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** 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 = 0.3565 r_free = 0.3565 target = 0.079603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.050527 restraints weight = 194405.788| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 5.32 r_work: 0.2675 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2680 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2680 r_free = 0.2680 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2680 r_free = 0.2680 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2680 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 18975 Z= 0.200 Angle : 0.617 8.737 25770 Z= 0.321 Chirality : 0.044 0.217 2877 Planarity : 0.004 0.057 3255 Dihedral : 12.017 163.531 2916 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.29 % Favored : 94.63 % Rotamer: Outliers : 1.10 % Allowed : 11.06 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.18), residues: 2331 helix: -0.14 (0.93), residues: 42 sheet: -0.21 (0.16), residues: 1080 loop : -1.07 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 29 TYR 0.021 0.002 TYR C 43 PHE 0.014 0.001 PHE H 153 TRP 0.013 0.001 TRP D 158 HIS 0.003 0.001 HIS B 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.20 (18963) covalent geometry : angle 0.61657 / 0.32 (25746) SS BOND : bond 0.00250 / 0.15 ( 12) SS BOND : angle 0.80408 / 0.50 ( 24) hydrogen bonds : bond 0.03264 / 2.17 ( 636) hydrogen bonds : angle 5.21276 / 3.51 ( 1728) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8381 (mm) REVERT: A 104 TYR cc_start: 0.8322 (OUTLIER) cc_final: 0.7376 (t80) REVERT: B 3 GLN cc_start: 0.8335 (pm20) cc_final: 0.8099 (pm20) REVERT: B 31 ASP cc_start: 0.8970 (m-30) cc_final: 0.8551 (m-30) REVERT: B 184 MET cc_start: 0.8237 (tpp) cc_final: 0.7494 (tmm) REVERT: D 104 TYR cc_start: 0.8229 (OUTLIER) cc_final: 0.7270 (t80) REVERT: D 113 LYS cc_start: 0.9013 (ptpp) cc_final: 0.8743 (ptmm) REVERT: E 184 MET cc_start: 0.8222 (tpp) cc_final: 0.7234 (tmm) REVERT: G 113 LYS cc_start: 0.9022 (ptmt) cc_final: 0.8782 (ptmm) outliers start: 16 outliers final: 12 residues processed: 132 average time/residue: 0.1253 time to fit residues: 25.8330 Evaluate side-chains 136 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 104 TYR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 104 TYR Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 104 TYR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain I residue 263 ILE Chi-restraints excluded: chain I residue 299 SER Chi-restraints excluded: chain I residue 318 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 23 optimal weight: 0.8980 chunk 164 optimal weight: 2.9990 chunk 71 optimal weight: 20.0000 chunk 4 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 102 optimal weight: 0.0870 chunk 49 optimal weight: 0.0370 chunk 159 optimal weight: 1.9990 chunk 171 optimal weight: 9.9990 chunk 172 optimal weight: 7.9990 chunk 33 optimal weight: 0.3980 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** 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 = 0.3587 r_free = 0.3587 target = 0.080663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.051704 restraints weight = 186794.404| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 5.27 r_work: 0.2707 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2716 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2716 r_free = 0.2716 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2716 r_free = 0.2716 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2716 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18975 Z= 0.123 Angle : 0.581 9.190 25770 Z= 0.303 Chirality : 0.043 0.196 2877 Planarity : 0.004 0.054 3255 Dihedral : 11.673 166.631 2916 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.85 % Favored : 95.06 % Rotamer: Outliers : 1.05 % Allowed : 11.11 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.17), residues: 2331 helix: -0.25 (0.91), residues: 42 sheet: -0.19 (0.16), residues: 1074 loop : -1.05 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 29 TYR 0.016 0.001 TYR H 152 PHE 0.013 0.001 PHE H 153 TRP 0.015 0.001 TRP I 246 HIS 0.003 0.001 HIS B 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (18963) covalent geometry : angle 0.58037 / 0.30 (25746) SS BOND : bond 0.00227 / 0.14 ( 12) SS BOND : angle 0.79027 / 0.50 ( 24) hydrogen bonds : bond 0.02998 / 1.99 ( 636) hydrogen bonds : angle 5.13447 / 3.46 ( 1728) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4557.40 seconds wall clock time: 78 minutes 52.66 seconds (4732.66 seconds total)