Starting phenix.real_space_refine on Fri Feb 16 19:07:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cha_30373/02_2024/7cha_30373_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cha_30373/02_2024/7cha_30373.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cha_30373/02_2024/7cha_30373_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cha_30373/02_2024/7cha_30373_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cha_30373/02_2024/7cha_30373_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cha_30373/02_2024/7cha_30373.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cha_30373/02_2024/7cha_30373.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cha_30373/02_2024/7cha_30373_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cha_30373/02_2024/7cha_30373_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.004 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 13 5.49 5 S 44 5.16 5 C 10414 2.51 5 N 2701 2.21 5 O 3059 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 109": "OE1" <-> "OE2" Residue "A ASP 119": "OD1" <-> "OD2" Residue "A GLU 120": "OE1" <-> "OE2" Residue "B GLU 7": "OE1" <-> "OE2" Residue "B PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 76": "OD1" <-> "OD2" Residue "B TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 121": "OD1" <-> "OD2" Residue "B ASP 140": "OD1" <-> "OD2" Residue "C ASP 38": "OD1" <-> "OD2" Residue "C ASP 121": "OD1" <-> "OD2" Residue "C ASP 125": "OD1" <-> "OD2" Residue "D ASP 76": "OD1" <-> "OD2" Residue "D GLU 85": "OE1" <-> "OE2" Residue "D TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 120": "OE1" <-> "OE2" Residue "D ASP 121": "OD1" <-> "OD2" Residue "D GLU 139": "OE1" <-> "OE2" Residue "E GLU 7": "OE1" <-> "OE2" Residue "E TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 119": "OD1" <-> "OD2" Residue "E GLU 120": "OE1" <-> "OE2" Residue "E GLU 139": "OE1" <-> "OE2" Residue "E ASP 140": "OD1" <-> "OD2" Residue "F TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 72": "OD1" <-> "OD2" Residue "F TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 119": "OD1" <-> "OD2" Residue "F GLU 120": "OE1" <-> "OE2" Residue "F ASP 131": "OD1" <-> "OD2" Residue "F GLU 139": "OE1" <-> "OE2" Residue "F PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 9": "NH1" <-> "NH2" Residue "G ARG 11": "NH1" <-> "NH2" Residue "G PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 15": "NH1" <-> "NH2" Residue "G ASP 19": "OD1" <-> "OD2" Residue "G ARG 26": "NH1" <-> "NH2" Residue "G PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 39": "NH1" <-> "NH2" Residue "G ARG 101": "NH1" <-> "NH2" Residue "G ARG 115": "NH1" <-> "NH2" Residue "G ASP 180": "OD1" <-> "OD2" Residue "G PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 201": "OE1" <-> "OE2" Residue "G PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 237": "NH1" <-> "NH2" Residue "G ARG 241": "NH1" <-> "NH2" Residue "H ARG 9": "NH1" <-> "NH2" Residue "H ARG 11": "NH1" <-> "NH2" Residue "H PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 15": "NH1" <-> "NH2" Residue "H ASP 19": "OD1" <-> "OD2" Residue "H ARG 26": "NH1" <-> "NH2" Residue "H PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 39": "NH1" <-> "NH2" Residue "H ARG 101": "NH1" <-> "NH2" Residue "H ARG 115": "NH1" <-> "NH2" Residue "H ASP 180": "OD1" <-> "OD2" Residue "H PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 201": "OE1" <-> "OE2" Residue "H PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 237": "NH1" <-> "NH2" Residue "H ARG 241": "NH1" <-> "NH2" Residue "I PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 18": "NH1" <-> "NH2" Residue "I ASP 28": "OD1" <-> "OD2" Residue "I ARG 33": "NH1" <-> "NH2" Residue "I ARG 59": "NH1" <-> "NH2" Residue "I ARG 77": "NH1" <-> "NH2" Residue "I ARG 84": "NH1" <-> "NH2" Residue "I PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 123": "OD1" <-> "OD2" Residue "I ARG 135": "NH1" <-> "NH2" Residue "I ARG 151": "NH1" <-> "NH2" Residue "I ARG 152": "NH1" <-> "NH2" Residue "I TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 170": "OE1" <-> "OE2" Residue "I PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 185": "NH1" <-> "NH2" Residue "I ASP 192": "OD1" <-> "OD2" Residue "I ASP 204": "OD1" <-> "OD2" Residue "I ARG 222": "NH1" <-> "NH2" Residue "I ARG 239": "NH1" <-> "NH2" Residue "I PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 259": "NH1" <-> "NH2" Residue "I ASP 264": "OD1" <-> "OD2" Residue "J PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 18": "NH1" <-> "NH2" Residue "J ASP 28": "OD1" <-> "OD2" Residue "J ARG 33": "NH1" <-> "NH2" Residue "J ARG 59": "NH1" <-> "NH2" Residue "J ARG 77": "NH1" <-> "NH2" Residue "J ARG 84": "NH1" <-> "NH2" Residue "J PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 123": "OD1" <-> "OD2" Residue "J ARG 135": "NH1" <-> "NH2" Residue "J ARG 151": "NH1" <-> "NH2" Residue "J ARG 152": "NH1" <-> "NH2" Residue "J TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 170": "OE1" <-> "OE2" Residue "J PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 185": "NH1" <-> "NH2" Residue "J ASP 192": "OD1" <-> "OD2" Residue "J ASP 204": "OD1" <-> "OD2" Residue "J ARG 222": "NH1" <-> "NH2" Residue "J ARG 239": "NH1" <-> "NH2" Residue "J PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 259": "NH1" <-> "NH2" Residue "J ASP 264": "OD1" <-> "OD2" Residue "K ARG 7": "NH1" <-> "NH2" Residue "K ARG 29": "NH1" <-> "NH2" Residue "K ARG 67": "NH1" <-> "NH2" Residue "K ARG 70": "NH1" <-> "NH2" Residue "K ARG 79": "NH1" <-> "NH2" Residue "L ARG 7": "NH1" <-> "NH2" Residue "L ARG 29": "NH1" <-> "NH2" Residue "L ARG 67": "NH1" <-> "NH2" Residue "L ARG 70": "NH1" <-> "NH2" Residue "L ARG 79": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16231 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1085 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 1, 'TRANS': 145} Chain: "B" Number of atoms: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1076 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 1, 'TRANS': 144} Chain: "C" Number of atoms: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1076 Classifications: {'peptide': 146} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 143} Chain: "D" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1082 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 1, 'TRANS': 145} Chain: "E" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1098 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 1, 'TRANS': 147} Chain: "F" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1068 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 1, 'TRANS': 143} Chain: "G" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1939 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 7, 'TRANS': 250} Chain: "H" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1939 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 7, 'TRANS': 250} Chain: "I" Number of atoms: 2028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2028 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 16, 'TRANS': 245} Chain: "J" Number of atoms: 2028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2028 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 16, 'TRANS': 245} Chain: "K" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 721 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "L" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 721 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "G" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 176 Unusual residues: {'LPP': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 132 Unusual residues: {'LPP': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.63, per 1000 atoms: 0.59 Number of scatterers: 16231 At special positions: 0 Unit cell: (98.8, 122.72, 145.6, 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 44 16.00 P 13 15.00 O 3059 8.00 N 2701 7.00 C 10414 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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=13, symmetry=0 Number of additional bonds: simple=13, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.38 Conformation dependent library (CDL) restraints added in 3.2 seconds 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3764 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 67 helices and 18 sheets defined 40.5% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.91 Creating SS restraints... Processing helix chain 'A' and resid 3 through 20 Processing helix chain 'A' and resid 140 through 143 No H-bonds generated for 'chain 'A' and resid 140 through 143' Processing helix chain 'B' and resid 5 through 25 Processing helix chain 'B' and resid 32 through 35 No H-bonds generated for 'chain 'B' and resid 32 through 35' Processing helix chain 'B' and resid 138 through 145 removed outlier: 3.786A pdb=" N PHE B 145 " --> pdb=" O LEU B 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 26 Processing helix chain 'C' and resid 138 through 144 Processing helix chain 'D' and resid 5 through 25 Processing helix chain 'D' and resid 138 through 143 Processing helix chain 'E' and resid 3 through 21 removed outlier: 4.029A pdb=" N LEU E 21 " --> pdb=" O GLY E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 146 Processing helix chain 'F' and resid 5 through 25 removed outlier: 4.777A pdb=" N GLY F 9 " --> pdb=" O LEU F 6 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N LEU F 19 " --> pdb=" O ALA F 16 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ALA F 20 " --> pdb=" O GLY F 17 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU F 22 " --> pdb=" O LEU F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 144 Processing helix chain 'G' and resid 6 through 36 Processing helix chain 'G' and resid 46 through 55 Processing helix chain 'G' and resid 60 through 85 removed outlier: 4.024A pdb=" N ASN G 80 " --> pdb=" O LEU G 76 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N SER G 84 " --> pdb=" O ASN G 80 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N TYR G 85 " --> pdb=" O ILE G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 95 removed outlier: 3.874A pdb=" N GLY G 92 " --> pdb=" O GLN G 89 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL G 95 " --> pdb=" O GLY G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 101 No H-bonds generated for 'chain 'G' and resid 98 through 101' Processing helix chain 'G' and resid 103 through 112 Processing helix chain 'G' and resid 121 through 129 Processing helix chain 'G' and resid 132 through 139 removed outlier: 3.716A pdb=" N LEU G 136 " --> pdb=" O GLN G 132 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLU G 137 " --> pdb=" O LEU G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 143 through 146 No H-bonds generated for 'chain 'G' and resid 143 through 146' Processing helix chain 'G' and resid 149 through 180 removed outlier: 3.553A pdb=" N SER G 158 " --> pdb=" O ALA G 154 " (cutoff:3.500A) Proline residue: G 160 - end of helix Processing helix chain 'G' and resid 186 through 196 removed outlier: 3.910A pdb=" N TRP G 190 " --> pdb=" O GLU G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 199 through 227 removed outlier: 4.699A pdb=" N LEU G 204 " --> pdb=" O THR G 200 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ASN G 205 " --> pdb=" O GLU G 201 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE G 213 " --> pdb=" O LYS G 209 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL G 222 " --> pdb=" O THR G 218 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLY G 225 " --> pdb=" O ALA G 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 259 removed outlier: 3.602A pdb=" N SER G 236 " --> pdb=" O SER G 232 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N THR G 240 " --> pdb=" O SER G 236 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL G 243 " --> pdb=" O THR G 239 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA G 246 " --> pdb=" O THR G 242 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL G 250 " --> pdb=" O ALA G 246 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 36 Processing helix chain 'H' and resid 46 through 55 Processing helix chain 'H' and resid 60 through 85 removed outlier: 4.025A pdb=" N ASN H 80 " --> pdb=" O LEU H 76 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N SER H 84 " --> pdb=" O ASN H 80 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N TYR H 85 " --> pdb=" O ILE H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 95 removed outlier: 3.875A pdb=" N GLY H 92 " --> pdb=" O GLN H 89 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL H 95 " --> pdb=" O GLY H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 98 through 101 No H-bonds generated for 'chain 'H' and resid 98 through 101' Processing helix chain 'H' and resid 103 through 112 Processing helix chain 'H' and resid 121 through 129 Processing helix chain 'H' and resid 132 through 139 removed outlier: 3.716A pdb=" N LEU H 136 " --> pdb=" O GLN H 132 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLU H 137 " --> pdb=" O LEU H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 143 through 146 No H-bonds generated for 'chain 'H' and resid 143 through 146' Processing helix chain 'H' and resid 149 through 180 removed outlier: 3.553A pdb=" N SER H 158 " --> pdb=" O ALA H 154 " (cutoff:3.500A) Proline residue: H 160 - end of helix Processing helix chain 'H' and resid 186 through 196 removed outlier: 3.909A pdb=" N TRP H 190 " --> pdb=" O GLU H 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 199 through 227 removed outlier: 4.699A pdb=" N LEU H 204 " --> pdb=" O THR H 200 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ASN H 205 " --> pdb=" O GLU H 201 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE H 213 " --> pdb=" O LYS H 209 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL H 222 " --> pdb=" O THR H 218 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLY H 225 " --> pdb=" O ALA H 221 " (cutoff:3.500A) Processing helix chain 'H' and resid 232 through 259 removed outlier: 3.602A pdb=" N SER H 236 " --> pdb=" O SER H 232 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N THR H 240 " --> pdb=" O SER H 236 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N VAL H 243 " --> pdb=" O THR H 239 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA H 246 " --> pdb=" O THR H 242 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL H 250 " --> pdb=" O ALA H 246 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 54 Processing helix chain 'I' and resid 77 through 86 removed outlier: 3.926A pdb=" N ASP I 82 " --> pdb=" O GLY I 78 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS I 85 " --> pdb=" O PHE I 81 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N GLN I 86 " --> pdb=" O ASP I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 113 Proline residue: I 109 - end of helix Processing helix chain 'I' and resid 118 through 132 removed outlier: 3.581A pdb=" N ARG I 122 " --> pdb=" O GLU I 118 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 144 No H-bonds generated for 'chain 'I' and resid 142 through 144' Processing helix chain 'I' and resid 149 through 162 removed outlier: 4.092A pdb=" N ALA I 154 " --> pdb=" O LYS I 150 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N LEU I 161 " --> pdb=" O ARG I 157 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ASP I 162 " --> pdb=" O ALA I 158 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 192 removed outlier: 3.585A pdb=" N ARG I 188 " --> pdb=" O VAL I 184 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASN I 191 " --> pdb=" O ILE I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 205 through 211 Processing helix chain 'I' and resid 229 through 234 removed outlier: 3.702A pdb=" N GLU I 234 " --> pdb=" O ASP I 230 " (cutoff:3.500A) Processing helix chain 'I' and resid 238 through 244 Processing helix chain 'I' and resid 263 through 266 No H-bonds generated for 'chain 'I' and resid 263 through 266' Processing helix chain 'J' and resid 47 through 54 Processing helix chain 'J' and resid 77 through 86 removed outlier: 3.926A pdb=" N ASP J 82 " --> pdb=" O GLY J 78 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS J 85 " --> pdb=" O PHE J 81 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N GLN J 86 " --> pdb=" O ASP J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 102 through 113 Proline residue: J 109 - end of helix Processing helix chain 'J' and resid 118 through 132 removed outlier: 3.581A pdb=" N ARG J 122 " --> pdb=" O GLU J 118 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 144 No H-bonds generated for 'chain 'J' and resid 142 through 144' Processing helix chain 'J' and resid 149 through 162 removed outlier: 4.092A pdb=" N ALA J 154 " --> pdb=" O LYS J 150 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N LEU J 161 " --> pdb=" O ARG J 157 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ASP J 162 " --> pdb=" O ALA J 158 " (cutoff:3.500A) Processing helix chain 'J' and resid 177 through 192 removed outlier: 3.586A pdb=" N ARG J 188 " --> pdb=" O VAL J 184 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASN J 191 " --> pdb=" O ILE J 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 205 through 211 Processing helix chain 'J' and resid 229 through 234 removed outlier: 3.703A pdb=" N GLU J 234 " --> pdb=" O ASP J 230 " (cutoff:3.500A) Processing helix chain 'J' and resid 238 through 244 Processing helix chain 'J' and resid 263 through 266 No H-bonds generated for 'chain 'J' and resid 263 through 266' Processing helix chain 'K' and resid 25 through 33 Processing helix chain 'K' and resid 56 through 71 removed outlier: 3.565A pdb=" N ILE K 66 " --> pdb=" O LEU K 62 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP K 68 " --> pdb=" O ALA K 64 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA K 69 " --> pdb=" O PHE K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 91 Processing helix chain 'L' and resid 25 through 33 Processing helix chain 'L' and resid 56 through 71 removed outlier: 3.565A pdb=" N ILE L 66 " --> pdb=" O LEU L 62 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP L 68 " --> pdb=" O ALA L 64 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA L 69 " --> pdb=" O PHE L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 91 Processing sheet with id= A, first strand: chain 'A' and resid 39 through 46 removed outlier: 3.927A pdb=" N THR A 79 " --> pdb=" O ASP A 74 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N GLU A 85 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N VAL A 68 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 98 through 103 removed outlier: 6.154A pdb=" N LEU A 60 " --> pdb=" O THR A 64 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N THR A 64 " --> pdb=" O LEU A 60 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 39 through 46 removed outlier: 5.826A pdb=" N GLU B 85 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N VAL B 68 " --> pdb=" O GLU B 85 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 99 through 103 removed outlier: 5.965A pdb=" N LYS B 57 " --> pdb=" O LYS B 110 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N LEU B 60 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N THR B 64 " --> pdb=" O LEU B 60 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 40 through 46 removed outlier: 3.644A pdb=" N TYR C 40 " --> pdb=" O ILE C 86 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N GLU C 85 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N VAL C 68 " --> pdb=" O GLU C 85 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 98 through 103 removed outlier: 5.137A pdb=" N LYS C 57 " --> pdb=" O LYS C 110 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N LEU C 60 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N THR C 64 " --> pdb=" O LEU C 60 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 39 through 46 removed outlier: 5.776A pdb=" N GLU D 85 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N VAL D 68 " --> pdb=" O GLU D 85 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 98 through 103 removed outlier: 5.460A pdb=" N LYS D 57 " --> pdb=" O LYS D 110 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LEU D 60 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N THR D 64 " --> pdb=" O LEU D 60 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 39 through 46 removed outlier: 3.924A pdb=" N THR E 79 " --> pdb=" O ASP E 74 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N GLU E 85 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N VAL E 68 " --> pdb=" O GLU E 85 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 98 through 101 removed outlier: 5.757A pdb=" N LEU E 60 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N THR E 64 " --> pdb=" O LEU E 60 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 40 through 46 removed outlier: 6.010A pdb=" N GLU F 85 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N VAL F 68 " --> pdb=" O GLU F 85 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 98 through 103 removed outlier: 5.896A pdb=" N LEU F 60 " --> pdb=" O THR F 64 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N THR F 64 " --> pdb=" O LEU F 60 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'I' and resid 64 through 67 removed outlier: 6.690A pdb=" N ILE I 31 " --> pdb=" O ALA I 8 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLU I 10 " --> pdb=" O VAL I 29 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL I 29 " --> pdb=" O GLU I 10 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'I' and resid 37 through 39 Processing sheet with id= O, first strand: chain 'J' and resid 64 through 67 removed outlier: 6.689A pdb=" N ILE J 31 " --> pdb=" O ALA J 8 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLU J 10 " --> pdb=" O VAL J 29 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL J 29 " --> pdb=" O GLU J 10 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'J' and resid 37 through 39 Processing sheet with id= Q, first strand: chain 'K' and resid 44 through 47 Processing sheet with id= R, first strand: chain 'L' and resid 44 through 47 684 hydrogen bonds defined for protein. 1941 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: 4.93 Time building geometry restraints manager: 7.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 2683 1.30 - 1.43: 3792 1.43 - 1.55: 9858 1.55 - 1.68: 25 1.68 - 1.81: 84 Bond restraints: 16442 Sorted by residual: bond pdb=" O3A ANP I 301 " pdb=" PB ANP I 301 " ideal model delta sigma weight residual 1.700 1.551 0.149 2.00e-02 2.50e+03 5.53e+01 bond pdb=" O3A ANP J 301 " pdb=" PB ANP J 301 " ideal model delta sigma weight residual 1.700 1.551 0.149 2.00e-02 2.50e+03 5.53e+01 bond pdb=" N3B ANP J 301 " pdb=" PG ANP J 301 " ideal model delta sigma weight residual 1.795 1.689 0.106 2.00e-02 2.50e+03 2.80e+01 bond pdb=" N3B ANP I 301 " pdb=" PG ANP I 301 " ideal model delta sigma weight residual 1.795 1.690 0.105 2.00e-02 2.50e+03 2.73e+01 bond pdb=" O5' ANP I 301 " pdb=" PA ANP I 301 " ideal model delta sigma weight residual 1.655 1.566 0.089 2.00e-02 2.50e+03 1.98e+01 ... (remaining 16437 not shown) Histogram of bond angle deviations from ideal: 98.10 - 105.27: 221 105.27 - 112.43: 9040 112.43 - 119.60: 5204 119.60 - 126.76: 7664 126.76 - 133.93: 124 Bond angle restraints: 22253 Sorted by residual: angle pdb=" N ILE E 65 " pdb=" CA ILE E 65 " pdb=" C ILE E 65 " ideal model delta sigma weight residual 113.42 107.71 5.71 1.17e+00 7.31e-01 2.38e+01 angle pdb=" N ILE D 65 " pdb=" CA ILE D 65 " pdb=" C ILE D 65 " ideal model delta sigma weight residual 113.42 108.05 5.37 1.17e+00 7.31e-01 2.11e+01 angle pdb=" PB ANP I 301 " pdb=" N3B ANP I 301 " pdb=" PG ANP I 301 " ideal model delta sigma weight residual 126.95 113.32 13.63 3.00e+00 1.11e-01 2.06e+01 angle pdb=" PB ANP J 301 " pdb=" N3B ANP J 301 " pdb=" PG ANP J 301 " ideal model delta sigma weight residual 126.95 113.34 13.61 3.00e+00 1.11e-01 2.06e+01 angle pdb=" C VAL B 95 " pdb=" N ASP B 96 " pdb=" CA ASP B 96 " ideal model delta sigma weight residual 122.65 115.15 7.50 1.66e+00 3.63e-01 2.04e+01 ... (remaining 22248 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.33: 8725 19.33 - 38.66: 809 38.66 - 57.99: 259 57.99 - 77.32: 48 77.32 - 96.65: 13 Dihedral angle restraints: 9854 sinusoidal: 3926 harmonic: 5928 Sorted by residual: dihedral pdb=" CA SER L 92 " pdb=" C SER L 92 " pdb=" N SER L 93 " pdb=" CA SER L 93 " ideal model delta harmonic sigma weight residual -180.00 -147.53 -32.47 0 5.00e+00 4.00e-02 4.22e+01 dihedral pdb=" CA SER K 92 " pdb=" C SER K 92 " pdb=" N SER K 93 " pdb=" CA SER K 93 " ideal model delta harmonic sigma weight residual -180.00 -147.53 -32.47 0 5.00e+00 4.00e-02 4.22e+01 dihedral pdb=" CA SER F 32 " pdb=" C SER F 32 " pdb=" N VAL F 33 " pdb=" CA VAL F 33 " ideal model delta harmonic sigma weight residual -180.00 -147.98 -32.02 0 5.00e+00 4.00e-02 4.10e+01 ... (remaining 9851 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2256 0.064 - 0.129: 398 0.129 - 0.193: 32 0.193 - 0.258: 4 0.258 - 0.322: 2 Chirality restraints: 2692 Sorted by residual: chirality pdb=" C3' ANP I 301 " pdb=" C2' ANP I 301 " pdb=" C4' ANP I 301 " pdb=" O3' ANP I 301 " both_signs ideal model delta sigma weight residual False -2.36 -2.68 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" C3' ANP J 301 " pdb=" C2' ANP J 301 " pdb=" C4' ANP J 301 " pdb=" O3' ANP J 301 " both_signs ideal model delta sigma weight residual False -2.36 -2.68 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA THR G 218 " pdb=" N THR G 218 " pdb=" C THR G 218 " pdb=" CB THR G 218 " both_signs ideal model delta sigma weight residual False 2.53 2.31 0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 2689 not shown) Planarity restraints: 2779 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR J 256 " -0.039 5.00e-02 4.00e+02 5.87e-02 5.52e+00 pdb=" N PRO J 257 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO J 257 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO J 257 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR I 256 " -0.039 5.00e-02 4.00e+02 5.84e-02 5.46e+00 pdb=" N PRO I 257 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO I 257 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO I 257 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA I 193 " 0.010 2.00e-02 2.50e+03 2.02e-02 4.06e+00 pdb=" C ALA I 193 " -0.035 2.00e-02 2.50e+03 pdb=" O ALA I 193 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU I 194 " 0.012 2.00e-02 2.50e+03 ... (remaining 2776 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 382 2.61 - 3.18: 16476 3.18 - 3.75: 25380 3.75 - 4.33: 34951 4.33 - 4.90: 55270 Nonbonded interactions: 132459 Sorted by model distance: nonbonded pdb=" O ALA B 25 " pdb=" OG SER B 29 " model vdw 2.033 2.440 nonbonded pdb=" O ALA C 99 " pdb=" OG1 THR C 132 " model vdw 2.111 2.440 nonbonded pdb=" CD2 TYR H 85 " pdb=" O10 LPP G 304 " model vdw 2.113 2.672 nonbonded pdb=" OD2 ASP J 123 " pdb=" NH2 ARG L 67 " model vdw 2.115 2.520 nonbonded pdb=" OD2 ASP D 74 " pdb=" OG SER D 77 " model vdw 2.123 2.440 ... (remaining 132454 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 3 through 147) selection = (chain 'B' and resid 3 through 147) selection = (chain 'C' and resid 3 through 147) selection = (chain 'D' and resid 3 through 147) selection = (chain 'E' and resid 3 through 147) selection = chain 'F' } ncs_group { reference = (chain 'G' and (resid 5 through 262 or resid 301 through 303)) selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 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: 4.510 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 47.220 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 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 : 0.009 0.149 16442 Z= 0.571 Angle : 1.040 13.631 22253 Z= 0.532 Chirality : 0.049 0.322 2692 Planarity : 0.005 0.059 2779 Dihedral : 17.313 96.650 6090 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 24.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 14.44 % Favored : 85.52 % Rotamer: Outliers : 5.12 % Allowed : 11.54 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.83 (0.14), residues: 2092 helix: -2.74 (0.14), residues: 863 sheet: -2.59 (0.26), residues: 297 loop : -3.86 (0.15), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 153 HIS 0.003 0.001 HIS I 203 PHE 0.017 0.002 PHE F 145 TYR 0.019 0.002 TYR F 40 ARG 0.009 0.001 ARG K 37 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 528 time to evaluate : 1.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.8752 (t0) cc_final: 0.8510 (t0) REVERT: B 19 LEU cc_start: 0.8783 (mt) cc_final: 0.8506 (tt) REVERT: B 133 GLN cc_start: 0.8144 (mm-40) cc_final: 0.7915 (mm110) REVERT: C 18 LEU cc_start: 0.9052 (mp) cc_final: 0.8831 (mp) REVERT: C 90 VAL cc_start: 0.7313 (t) cc_final: 0.7036 (t) REVERT: D 84 MET cc_start: 0.8225 (pmm) cc_final: 0.7952 (pmm) REVERT: E 7 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7593 (mt-10) REVERT: E 14 LEU cc_start: 0.8707 (tp) cc_final: 0.8363 (tt) REVERT: E 111 TYR cc_start: 0.8998 (p90) cc_final: 0.8402 (p90) REVERT: F 67 LYS cc_start: 0.8896 (ptmt) cc_final: 0.8499 (ptpt) REVERT: F 101 ILE cc_start: 0.9506 (mp) cc_final: 0.9279 (mt) REVERT: G 7 LEU cc_start: 0.7572 (pp) cc_final: 0.7325 (mt) REVERT: G 8 GLU cc_start: 0.8243 (tt0) cc_final: 0.7883 (mp0) REVERT: G 167 SER cc_start: 0.9357 (OUTLIER) cc_final: 0.9149 (m) REVERT: G 172 TRP cc_start: 0.7374 (t60) cc_final: 0.6311 (m-10) REVERT: G 186 GLU cc_start: 0.8205 (mp0) cc_final: 0.8005 (mp0) REVERT: H 19 ASP cc_start: 0.8767 (OUTLIER) cc_final: 0.8418 (m-30) REVERT: H 185 TYR cc_start: 0.8099 (t80) cc_final: 0.7370 (t80) REVERT: H 223 TYR cc_start: 0.9147 (t80) cc_final: 0.8781 (t80) REVERT: I 10 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7106 (mp0) REVERT: I 101 ASP cc_start: 0.8208 (p0) cc_final: 0.7963 (p0) REVERT: I 159 ILE cc_start: 0.9553 (pt) cc_final: 0.9300 (mt) REVERT: I 175 GLN cc_start: 0.8517 (pm20) cc_final: 0.8279 (pm20) REVERT: I 202 SER cc_start: 0.8817 (t) cc_final: 0.8602 (t) REVERT: J 233 LYS cc_start: 0.8889 (tppp) cc_final: 0.8626 (mmmm) REVERT: K 45 VAL cc_start: 0.8132 (t) cc_final: 0.7886 (p) REVERT: K 70 ARG cc_start: 0.8402 (ttt-90) cc_final: 0.8077 (ttp80) REVERT: L 44 LEU cc_start: 0.6445 (OUTLIER) cc_final: 0.5984 (mm) outliers start: 87 outliers final: 18 residues processed: 563 average time/residue: 0.3205 time to fit residues: 254.1070 Evaluate side-chains 383 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 362 time to evaluate : 1.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 19 ASP Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 244 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 228 THR Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain K residue 37 ARG Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain L residue 44 LEU Chi-restraints excluded: chain L residue 52 GLU Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 61 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 0.9990 chunk 154 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 52 optimal weight: 0.3980 chunk 104 optimal weight: 0.9990 chunk 82 optimal weight: 20.0000 chunk 159 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 185 optimal weight: 4.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 88 GLN A 133 GLN D 148 ASN E 2 GLN E 35 ASN E 87 ASN ** E 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 ASN F 133 GLN ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 195 ASN G 224 GLN ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 GLN ** I 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 68 ASN ** J 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 191 ASN ** J 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16442 Z= 0.224 Angle : 0.744 13.550 22253 Z= 0.373 Chirality : 0.044 0.244 2692 Planarity : 0.005 0.085 2779 Dihedral : 13.178 83.135 2609 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 21.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 4.36 % Allowed : 21.50 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.28 (0.16), residues: 2092 helix: -1.18 (0.17), residues: 846 sheet: -2.30 (0.27), residues: 292 loop : -3.09 (0.16), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP I 66 HIS 0.003 0.001 HIS A 130 PHE 0.023 0.002 PHE G 213 TYR 0.024 0.002 TYR D 40 ARG 0.010 0.001 ARG K 67 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 453 time to evaluate : 1.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.8789 (t0) cc_final: 0.8457 (t0) REVERT: A 67 LYS cc_start: 0.8213 (mmmt) cc_final: 0.7860 (mmmm) REVERT: B 19 LEU cc_start: 0.8677 (mt) cc_final: 0.8401 (tt) REVERT: C 67 LYS cc_start: 0.9126 (ptpt) cc_final: 0.8615 (ptpt) REVERT: D 89 ASN cc_start: 0.7806 (p0) cc_final: 0.7590 (m110) REVERT: E 48 ASN cc_start: 0.7781 (t0) cc_final: 0.7202 (m-40) REVERT: E 139 GLU cc_start: 0.7498 (tp30) cc_final: 0.7250 (mm-30) REVERT: F 4 ARG cc_start: 0.7521 (mtt180) cc_final: 0.6639 (mtp-110) REVERT: F 43 TYR cc_start: 0.8268 (m-80) cc_final: 0.8021 (m-80) REVERT: F 67 LYS cc_start: 0.8664 (ptmt) cc_final: 0.8348 (ttpp) REVERT: F 101 ILE cc_start: 0.9403 (mp) cc_final: 0.9168 (mm) REVERT: G 138 MET cc_start: 0.8445 (mpp) cc_final: 0.8237 (mpp) REVERT: G 172 TRP cc_start: 0.7163 (t60) cc_final: 0.6357 (m-10) REVERT: G 185 TYR cc_start: 0.6734 (t80) cc_final: 0.6514 (t80) REVERT: G 255 PHE cc_start: 0.8607 (t80) cc_final: 0.8344 (t80) REVERT: H 19 ASP cc_start: 0.8651 (m-30) cc_final: 0.8291 (m-30) REVERT: H 223 TYR cc_start: 0.8930 (t80) cc_final: 0.8546 (t80) REVERT: I 116 LEU cc_start: 0.8838 (mt) cc_final: 0.8328 (mp) REVERT: I 159 ILE cc_start: 0.9546 (pt) cc_final: 0.9327 (mt) REVERT: I 202 SER cc_start: 0.8655 (t) cc_final: 0.8447 (t) REVERT: K 70 ARG cc_start: 0.8480 (ttt-90) cc_final: 0.8170 (ttp80) REVERT: L 71 LYS cc_start: 0.8912 (tttt) cc_final: 0.8676 (ptpt) REVERT: L 87 GLU cc_start: 0.8518 (tt0) cc_final: 0.8268 (tt0) outliers start: 74 outliers final: 45 residues processed: 491 average time/residue: 0.2880 time to fit residues: 206.9428 Evaluate side-chains 400 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 355 time to evaluate : 1.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain G residue 201 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 56 SER Chi-restraints excluded: chain I residue 64 GLU Chi-restraints excluded: chain I residue 120 MET Chi-restraints excluded: chain I residue 143 ASP Chi-restraints excluded: chain I residue 149 MET Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain I residue 235 THR Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 68 ASN Chi-restraints excluded: chain J residue 99 ASP Chi-restraints excluded: chain J residue 110 LEU Chi-restraints excluded: chain J residue 139 GLU Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 228 THR Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain J residue 235 THR Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain L residue 61 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 154 optimal weight: 9.9990 chunk 126 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 185 optimal weight: 9.9990 chunk 200 optimal weight: 5.9990 chunk 165 optimal weight: 9.9990 chunk 184 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 chunk 148 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 133 GLN G 77 GLN ** G 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 86 GLN ** J 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 113 HIS ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 16442 Z= 0.370 Angle : 0.794 10.059 22253 Z= 0.395 Chirality : 0.047 0.284 2692 Planarity : 0.005 0.051 2779 Dihedral : 11.961 83.102 2584 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 21.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.28 % Favored : 89.72 % Rotamer: Outliers : 7.07 % Allowed : 22.97 % Favored : 69.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.17), residues: 2092 helix: -0.79 (0.17), residues: 865 sheet: -2.01 (0.28), residues: 282 loop : -3.06 (0.17), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP G 153 HIS 0.003 0.001 HIS J 226 PHE 0.033 0.002 PHE G 213 TYR 0.044 0.002 TYR G 85 ARG 0.007 0.001 ARG J 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 370 time to evaluate : 1.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.8851 (t0) cc_final: 0.8518 (t0) REVERT: A 57 LYS cc_start: 0.8462 (mtpp) cc_final: 0.8140 (tppp) REVERT: A 111 TYR cc_start: 0.8572 (p90) cc_final: 0.8254 (p90) REVERT: B 19 LEU cc_start: 0.8742 (mt) cc_final: 0.8465 (tt) REVERT: C 18 LEU cc_start: 0.9115 (mt) cc_final: 0.8856 (mp) REVERT: C 67 LYS cc_start: 0.9209 (ptpt) cc_final: 0.8977 (ptpt) REVERT: F 4 ARG cc_start: 0.7590 (mtt180) cc_final: 0.6321 (mmm-85) REVERT: F 7 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7612 (mp0) REVERT: F 47 ASP cc_start: 0.8165 (m-30) cc_final: 0.7736 (t0) REVERT: F 101 ILE cc_start: 0.9430 (mp) cc_final: 0.9187 (mm) REVERT: G 172 TRP cc_start: 0.7546 (t60) cc_final: 0.6511 (m-10) REVERT: G 255 PHE cc_start: 0.8667 (t80) cc_final: 0.8413 (t80) REVERT: H 19 ASP cc_start: 0.8679 (m-30) cc_final: 0.8388 (m-30) REVERT: H 185 TYR cc_start: 0.7521 (t80) cc_final: 0.7248 (t80) REVERT: H 223 TYR cc_start: 0.9071 (t80) cc_final: 0.8721 (t80) REVERT: I 10 GLU cc_start: 0.7444 (mp0) cc_final: 0.7199 (mp0) REVERT: I 139 GLU cc_start: 0.7874 (tp30) cc_final: 0.7644 (tp30) REVERT: I 159 ILE cc_start: 0.9575 (pt) cc_final: 0.9227 (mt) REVERT: J 51 LEU cc_start: 0.9425 (tp) cc_final: 0.9211 (tp) REVERT: K 70 ARG cc_start: 0.8487 (ttt-90) cc_final: 0.8179 (ttp80) outliers start: 120 outliers final: 76 residues processed: 450 average time/residue: 0.2701 time to fit residues: 179.9609 Evaluate side-chains 394 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 318 time to evaluate : 1.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 91 ASN Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 91 ASN Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 201 GLU Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 261 MET Chi-restraints excluded: chain H residue 8 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 30 PHE Chi-restraints excluded: chain H residue 94 MET Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 240 THR Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 57 GLN Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 143 ASP Chi-restraints excluded: chain I residue 149 MET Chi-restraints excluded: chain I residue 167 LEU Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain I residue 215 ILE Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 235 THR Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 99 ASP Chi-restraints excluded: chain J residue 110 LEU Chi-restraints excluded: chain J residue 119 GLU Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 228 THR Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain J residue 235 THR Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 91 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 chunk 96 optimal weight: 0.5980 chunk 20 optimal weight: 10.0000 chunk 88 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 186 optimal weight: 7.9990 chunk 197 optimal weight: 7.9990 chunk 97 optimal weight: 0.9980 chunk 176 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 89 ASN ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 GLN ** G 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 GLN ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16442 Z= 0.202 Angle : 0.724 12.837 22253 Z= 0.360 Chirality : 0.045 0.247 2692 Planarity : 0.004 0.050 2779 Dihedral : 11.328 85.961 2581 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 18.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 5.30 % Allowed : 25.62 % Favored : 69.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.17), residues: 2092 helix: -0.36 (0.18), residues: 866 sheet: -1.89 (0.29), residues: 277 loop : -2.89 (0.17), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 190 HIS 0.003 0.001 HIS J 203 PHE 0.030 0.002 PHE H 199 TYR 0.041 0.002 TYR D 40 ARG 0.005 0.000 ARG G 151 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 379 time to evaluate : 1.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.6797 (OUTLIER) cc_final: 0.6388 (p) REVERT: A 48 ASN cc_start: 0.8879 (t0) cc_final: 0.8554 (t0) REVERT: A 111 TYR cc_start: 0.8435 (p90) cc_final: 0.8181 (p90) REVERT: B 19 LEU cc_start: 0.8662 (mt) cc_final: 0.8410 (tt) REVERT: C 67 LYS cc_start: 0.9210 (ptpt) cc_final: 0.8849 (ptpt) REVERT: C 82 VAL cc_start: 0.8598 (p) cc_final: 0.8265 (m) REVERT: C 84 MET cc_start: 0.8288 (pmm) cc_final: 0.6803 (pmm) REVERT: E 7 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7182 (mt-10) REVERT: E 48 ASN cc_start: 0.7822 (t0) cc_final: 0.7126 (m-40) REVERT: E 101 ILE cc_start: 0.9254 (mt) cc_final: 0.8839 (mt) REVERT: F 4 ARG cc_start: 0.7565 (mtt180) cc_final: 0.6271 (mmm-85) REVERT: F 7 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7478 (mp0) REVERT: F 101 ILE cc_start: 0.9421 (mp) cc_final: 0.9117 (mm) REVERT: G 77 GLN cc_start: 0.8649 (tp40) cc_final: 0.8431 (tp40) REVERT: G 172 TRP cc_start: 0.7385 (t60) cc_final: 0.6534 (m-10) REVERT: G 193 MET cc_start: 0.7771 (OUTLIER) cc_final: 0.7356 (ttp) REVERT: H 36 LEU cc_start: 0.7976 (mt) cc_final: 0.7504 (pp) REVERT: H 223 TYR cc_start: 0.8804 (t80) cc_final: 0.8445 (t80) REVERT: H 224 GLN cc_start: 0.8880 (mm-40) cc_final: 0.8596 (mm-40) REVERT: I 10 GLU cc_start: 0.7361 (mp0) cc_final: 0.7138 (mp0) REVERT: I 116 LEU cc_start: 0.8860 (mt) cc_final: 0.8482 (mp) REVERT: I 159 ILE cc_start: 0.9556 (pt) cc_final: 0.9299 (mt) REVERT: J 57 GLN cc_start: 0.8862 (tm-30) cc_final: 0.8288 (tm-30) REVERT: J 120 MET cc_start: 0.8152 (tpp) cc_final: 0.7838 (tpp) REVERT: J 215 ILE cc_start: 0.9269 (OUTLIER) cc_final: 0.9017 (tt) REVERT: J 261 TYR cc_start: 0.7768 (t80) cc_final: 0.7524 (t80) REVERT: K 70 ARG cc_start: 0.8447 (ttt-90) cc_final: 0.8134 (ttp80) REVERT: L 31 GLN cc_start: 0.7520 (OUTLIER) cc_final: 0.6891 (pp30) REVERT: L 87 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8363 (mt-10) outliers start: 90 outliers final: 55 residues processed: 437 average time/residue: 0.2809 time to fit residues: 180.4122 Evaluate side-chains 389 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 329 time to evaluate : 1.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 193 MET Chi-restraints excluded: chain G residue 201 GLU Chi-restraints excluded: chain G residue 261 MET Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 94 MET Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 143 ASP Chi-restraints excluded: chain I residue 149 MET Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 167 LEU Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain I residue 202 SER Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 99 ASP Chi-restraints excluded: chain J residue 119 GLU Chi-restraints excluded: chain J residue 150 LYS Chi-restraints excluded: chain J residue 215 ILE Chi-restraints excluded: chain J residue 228 THR Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain K residue 53 ARG Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain L residue 30 GLU Chi-restraints excluded: chain L residue 31 GLN Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 91 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 146 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 chunk 168 optimal weight: 3.9990 chunk 136 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 chunk 176 optimal weight: 0.8980 chunk 49 optimal weight: 6.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 GLN ** G 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 ASN ** H 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 GLN ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16442 Z= 0.282 Angle : 0.744 10.918 22253 Z= 0.374 Chirality : 0.045 0.325 2692 Planarity : 0.004 0.047 2779 Dihedral : 11.056 88.749 2579 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 6.71 % Allowed : 26.03 % Favored : 67.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.17), residues: 2092 helix: -0.25 (0.18), residues: 866 sheet: -1.76 (0.28), residues: 299 loop : -2.89 (0.17), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 190 HIS 0.002 0.001 HIS I 113 PHE 0.028 0.002 PHE G 213 TYR 0.051 0.002 TYR D 40 ARG 0.007 0.000 ARG E 75 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 350 time to evaluate : 1.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.6750 (OUTLIER) cc_final: 0.6500 (p) REVERT: A 48 ASN cc_start: 0.8929 (t0) cc_final: 0.8509 (t0) REVERT: B 19 LEU cc_start: 0.8684 (mt) cc_final: 0.8442 (tt) REVERT: C 67 LYS cc_start: 0.9212 (ptpt) cc_final: 0.8813 (ptpt) REVERT: C 84 MET cc_start: 0.8350 (pmm) cc_final: 0.6902 (pmm) REVERT: D 67 LYS cc_start: 0.8778 (ptpt) cc_final: 0.8452 (pttp) REVERT: D 86 ILE cc_start: 0.7724 (mp) cc_final: 0.7315 (pt) REVERT: E 14 LEU cc_start: 0.8814 (tp) cc_final: 0.8465 (tt) REVERT: E 48 ASN cc_start: 0.7860 (t0) cc_final: 0.7228 (m-40) REVERT: E 101 ILE cc_start: 0.9175 (mt) cc_final: 0.8756 (mt) REVERT: E 146 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7107 (pt) REVERT: F 4 ARG cc_start: 0.7587 (mtt180) cc_final: 0.6284 (mmm-85) REVERT: F 7 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7521 (mp0) REVERT: F 101 ILE cc_start: 0.9429 (mp) cc_final: 0.9160 (mm) REVERT: G 77 GLN cc_start: 0.8740 (tp40) cc_final: 0.8235 (tt0) REVERT: G 138 MET cc_start: 0.8287 (mpp) cc_final: 0.8076 (mpp) REVERT: G 172 TRP cc_start: 0.7531 (t60) cc_final: 0.6553 (m-10) REVERT: G 185 TYR cc_start: 0.6982 (t80) cc_final: 0.6652 (t80) REVERT: H 8 GLU cc_start: 0.8686 (tp30) cc_final: 0.8450 (mm-30) REVERT: H 19 ASP cc_start: 0.8725 (m-30) cc_final: 0.8432 (m-30) REVERT: H 102 GLU cc_start: 0.5644 (tm-30) cc_final: 0.5403 (tm-30) REVERT: H 223 TYR cc_start: 0.8896 (t80) cc_final: 0.8552 (t80) REVERT: I 10 GLU cc_start: 0.7440 (mp0) cc_final: 0.7234 (mp0) REVERT: I 17 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8597 (tttm) REVERT: I 127 MET cc_start: 0.7864 (ttp) cc_final: 0.7523 (ttm) REVERT: I 159 ILE cc_start: 0.9579 (pt) cc_final: 0.9253 (mt) REVERT: J 57 GLN cc_start: 0.8847 (tm-30) cc_final: 0.8262 (tm-30) REVERT: K 70 ARG cc_start: 0.8477 (ttt-90) cc_final: 0.8145 (ttp80) outliers start: 114 outliers final: 73 residues processed: 430 average time/residue: 0.2908 time to fit residues: 184.6024 Evaluate side-chains 406 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 330 time to evaluate : 1.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain C residue 4 ARG Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain G residue 201 GLU Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 261 MET Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 94 MET Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain H residue 240 THR Chi-restraints excluded: chain I residue 17 LYS Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain I residue 143 ASP Chi-restraints excluded: chain I residue 149 MET Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 167 LEU Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain I residue 202 SER Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 99 ASP Chi-restraints excluded: chain J residue 119 GLU Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 91 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 6.9990 chunk 177 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 chunk 115 optimal weight: 0.7980 chunk 48 optimal weight: 10.0000 chunk 197 optimal weight: 0.6980 chunk 163 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 65 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 GLN ** H 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 GLN ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16442 Z= 0.225 Angle : 0.717 12.616 22253 Z= 0.358 Chirality : 0.044 0.254 2692 Planarity : 0.004 0.048 2779 Dihedral : 10.798 90.465 2577 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 18.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 5.95 % Allowed : 27.39 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.17), residues: 2092 helix: -0.00 (0.18), residues: 858 sheet: -1.77 (0.28), residues: 304 loop : -2.82 (0.18), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 66 HIS 0.002 0.000 HIS I 113 PHE 0.024 0.002 PHE G 213 TYR 0.048 0.002 TYR D 40 ARG 0.006 0.000 ARG G 151 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 362 time to evaluate : 1.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.6878 (OUTLIER) cc_final: 0.6631 (p) REVERT: A 48 ASN cc_start: 0.8980 (t0) cc_final: 0.8518 (t0) REVERT: A 75 ARG cc_start: 0.6361 (mmm160) cc_final: 0.5073 (mmm160) REVERT: B 19 LEU cc_start: 0.8599 (mt) cc_final: 0.8398 (tt) REVERT: B 67 LYS cc_start: 0.9061 (tmmt) cc_final: 0.8835 (tttt) REVERT: B 107 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7395 (mm) REVERT: C 18 LEU cc_start: 0.9161 (mp) cc_final: 0.8497 (tp) REVERT: C 91 ASN cc_start: 0.6987 (OUTLIER) cc_final: 0.6716 (m-40) REVERT: D 67 LYS cc_start: 0.8751 (ptpt) cc_final: 0.8485 (pttp) REVERT: E 7 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7347 (mt-10) REVERT: E 14 LEU cc_start: 0.8812 (tp) cc_final: 0.8487 (tt) REVERT: E 48 ASN cc_start: 0.7835 (t0) cc_final: 0.7153 (m-40) REVERT: E 146 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7185 (pt) REVERT: F 4 ARG cc_start: 0.7576 (mtt180) cc_final: 0.6260 (mmm-85) REVERT: F 7 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7559 (mp0) REVERT: F 47 ASP cc_start: 0.8037 (m-30) cc_final: 0.7683 (t0) REVERT: F 101 ILE cc_start: 0.9439 (mp) cc_final: 0.9100 (mm) REVERT: G 77 GLN cc_start: 0.8773 (tp40) cc_final: 0.8281 (tt0) REVERT: G 172 TRP cc_start: 0.7508 (t60) cc_final: 0.6586 (m-10) REVERT: H 8 GLU cc_start: 0.8554 (tp30) cc_final: 0.8306 (mm-30) REVERT: H 223 TYR cc_start: 0.8795 (t80) cc_final: 0.8460 (t80) REVERT: H 224 GLN cc_start: 0.8945 (mm-40) cc_final: 0.8690 (mm-40) REVERT: I 104 GLU cc_start: 0.7155 (mp0) cc_final: 0.6940 (mp0) REVERT: I 116 LEU cc_start: 0.8921 (mt) cc_final: 0.8563 (mp) REVERT: I 127 MET cc_start: 0.7825 (ttp) cc_final: 0.7524 (ttm) REVERT: I 159 ILE cc_start: 0.9566 (pt) cc_final: 0.9254 (mt) REVERT: J 57 GLN cc_start: 0.8823 (tm-30) cc_final: 0.8302 (tm-30) REVERT: K 70 ARG cc_start: 0.8488 (ttt-90) cc_final: 0.8135 (ttp80) REVERT: L 31 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.7131 (pp30) outliers start: 101 outliers final: 71 residues processed: 434 average time/residue: 0.2752 time to fit residues: 177.2506 Evaluate side-chains 401 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 325 time to evaluate : 1.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 91 ASN Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain G residue 201 GLU Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 94 MET Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 161 LEU Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain H residue 240 THR Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 57 GLN Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 143 ASP Chi-restraints excluded: chain I residue 149 MET Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 167 LEU Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain I residue 215 ILE Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 99 ASP Chi-restraints excluded: chain J residue 119 GLU Chi-restraints excluded: chain J residue 120 MET Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 228 THR Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain L residue 31 GLN Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 91 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 144 optimal weight: 0.3980 chunk 111 optimal weight: 0.9990 chunk 166 optimal weight: 0.0470 chunk 110 optimal weight: 0.9980 chunk 196 optimal weight: 9.9990 chunk 123 optimal weight: 0.6980 chunk 119 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 148 ASN ** G 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 205 ASN ** I 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 GLN ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.4429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16442 Z= 0.190 Angle : 0.716 11.670 22253 Z= 0.356 Chirality : 0.044 0.245 2692 Planarity : 0.004 0.060 2779 Dihedral : 10.560 92.185 2577 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 17.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 5.01 % Allowed : 29.33 % Favored : 65.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.18), residues: 2092 helix: 0.21 (0.18), residues: 854 sheet: -1.79 (0.29), residues: 297 loop : -2.76 (0.18), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 66 HIS 0.002 0.001 HIS J 203 PHE 0.021 0.002 PHE G 213 TYR 0.086 0.002 TYR H 85 ARG 0.005 0.000 ARG G 151 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 363 time to evaluate : 1.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.9021 (t0) cc_final: 0.8604 (t0) REVERT: A 75 ARG cc_start: 0.6383 (mmm160) cc_final: 0.6114 (mmm160) REVERT: B 107 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7429 (mm) REVERT: B 120 GLU cc_start: 0.7067 (tm-30) cc_final: 0.6845 (tm-30) REVERT: C 18 LEU cc_start: 0.9153 (mp) cc_final: 0.8454 (tp) REVERT: C 67 LYS cc_start: 0.9359 (ptpt) cc_final: 0.8904 (ptpt) REVERT: D 67 LYS cc_start: 0.8685 (ptpt) cc_final: 0.8432 (pttp) REVERT: E 7 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7379 (mt-10) REVERT: E 14 LEU cc_start: 0.8796 (tp) cc_final: 0.8469 (tt) REVERT: E 48 ASN cc_start: 0.7828 (t0) cc_final: 0.7129 (m-40) REVERT: E 146 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7191 (pt) REVERT: F 4 ARG cc_start: 0.7494 (mtt180) cc_final: 0.6224 (mmm-85) REVERT: F 7 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7644 (mp0) REVERT: F 27 ARG cc_start: 0.5984 (OUTLIER) cc_final: 0.5682 (ttp80) REVERT: F 47 ASP cc_start: 0.8089 (m-30) cc_final: 0.7675 (t0) REVERT: F 67 LYS cc_start: 0.8333 (ptmt) cc_final: 0.7959 (ptmt) REVERT: F 101 ILE cc_start: 0.9439 (mp) cc_final: 0.9116 (mm) REVERT: F 147 LEU cc_start: 0.3964 (OUTLIER) cc_final: 0.3120 (mp) REVERT: G 77 GLN cc_start: 0.8619 (tp40) cc_final: 0.8315 (tt0) REVERT: G 172 TRP cc_start: 0.7450 (t60) cc_final: 0.6602 (m-10) REVERT: H 8 GLU cc_start: 0.8504 (tp30) cc_final: 0.8266 (mm-30) REVERT: H 36 LEU cc_start: 0.8004 (mt) cc_final: 0.7557 (pp) REVERT: H 185 TYR cc_start: 0.7279 (t80) cc_final: 0.6872 (t80) REVERT: H 186 GLU cc_start: 0.6590 (tp30) cc_final: 0.6359 (tp30) REVERT: H 224 GLN cc_start: 0.8880 (mm-40) cc_final: 0.8660 (mm-40) REVERT: I 101 ASP cc_start: 0.7811 (p0) cc_final: 0.6897 (p0) REVERT: I 116 LEU cc_start: 0.8909 (mt) cc_final: 0.8487 (mp) REVERT: I 159 ILE cc_start: 0.9547 (pt) cc_final: 0.9248 (mt) REVERT: J 40 MET cc_start: 0.8431 (ptp) cc_final: 0.8068 (ptp) REVERT: J 57 GLN cc_start: 0.8798 (tm-30) cc_final: 0.8268 (tm-30) REVERT: J 150 LYS cc_start: 0.9111 (tttt) cc_final: 0.8723 (tttm) REVERT: K 70 ARG cc_start: 0.8472 (ttt-90) cc_final: 0.8118 (ttp80) REVERT: L 31 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7349 (pp30) REVERT: L 43 GLU cc_start: 0.5308 (OUTLIER) cc_final: 0.4878 (pp20) REVERT: L 87 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8289 (mt-10) outliers start: 85 outliers final: 61 residues processed: 422 average time/residue: 0.2734 time to fit residues: 170.5727 Evaluate side-chains 397 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 329 time to evaluate : 1.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain F residue 27 ARG Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 94 MET Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain H residue 205 ASN Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 143 ASP Chi-restraints excluded: chain I residue 149 MET Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 167 LEU Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain I residue 202 SER Chi-restraints excluded: chain I residue 215 ILE Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 99 ASP Chi-restraints excluded: chain J residue 119 GLU Chi-restraints excluded: chain J residue 120 MET Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 228 THR Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain L residue 31 GLN Chi-restraints excluded: chain L residue 43 GLU Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 91 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 chunk 59 optimal weight: 0.2980 chunk 38 optimal weight: 6.9990 chunk 125 optimal weight: 5.9990 chunk 133 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 154 optimal weight: 10.0000 chunk 178 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 51 GLN ** G 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 205 ASN ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 126 ASN ** H 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 205 ASN ** I 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 191 ASN J 26 ASN ** J 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.4618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16442 Z= 0.197 Angle : 0.727 11.844 22253 Z= 0.363 Chirality : 0.044 0.331 2692 Planarity : 0.004 0.051 2779 Dihedral : 10.370 93.008 2574 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 4.83 % Allowed : 29.92 % Favored : 65.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.18), residues: 2092 helix: 0.21 (0.18), residues: 870 sheet: -1.61 (0.29), residues: 294 loop : -2.86 (0.17), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 66 HIS 0.002 0.001 HIS J 113 PHE 0.023 0.002 PHE H 213 TYR 0.061 0.002 TYR H 85 ARG 0.015 0.000 ARG H 11 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 347 time to evaluate : 1.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.9034 (t0) cc_final: 0.8596 (t0) REVERT: B 107 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7444 (mm) REVERT: C 18 LEU cc_start: 0.9164 (mp) cc_final: 0.8497 (tp) REVERT: C 60 LEU cc_start: 0.8193 (mm) cc_final: 0.7732 (mm) REVERT: C 67 LYS cc_start: 0.9340 (ptpt) cc_final: 0.8857 (ptpt) REVERT: E 14 LEU cc_start: 0.8804 (tp) cc_final: 0.8465 (tt) REVERT: E 48 ASN cc_start: 0.7938 (t0) cc_final: 0.7090 (m-40) REVERT: E 146 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7215 (pt) REVERT: F 4 ARG cc_start: 0.7501 (mtt180) cc_final: 0.6385 (mmm-85) REVERT: F 27 ARG cc_start: 0.6002 (OUTLIER) cc_final: 0.5583 (ttp80) REVERT: F 47 ASP cc_start: 0.8091 (m-30) cc_final: 0.7677 (t0) REVERT: F 67 LYS cc_start: 0.8289 (ptmt) cc_final: 0.7897 (ptmt) REVERT: F 101 ILE cc_start: 0.9480 (mp) cc_final: 0.9111 (mm) REVERT: F 147 LEU cc_start: 0.3820 (OUTLIER) cc_final: 0.2985 (mp) REVERT: G 51 GLN cc_start: 0.7543 (OUTLIER) cc_final: 0.7340 (mt0) REVERT: G 77 GLN cc_start: 0.8538 (tp40) cc_final: 0.8254 (tt0) REVERT: G 79 TYR cc_start: 0.6962 (t80) cc_final: 0.6728 (t80) REVERT: G 172 TRP cc_start: 0.7437 (t60) cc_final: 0.6619 (m-10) REVERT: H 36 LEU cc_start: 0.7981 (mt) cc_final: 0.7483 (pp) REVERT: I 116 LEU cc_start: 0.8874 (mt) cc_final: 0.8479 (mp) REVERT: I 159 ILE cc_start: 0.9544 (pt) cc_final: 0.9226 (mt) REVERT: J 57 GLN cc_start: 0.8714 (tm-30) cc_final: 0.8281 (tm-30) REVERT: J 150 LYS cc_start: 0.9106 (tttt) cc_final: 0.8775 (tttm) REVERT: K 70 ARG cc_start: 0.8463 (ttt-90) cc_final: 0.8096 (ttp80) REVERT: L 43 GLU cc_start: 0.5378 (OUTLIER) cc_final: 0.4896 (pp20) REVERT: L 87 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8287 (mt-10) outliers start: 82 outliers final: 62 residues processed: 403 average time/residue: 0.2754 time to fit residues: 164.0958 Evaluate side-chains 394 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 325 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain F residue 27 ARG Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 51 GLN Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain G residue 201 GLU Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain H residue 94 MET Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 143 ASP Chi-restraints excluded: chain I residue 149 MET Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 167 LEU Chi-restraints excluded: chain I residue 191 ASN Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain I residue 202 SER Chi-restraints excluded: chain I residue 215 ILE Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 99 ASP Chi-restraints excluded: chain J residue 119 GLU Chi-restraints excluded: chain J residue 120 MET Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 228 THR Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain J residue 235 THR Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain L residue 43 GLU Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 91 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 3.9990 chunk 171 optimal weight: 5.9990 chunk 183 optimal weight: 0.6980 chunk 110 optimal weight: 0.9980 chunk 79 optimal weight: 8.9990 chunk 143 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 chunk 165 optimal weight: 10.0000 chunk 173 optimal weight: 8.9990 chunk 182 optimal weight: 1.9990 chunk 120 optimal weight: 0.0030 overall best weight: 1.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 205 ASN ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 126 ASN ** H 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 191 ASN J 26 ASN ** J 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 GLN ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.4731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16442 Z= 0.214 Angle : 0.740 11.598 22253 Z= 0.370 Chirality : 0.044 0.234 2692 Planarity : 0.004 0.046 2779 Dihedral : 10.194 93.005 2572 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 18.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 4.71 % Allowed : 30.80 % Favored : 64.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.18), residues: 2092 helix: 0.31 (0.18), residues: 857 sheet: -1.67 (0.28), residues: 314 loop : -2.76 (0.18), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 190 HIS 0.004 0.001 HIS J 113 PHE 0.023 0.002 PHE G 213 TYR 0.047 0.002 TYR H 85 ARG 0.010 0.001 ARG H 11 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 333 time to evaluate : 1.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.9015 (t0) cc_final: 0.8566 (t0) REVERT: C 18 LEU cc_start: 0.9152 (mp) cc_final: 0.8453 (tp) REVERT: C 60 LEU cc_start: 0.8266 (mm) cc_final: 0.7823 (mm) REVERT: C 67 LYS cc_start: 0.9341 (ptpt) cc_final: 0.8961 (ptpt) REVERT: D 67 LYS cc_start: 0.8721 (ptpt) cc_final: 0.8384 (pttp) REVERT: E 7 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7327 (mt-10) REVERT: E 14 LEU cc_start: 0.8860 (tp) cc_final: 0.8489 (tt) REVERT: E 48 ASN cc_start: 0.7924 (t0) cc_final: 0.7149 (m-40) REVERT: E 101 ILE cc_start: 0.9090 (mp) cc_final: 0.8839 (mt) REVERT: E 146 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7213 (pt) REVERT: F 4 ARG cc_start: 0.7636 (mtt180) cc_final: 0.6374 (mmm-85) REVERT: F 27 ARG cc_start: 0.6017 (OUTLIER) cc_final: 0.5628 (ttp80) REVERT: F 47 ASP cc_start: 0.8089 (m-30) cc_final: 0.7666 (t0) REVERT: F 67 LYS cc_start: 0.8237 (ptmt) cc_final: 0.8012 (ptmt) REVERT: F 101 ILE cc_start: 0.9477 (mp) cc_final: 0.9128 (mm) REVERT: F 147 LEU cc_start: 0.3625 (OUTLIER) cc_final: 0.2761 (mp) REVERT: G 77 GLN cc_start: 0.8576 (tp40) cc_final: 0.8283 (tt0) REVERT: G 172 TRP cc_start: 0.7509 (t60) cc_final: 0.6654 (m-10) REVERT: H 36 LEU cc_start: 0.7953 (mt) cc_final: 0.7536 (pp) REVERT: I 116 LEU cc_start: 0.8820 (mt) cc_final: 0.8474 (mp) REVERT: I 159 ILE cc_start: 0.9549 (pt) cc_final: 0.9220 (mt) REVERT: J 40 MET cc_start: 0.8484 (ptp) cc_final: 0.7992 (ptp) REVERT: J 51 LEU cc_start: 0.9424 (tp) cc_final: 0.9168 (tp) REVERT: J 57 GLN cc_start: 0.8694 (tm-30) cc_final: 0.8278 (tm-30) REVERT: J 150 LYS cc_start: 0.9127 (tttt) cc_final: 0.8798 (tttm) REVERT: K 70 ARG cc_start: 0.8457 (ttt-90) cc_final: 0.8086 (ttp80) REVERT: L 31 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7628 (pp30) REVERT: L 43 GLU cc_start: 0.5413 (OUTLIER) cc_final: 0.4931 (pp20) REVERT: L 87 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8239 (mt-10) outliers start: 80 outliers final: 64 residues processed: 391 average time/residue: 0.2782 time to fit residues: 161.3418 Evaluate side-chains 393 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 323 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain F residue 27 ARG Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 94 MET Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 57 GLN Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 143 ASP Chi-restraints excluded: chain I residue 149 MET Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 167 LEU Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain I residue 202 SER Chi-restraints excluded: chain I residue 215 ILE Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 99 ASP Chi-restraints excluded: chain J residue 120 MET Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 228 THR Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain J residue 235 THR Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain L residue 31 GLN Chi-restraints excluded: chain L residue 43 GLU Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 94 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 9.9990 chunk 118 optimal weight: 0.0970 chunk 91 optimal weight: 0.7980 chunk 134 optimal weight: 7.9990 chunk 203 optimal weight: 0.9980 chunk 187 optimal weight: 6.9990 chunk 161 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 205 ASN ** H 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 26 ASN ** J 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 GLN ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.4845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 16442 Z= 0.216 Angle : 0.745 11.566 22253 Z= 0.372 Chirality : 0.044 0.241 2692 Planarity : 0.004 0.044 2779 Dihedral : 10.115 92.988 2572 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 4.53 % Allowed : 31.10 % Favored : 64.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.18), residues: 2092 helix: 0.33 (0.18), residues: 857 sheet: -1.72 (0.29), residues: 300 loop : -2.72 (0.17), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 190 HIS 0.003 0.001 HIS J 113 PHE 0.024 0.002 PHE G 255 TYR 0.041 0.002 TYR H 85 ARG 0.009 0.000 ARG L 29 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 336 time to evaluate : 2.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.9036 (t0) cc_final: 0.8585 (t0) REVERT: C 18 LEU cc_start: 0.9106 (mp) cc_final: 0.8429 (tp) REVERT: C 60 LEU cc_start: 0.8271 (mm) cc_final: 0.7881 (mm) REVERT: C 67 LYS cc_start: 0.9358 (ptpt) cc_final: 0.9046 (ptpt) REVERT: E 7 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7352 (mt-10) REVERT: E 14 LEU cc_start: 0.8845 (tp) cc_final: 0.8588 (tt) REVERT: E 48 ASN cc_start: 0.7816 (t0) cc_final: 0.6925 (m-40) REVERT: E 146 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7204 (pt) REVERT: F 4 ARG cc_start: 0.7476 (mtt180) cc_final: 0.6241 (mmm-85) REVERT: F 47 ASP cc_start: 0.8080 (m-30) cc_final: 0.7669 (t0) REVERT: F 67 LYS cc_start: 0.8225 (ptmt) cc_final: 0.7851 (ptmt) REVERT: F 101 ILE cc_start: 0.9484 (mp) cc_final: 0.9125 (mm) REVERT: G 77 GLN cc_start: 0.8592 (tp40) cc_final: 0.8326 (tt0) REVERT: G 172 TRP cc_start: 0.7531 (t60) cc_final: 0.6656 (m-10) REVERT: H 36 LEU cc_start: 0.7976 (mt) cc_final: 0.7554 (pp) REVERT: H 185 TYR cc_start: 0.7368 (t80) cc_final: 0.7087 (t80) REVERT: I 116 LEU cc_start: 0.8801 (mt) cc_final: 0.8436 (mp) REVERT: I 139 GLU cc_start: 0.7630 (tp30) cc_final: 0.7413 (tp30) REVERT: I 159 ILE cc_start: 0.9542 (pt) cc_final: 0.9223 (mt) REVERT: J 40 MET cc_start: 0.8502 (ptp) cc_final: 0.8012 (ptp) REVERT: J 57 GLN cc_start: 0.8606 (tm-30) cc_final: 0.8139 (tm-30) REVERT: J 150 LYS cc_start: 0.9128 (tttt) cc_final: 0.8780 (tttm) REVERT: K 70 ARG cc_start: 0.8420 (ttt-90) cc_final: 0.8047 (ttp80) REVERT: L 31 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7702 (pp30) REVERT: L 43 GLU cc_start: 0.5529 (OUTLIER) cc_final: 0.5034 (pp20) REVERT: L 87 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8258 (mt-10) outliers start: 77 outliers final: 66 residues processed: 387 average time/residue: 0.2809 time to fit residues: 162.1427 Evaluate side-chains 396 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 326 time to evaluate : 1.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 137 GLU Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 94 MET Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 57 GLN Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 143 ASP Chi-restraints excluded: chain I residue 149 MET Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 167 LEU Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain I residue 202 SER Chi-restraints excluded: chain I residue 215 ILE Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 120 MET Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 228 THR Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain J residue 235 THR Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain L residue 30 GLU Chi-restraints excluded: chain L residue 31 GLN Chi-restraints excluded: chain L residue 43 GLU Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 94 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 149 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 44 optimal weight: 9.9990 chunk 162 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 166 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 142 optimal weight: 0.0030 overall best weight: 1.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 205 ASN ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 40 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 = 0.3746 r_free = 0.3746 target = 0.113072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.085473 restraints weight = 40447.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.085657 restraints weight = 29991.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.085523 restraints weight = 24838.863| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.4918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16442 Z= 0.225 Angle : 0.752 12.124 22253 Z= 0.374 Chirality : 0.044 0.219 2692 Planarity : 0.004 0.044 2779 Dihedral : 10.112 92.855 2572 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 18.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 4.30 % Allowed : 31.45 % Favored : 64.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.18), residues: 2092 helix: 0.46 (0.18), residues: 845 sheet: -1.79 (0.30), residues: 293 loop : -2.69 (0.17), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 190 HIS 0.003 0.001 HIS J 113 PHE 0.025 0.002 PHE G 213 TYR 0.037 0.002 TYR H 85 ARG 0.008 0.001 ARG H 11 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3774.94 seconds wall clock time: 69 minutes 22.02 seconds (4162.02 seconds total)