Starting phenix.real_space_refine on Thu Feb 15 16:42:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s3r_10095/02_2024/6s3r_10095.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s3r_10095/02_2024/6s3r_10095.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s3r_10095/02_2024/6s3r_10095.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s3r_10095/02_2024/6s3r_10095.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s3r_10095/02_2024/6s3r_10095.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s3r_10095/02_2024/6s3r_10095.pdb" } resolution = 3.5 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 117 5.16 5 C 8592 2.51 5 N 1970 2.21 5 O 2176 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 115": "OD1" <-> "OD2" Residue "A TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 129": "OD1" <-> "OD2" Residue "A ASP 140": "OD1" <-> "OD2" Residue "A GLU 152": "OE1" <-> "OE2" Residue "A PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 234": "OD1" <-> "OD2" Residue "B PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 110": "OD1" <-> "OD2" Residue "B TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 140": "OD1" <-> "OD2" Residue "B GLU 152": "OE1" <-> "OE2" Residue "B PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 182": "OE1" <-> "OE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 115": "OD1" <-> "OD2" Residue "C TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 129": "OD1" <-> "OD2" Residue "C ASP 140": "OD1" <-> "OD2" Residue "C PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 234": "OD1" <-> "OD2" Residue "D PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 115": "OD1" <-> "OD2" Residue "D TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 129": "OD1" <-> "OD2" Residue "D ASP 140": "OD1" <-> "OD2" Residue "D GLU 152": "OE1" <-> "OE2" Residue "D PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 162": "OD1" <-> "OD2" Residue "D ASP 167": "OD1" <-> "OD2" Residue "D PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 201": "OD1" <-> "OD2" Residue "D PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 115": "OD1" <-> "OD2" Residue "E TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 140": "OD1" <-> "OD2" Residue "E PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 174": "OE1" <-> "OE2" Residue "F ASP 238": "OD1" <-> "OD2" Residue "F TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 4": "OE1" <-> "OE2" Residue "G PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 54": "NH1" <-> "NH2" Residue "G PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 4": "OE1" <-> "OE2" Residue "H PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 54": "NH1" <-> "NH2" Residue "H PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 4": "OE1" <-> "OE2" Residue "I PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 54": "NH1" <-> "NH2" Residue "I PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 4": "OE1" <-> "OE2" Residue "J PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 54": "NH1" <-> "NH2" Residue "J PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 11": "NH1" <-> "NH2" Residue "K GLU 12": "OE1" <-> "OE2" Residue "K ARG 54": "NH1" <-> "NH2" Residue "K PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12855 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1510 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 12, 'TRANS': 183} Chain: "B" Number of atoms: 1522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1522 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 12, 'TRANS': 185} Chain: "C" Number of atoms: 1522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1522 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 12, 'TRANS': 185} Chain: "D" Number of atoms: 1522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1522 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 12, 'TRANS': 185} Chain: "E" Number of atoms: 1522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1522 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 12, 'TRANS': 185} Chain: "F" Number of atoms: 1907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1907 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 13, 'TRANS': 238} Chain: "G" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 695 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "H" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 695 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "I" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 695 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "J" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 695 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "K" Number of atoms: 570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 570 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 5, 'TRANS': 67} Chain breaks: 1 Time building chain proxies: 6.78, per 1000 atoms: 0.53 Number of scatterers: 12855 At special positions: 0 Unit cell: (107.682, 98.64, 120.834, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 117 16.00 O 2176 8.00 N 1970 7.00 C 8592 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=0, symmetry=0 Time building additional restraints: 5.43 Conformation dependent library (CDL) restraints added in 2.1 seconds 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3174 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 0 sheets defined 81.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 56 through 66 removed outlier: 3.556A pdb=" N PHE A 61 " --> pdb=" O PHE A 57 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL A 62 " --> pdb=" O ILE A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 82 Processing helix chain 'A' and resid 91 through 116 removed outlier: 3.610A pdb=" N GLY A 95 " --> pdb=" O GLN A 91 " (cutoff:3.500A) Proline residue: A 107 - end of helix Processing helix chain 'A' and resid 118 through 122 removed outlier: 4.156A pdb=" N LEU A 121 " --> pdb=" O GLN A 118 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA A 122 " --> pdb=" O PRO A 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 118 through 122' Processing helix chain 'A' and resid 129 through 144 Proline residue: A 137 - end of helix Processing helix chain 'A' and resid 147 through 159 removed outlier: 3.556A pdb=" N LEU A 151 " --> pdb=" O ARG A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 211 Proline residue: A 196 - end of helix Processing helix chain 'A' and resid 217 through 233 removed outlier: 3.943A pdb=" N ILE A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Proline residue: A 224 - end of helix Processing helix chain 'A' and resid 235 through 248 removed outlier: 4.354A pdb=" N GLY A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 62 Processing helix chain 'B' and resid 67 through 82 Processing helix chain 'B' and resid 90 through 105 Processing helix chain 'B' and resid 105 through 116 Processing helix chain 'B' and resid 129 through 144 Proline residue: B 137 - end of helix Processing helix chain 'B' and resid 147 through 159 Processing helix chain 'B' and resid 173 through 211 removed outlier: 3.881A pdb=" N ALA B 177 " --> pdb=" O ILE B 173 " (cutoff:3.500A) Proline residue: B 196 - end of helix Processing helix chain 'B' and resid 217 through 233 removed outlier: 3.777A pdb=" N ILE B 221 " --> pdb=" O SER B 217 " (cutoff:3.500A) Proline residue: B 224 - end of helix Processing helix chain 'B' and resid 235 through 248 removed outlier: 4.006A pdb=" N GLY B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 65 Proline residue: C 59 - end of helix Processing helix chain 'C' and resid 67 through 82 removed outlier: 3.520A pdb=" N ILE C 73 " --> pdb=" O THR C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 116 Proline residue: C 107 - end of helix Processing helix chain 'C' and resid 118 through 122 removed outlier: 4.250A pdb=" N LEU C 121 " --> pdb=" O GLN C 118 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA C 122 " --> pdb=" O PRO C 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 118 through 122' Processing helix chain 'C' and resid 129 through 146 Proline residue: C 137 - end of helix removed outlier: 3.725A pdb=" N GLN C 145 " --> pdb=" O PHE C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 159 Processing helix chain 'C' and resid 170 through 211 removed outlier: 3.704A pdb=" N LEU C 174 " --> pdb=" O PRO C 170 " (cutoff:3.500A) Proline residue: C 176 - end of helix Proline residue: C 196 - end of helix Processing helix chain 'C' and resid 217 through 233 removed outlier: 3.730A pdb=" N ILE C 221 " --> pdb=" O SER C 217 " (cutoff:3.500A) Proline residue: C 224 - end of helix Processing helix chain 'C' and resid 235 through 248 removed outlier: 4.133A pdb=" N GLY C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 65 Proline residue: D 59 - end of helix removed outlier: 3.824A pdb=" N MET D 65 " --> pdb=" O PHE D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 82 removed outlier: 3.727A pdb=" N ILE D 73 " --> pdb=" O THR D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 105 removed outlier: 3.718A pdb=" N GLY D 95 " --> pdb=" O GLN D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 116 Processing helix chain 'D' and resid 118 through 122 removed outlier: 4.143A pdb=" N LEU D 121 " --> pdb=" O GLN D 118 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA D 122 " --> pdb=" O PRO D 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 118 through 122' Processing helix chain 'D' and resid 129 through 146 Proline residue: D 137 - end of helix removed outlier: 3.710A pdb=" N GLN D 145 " --> pdb=" O PHE D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 159 Processing helix chain 'D' and resid 170 through 211 removed outlier: 3.749A pdb=" N LEU D 174 " --> pdb=" O PRO D 170 " (cutoff:3.500A) Proline residue: D 176 - end of helix Proline residue: D 196 - end of helix Processing helix chain 'D' and resid 217 through 233 removed outlier: 3.742A pdb=" N ILE D 221 " --> pdb=" O SER D 217 " (cutoff:3.500A) Proline residue: D 224 - end of helix Processing helix chain 'D' and resid 235 through 248 removed outlier: 4.007A pdb=" N GLY D 248 " --> pdb=" O ALA D 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 62 removed outlier: 3.576A pdb=" N ILE E 58 " --> pdb=" O ALA E 54 " (cutoff:3.500A) Proline residue: E 59 - end of helix Processing helix chain 'E' and resid 67 through 82 Processing helix chain 'E' and resid 91 through 116 removed outlier: 3.592A pdb=" N GLY E 95 " --> pdb=" O GLN E 91 " (cutoff:3.500A) Proline residue: E 107 - end of helix Processing helix chain 'E' and resid 118 through 122 removed outlier: 4.059A pdb=" N LEU E 121 " --> pdb=" O GLN E 118 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA E 122 " --> pdb=" O PRO E 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 118 through 122' Processing helix chain 'E' and resid 129 through 146 Proline residue: E 137 - end of helix removed outlier: 3.812A pdb=" N GLN E 145 " --> pdb=" O PHE E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 159 Processing helix chain 'E' and resid 173 through 211 removed outlier: 3.843A pdb=" N ALA E 177 " --> pdb=" O ILE E 173 " (cutoff:3.500A) Proline residue: E 196 - end of helix Processing helix chain 'E' and resid 217 through 233 removed outlier: 3.661A pdb=" N ILE E 221 " --> pdb=" O SER E 217 " (cutoff:3.500A) Proline residue: E 224 - end of helix removed outlier: 3.592A pdb=" N VAL E 233 " --> pdb=" O LEU E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 248 removed outlier: 3.858A pdb=" N GLY E 248 " --> pdb=" O ALA E 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 32 removed outlier: 3.805A pdb=" N PHE F 24 " --> pdb=" O MET F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 58 Processing helix chain 'F' and resid 73 through 111 removed outlier: 4.115A pdb=" N PHE F 95 " --> pdb=" O SER F 91 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N PHE F 96 " --> pdb=" O LEU F 92 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N PHE F 99 " --> pdb=" O PHE F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 129 through 144 Processing helix chain 'F' and resid 145 through 161 removed outlier: 4.321A pdb=" N LEU F 151 " --> pdb=" O HIS F 147 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR F 159 " --> pdb=" O VAL F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 177 Processing helix chain 'F' and resid 177 through 211 removed outlier: 4.289A pdb=" N TRP F 181 " --> pdb=" O ASN F 177 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA F 182 " --> pdb=" O GLY F 178 " (cutoff:3.500A) Proline residue: F 192 - end of helix removed outlier: 3.844A pdb=" N ALA F 196 " --> pdb=" O PRO F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 219 through 260 removed outlier: 3.553A pdb=" N VAL F 230 " --> pdb=" O VAL F 226 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY F 237 " --> pdb=" O TRP F 233 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASP F 238 " --> pdb=" O MET F 234 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N LEU F 240 " --> pdb=" O MET F 236 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N ASN F 241 " --> pdb=" O GLY F 237 " (cutoff:3.500A) Proline residue: F 245 - end of helix removed outlier: 3.515A pdb=" N SER F 248 " --> pdb=" O GLN F 244 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 42 Proline residue: G 27 - end of helix removed outlier: 3.654A pdb=" N THR G 42 " --> pdb=" O PHE G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 66 Processing helix chain 'G' and resid 66 through 88 Proline residue: G 85 - end of helix Processing helix chain 'H' and resid 2 through 42 Proline residue: H 27 - end of helix removed outlier: 3.655A pdb=" N THR H 42 " --> pdb=" O PHE H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 66 Processing helix chain 'H' and resid 66 through 88 Proline residue: H 85 - end of helix Processing helix chain 'I' and resid 2 through 42 Proline residue: I 27 - end of helix removed outlier: 3.654A pdb=" N THR I 42 " --> pdb=" O PHE I 38 " (cutoff:3.500A) Processing helix chain 'I' and resid 51 through 66 Processing helix chain 'I' and resid 66 through 88 Proline residue: I 85 - end of helix Processing helix chain 'J' and resid 2 through 42 Proline residue: J 27 - end of helix removed outlier: 3.656A pdb=" N THR J 42 " --> pdb=" O PHE J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 51 through 66 Processing helix chain 'J' and resid 66 through 88 Proline residue: J 85 - end of helix Processing helix chain 'K' and resid 3 through 35 Proline residue: K 27 - end of helix Processing helix chain 'K' and resid 53 through 66 Processing helix chain 'K' and resid 66 through 89 removed outlier: 3.601A pdb=" N LEU K 70 " --> pdb=" O GLY K 66 " (cutoff:3.500A) Proline residue: K 85 - end of helix removed outlier: 3.907A pdb=" N GLY K 89 " --> pdb=" O PRO K 85 " (cutoff:3.500A) 931 hydrogen bonds defined for protein. 2793 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.41 Time building geometry restraints manager: 5.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3839 1.34 - 1.46: 2590 1.46 - 1.58: 6459 1.58 - 1.70: 0 1.70 - 1.81: 229 Bond restraints: 13117 Sorted by residual: bond pdb=" CA ASN F 177 " pdb=" C ASN F 177 " ideal model delta sigma weight residual 1.523 1.488 0.034 1.41e-02 5.03e+03 5.98e+00 bond pdb=" CA ILE G 84 " pdb=" CB ILE G 84 " ideal model delta sigma weight residual 1.537 1.525 0.012 5.00e-03 4.00e+04 5.80e+00 bond pdb=" CA ILE I 84 " pdb=" CB ILE I 84 " ideal model delta sigma weight residual 1.537 1.525 0.012 5.00e-03 4.00e+04 5.49e+00 bond pdb=" CA ILE J 84 " pdb=" CB ILE J 84 " ideal model delta sigma weight residual 1.537 1.525 0.011 5.00e-03 4.00e+04 5.20e+00 bond pdb=" CA ILE H 84 " pdb=" CB ILE H 84 " ideal model delta sigma weight residual 1.537 1.526 0.011 5.00e-03 4.00e+04 5.10e+00 ... (remaining 13112 not shown) Histogram of bond angle deviations from ideal: 98.20 - 105.38: 434 105.38 - 112.55: 7192 112.55 - 119.72: 4159 119.72 - 126.90: 5931 126.90 - 134.07: 155 Bond angle restraints: 17871 Sorted by residual: angle pdb=" C ILE K 84 " pdb=" CA ILE K 84 " pdb=" CB ILE K 84 " ideal model delta sigma weight residual 113.70 109.64 4.06 9.50e-01 1.11e+00 1.82e+01 angle pdb=" C PRO A 88 " pdb=" N SER A 89 " pdb=" CA SER A 89 " ideal model delta sigma weight residual 121.54 128.93 -7.39 1.91e+00 2.74e-01 1.50e+01 angle pdb=" N ASP E 234 " pdb=" CA ASP E 234 " pdb=" CB ASP E 234 " ideal model delta sigma weight residual 114.17 109.77 4.40 1.14e+00 7.69e-01 1.49e+01 angle pdb=" C VAL F 118 " pdb=" N ASP F 119 " pdb=" CA ASP F 119 " ideal model delta sigma weight residual 121.80 130.63 -8.83 2.44e+00 1.68e-01 1.31e+01 angle pdb=" C PRO F 34 " pdb=" N VAL F 35 " pdb=" CA VAL F 35 " ideal model delta sigma weight residual 123.08 119.69 3.39 1.01e+00 9.80e-01 1.12e+01 ... (remaining 17866 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 6959 17.23 - 34.45: 753 34.45 - 51.68: 147 51.68 - 68.91: 23 68.91 - 86.14: 18 Dihedral angle restraints: 7900 sinusoidal: 3052 harmonic: 4848 Sorted by residual: dihedral pdb=" CA THR B 87 " pdb=" C THR B 87 " pdb=" N PRO B 88 " pdb=" CA PRO B 88 " ideal model delta harmonic sigma weight residual 180.00 119.23 60.77 0 5.00e+00 4.00e-02 1.48e+02 dihedral pdb=" CA THR A 87 " pdb=" C THR A 87 " pdb=" N PRO A 88 " pdb=" CA PRO A 88 " ideal model delta harmonic sigma weight residual 180.00 119.46 60.54 0 5.00e+00 4.00e-02 1.47e+02 dihedral pdb=" CA THR C 87 " pdb=" C THR C 87 " pdb=" N PRO C 88 " pdb=" CA PRO C 88 " ideal model delta harmonic sigma weight residual 180.00 120.51 59.49 0 5.00e+00 4.00e-02 1.42e+02 ... (remaining 7897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1656 0.046 - 0.093: 487 0.093 - 0.139: 134 0.139 - 0.185: 7 0.185 - 0.232: 4 Chirality restraints: 2288 Sorted by residual: chirality pdb=" CA GLU J 75 " pdb=" N GLU J 75 " pdb=" C GLU J 75 " pdb=" CB GLU J 75 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA GLU G 75 " pdb=" N GLU G 75 " pdb=" C GLU G 75 " pdb=" CB GLU G 75 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA GLU I 75 " pdb=" N GLU I 75 " pdb=" C GLU I 75 " pdb=" CB GLU I 75 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 2285 not shown) Planarity restraints: 2149 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP F 119 " -0.065 5.00e-02 4.00e+02 9.95e-02 1.58e+01 pdb=" N PRO F 120 " 0.172 5.00e-02 4.00e+02 pdb=" CA PRO F 120 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO F 120 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 87 " 0.064 5.00e-02 4.00e+02 9.72e-02 1.51e+01 pdb=" N PRO A 88 " -0.168 5.00e-02 4.00e+02 pdb=" CA PRO A 88 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 88 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 87 " -0.061 5.00e-02 4.00e+02 9.34e-02 1.39e+01 pdb=" N PRO D 88 " 0.162 5.00e-02 4.00e+02 pdb=" CA PRO D 88 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO D 88 " -0.051 5.00e-02 4.00e+02 ... (remaining 2146 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 99 2.61 - 3.18: 12476 3.18 - 3.75: 20709 3.75 - 4.33: 27378 4.33 - 4.90: 45488 Nonbonded interactions: 106150 Sorted by model distance: nonbonded pdb=" O LEU J 78 " pdb=" OG1 THR J 82 " model vdw 2.035 2.440 nonbonded pdb=" O LEU G 78 " pdb=" OG1 THR G 82 " model vdw 2.035 2.440 nonbonded pdb=" O LEU I 78 " pdb=" OG1 THR I 82 " model vdw 2.035 2.440 nonbonded pdb=" O LEU H 78 " pdb=" OG1 THR H 82 " model vdw 2.035 2.440 nonbonded pdb=" O VAL C 62 " pdb=" OG1 THR C 66 " model vdw 2.163 2.440 ... (remaining 106145 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' selection = (chain 'B' and resid 55 through 250) selection = (chain 'C' and resid 55 through 250) selection = (chain 'D' and resid 55 through 250) selection = (chain 'E' and resid 55 through 250) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 1.480 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: 5.710 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 35.140 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 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 : 0.006 0.049 13117 Z= 0.376 Angle : 0.886 8.831 17871 Z= 0.467 Chirality : 0.046 0.232 2288 Planarity : 0.007 0.100 2149 Dihedral : 15.344 86.137 4726 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 18.37 Ramachandran Plot: Outliers : 0.79 % Allowed : 8.39 % Favored : 90.82 % Rotamer: Outliers : 2.22 % Allowed : 5.42 % Favored : 92.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.12 % Twisted General : 0.19 % 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: -3.03 (0.18), residues: 1645 helix: -1.31 (0.13), residues: 1302 sheet: None (None), residues: 0 loop : -4.26 (0.29), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP J 68 HIS 0.005 0.002 HIS F 97 PHE 0.029 0.002 PHE F 132 TYR 0.012 0.002 TYR J 76 ARG 0.010 0.001 ARG A 70 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 376 time to evaluate : 1.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LYS cc_start: 0.8357 (ttmt) cc_final: 0.7914 (tttt) REVERT: A 211 MET cc_start: 0.7489 (mmm) cc_final: 0.7261 (mmm) REVERT: A 220 ILE cc_start: 0.8731 (tt) cc_final: 0.8497 (tt) REVERT: B 170 PRO cc_start: 0.5769 (Cg_endo) cc_final: 0.5496 (Cg_exo) REVERT: C 182 GLU cc_start: 0.7463 (tp30) cc_final: 0.7180 (tp30) REVERT: D 96 MET cc_start: 0.7659 (tpt) cc_final: 0.7163 (ttm) REVERT: D 98 LEU cc_start: 0.8623 (tp) cc_final: 0.8277 (tt) REVERT: D 182 GLU cc_start: 0.7414 (tp30) cc_final: 0.7190 (tp30) REVERT: E 209 MET cc_start: 0.3688 (ppp) cc_final: 0.2756 (ppp) REVERT: F 117 MET cc_start: 0.5891 (pmm) cc_final: 0.5481 (pmm) REVERT: F 219 ILE cc_start: 0.8821 (mm) cc_final: 0.8611 (mm) REVERT: H 29 LEU cc_start: 0.8355 (tt) cc_final: 0.8151 (tt) REVERT: H 34 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7361 (tp) REVERT: J 23 ILE cc_start: 0.8869 (OUTLIER) cc_final: 0.8570 (mm) REVERT: K 58 MET cc_start: 0.8273 (tpp) cc_final: 0.8056 (tpp) REVERT: K 71 LYS cc_start: 0.6237 (tttp) cc_final: 0.5460 (mptt) outliers start: 32 outliers final: 5 residues processed: 393 average time/residue: 0.2321 time to fit residues: 134.0495 Evaluate side-chains 302 residues out of total 1439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 295 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain I residue 23 ILE Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 37 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 0.5980 chunk 120 optimal weight: 0.0980 chunk 66 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 64 optimal weight: 9.9990 chunk 124 optimal weight: 8.9990 chunk 48 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 ASN E 118 GLN F 11 GLN F 97 HIS F 109 GLN ** F 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN J 39 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 13117 Z= 0.241 Angle : 0.792 13.392 17871 Z= 0.392 Chirality : 0.045 0.301 2288 Planarity : 0.006 0.085 2149 Dihedral : 6.824 58.191 1739 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.09 % Favored : 91.67 % Rotamer: Outliers : 2.64 % Allowed : 14.18 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.12 % Twisted General : 0.06 % 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: -0.95 (0.21), residues: 1645 helix: 0.20 (0.14), residues: 1332 sheet: None (None), residues: 0 loop : -4.07 (0.30), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP G 68 HIS 0.003 0.001 HIS F 97 PHE 0.025 0.002 PHE D 109 TYR 0.020 0.002 TYR B 120 ARG 0.004 0.001 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 312 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 LYS cc_start: 0.8278 (ttmt) cc_final: 0.7882 (tttm) REVERT: A 220 ILE cc_start: 0.8647 (tt) cc_final: 0.8447 (tt) REVERT: C 139 LYS cc_start: 0.8682 (ttmm) cc_final: 0.8446 (mtpt) REVERT: C 192 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.7100 (mpp) REVERT: D 173 ILE cc_start: 0.7556 (tt) cc_final: 0.6926 (mt) REVERT: D 211 MET cc_start: 0.7113 (mmm) cc_final: 0.6453 (mtm) REVERT: E 142 MET cc_start: 0.8444 (mtp) cc_final: 0.8205 (mtm) REVERT: E 209 MET cc_start: 0.4179 (ppp) cc_final: 0.1441 (tpp) REVERT: G 68 TRP cc_start: 0.6788 (p-90) cc_final: 0.5493 (m-90) REVERT: I 23 ILE cc_start: 0.8876 (mm) cc_final: 0.8626 (mt) REVERT: K 58 MET cc_start: 0.8152 (tpp) cc_final: 0.7879 (tpp) REVERT: K 71 LYS cc_start: 0.6196 (tttp) cc_final: 0.5406 (mptt) outliers start: 38 outliers final: 16 residues processed: 333 average time/residue: 0.2124 time to fit residues: 106.6490 Evaluate side-chains 299 residues out of total 1439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 282 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 87 LEU Chi-restraints excluded: chain J residue 70 LEU Chi-restraints excluded: chain K residue 72 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 120 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 144 optimal weight: 0.4980 chunk 156 optimal weight: 5.9990 chunk 128 optimal weight: 0.8980 chunk 143 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 chunk 116 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 45 ASN I 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13117 Z= 0.244 Angle : 0.756 12.945 17871 Z= 0.370 Chirality : 0.043 0.248 2288 Planarity : 0.006 0.086 2149 Dihedral : 6.381 57.470 1725 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.78 % Favored : 92.10 % Rotamer: Outliers : 2.99 % Allowed : 17.65 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.12 % Twisted General : 0.06 % 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: -0.13 (0.21), residues: 1645 helix: 0.92 (0.15), residues: 1287 sheet: None (None), residues: 0 loop : -3.91 (0.28), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 68 HIS 0.005 0.002 HIS F 147 PHE 0.033 0.002 PHE B 247 TYR 0.021 0.002 TYR A 120 ARG 0.007 0.000 ARG C 111 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 297 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LYS cc_start: 0.8251 (ttmt) cc_final: 0.7954 (tttm) REVERT: A 220 ILE cc_start: 0.8603 (tt) cc_final: 0.8369 (tt) REVERT: B 70 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.7895 (ptp-170) REVERT: B 175 VAL cc_start: 0.9307 (t) cc_final: 0.9034 (t) REVERT: C 192 MET cc_start: 0.7753 (OUTLIER) cc_final: 0.7104 (mpp) REVERT: D 100 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.7945 (tt) REVERT: D 109 PHE cc_start: 0.7710 (m-80) cc_final: 0.7310 (m-80) REVERT: E 105 MET cc_start: 0.7327 (mmm) cc_final: 0.6373 (mmm) REVERT: E 142 MET cc_start: 0.8405 (mtp) cc_final: 0.8149 (mtm) REVERT: E 182 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.6506 (mp0) REVERT: E 209 MET cc_start: 0.4351 (ppp) cc_final: 0.2200 (tpp) REVERT: F 43 ARG cc_start: 0.7622 (mtm-85) cc_final: 0.7357 (ttp80) REVERT: F 78 ILE cc_start: 0.8865 (mt) cc_final: 0.8655 (mt) REVERT: F 187 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8148 (mm) REVERT: H 37 MET cc_start: 0.6240 (ttt) cc_final: 0.5248 (mtt) REVERT: I 23 ILE cc_start: 0.8857 (mm) cc_final: 0.8508 (mt) REVERT: K 58 MET cc_start: 0.8102 (tpp) cc_final: 0.7848 (tpp) REVERT: K 71 LYS cc_start: 0.6120 (tttp) cc_final: 0.5402 (mptt) outliers start: 43 outliers final: 23 residues processed: 324 average time/residue: 0.2077 time to fit residues: 102.1876 Evaluate side-chains 312 residues out of total 1439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 284 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 182 GLU Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 72 ILE Chi-restraints excluded: chain I residue 87 LEU Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 72 ILE Chi-restraints excluded: chain K residue 79 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 0.6980 chunk 108 optimal weight: 0.6980 chunk 75 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 97 optimal weight: 0.4980 chunk 145 optimal weight: 0.9980 chunk 153 optimal weight: 0.9980 chunk 137 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 109 GLN G 45 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13117 Z= 0.207 Angle : 0.721 12.867 17871 Z= 0.352 Chirality : 0.042 0.220 2288 Planarity : 0.006 0.084 2149 Dihedral : 6.133 58.299 1723 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.54 % Favored : 92.34 % Rotamer: Outliers : 3.89 % Allowed : 19.39 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.12 % Twisted General : 0.06 % 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: 0.15 (0.22), residues: 1645 helix: 1.10 (0.15), residues: 1307 sheet: None (None), residues: 0 loop : -4.00 (0.28), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 68 HIS 0.002 0.001 HIS F 147 PHE 0.022 0.002 PHE D 247 TYR 0.007 0.001 TYR C 120 ARG 0.005 0.000 ARG C 111 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 297 time to evaluate : 1.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.7911 (mtt) cc_final: 0.7707 (mtt) REVERT: A 139 LYS cc_start: 0.8357 (ttmt) cc_final: 0.7931 (tttt) REVERT: A 220 ILE cc_start: 0.8563 (tt) cc_final: 0.8356 (tt) REVERT: B 70 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.7864 (ptp-170) REVERT: B 175 VAL cc_start: 0.9297 (t) cc_final: 0.9020 (t) REVERT: B 247 PHE cc_start: 0.7873 (OUTLIER) cc_final: 0.7595 (m-80) REVERT: C 192 MET cc_start: 0.7738 (OUTLIER) cc_final: 0.7098 (mpp) REVERT: D 100 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.7967 (tt) REVERT: D 109 PHE cc_start: 0.7793 (m-80) cc_final: 0.7423 (m-80) REVERT: D 211 MET cc_start: 0.7249 (mmm) cc_final: 0.6576 (mtm) REVERT: D 229 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7739 (mm) REVERT: E 105 MET cc_start: 0.7275 (mmm) cc_final: 0.6383 (mmm) REVERT: E 182 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.6519 (mp0) REVERT: E 209 MET cc_start: 0.4523 (ppp) cc_final: 0.2757 (tpp) REVERT: F 43 ARG cc_start: 0.7495 (mtm-85) cc_final: 0.7240 (ttp80) REVERT: F 94 MET cc_start: 0.8480 (mpp) cc_final: 0.8200 (mpp) REVERT: F 187 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8154 (mm) REVERT: H 37 MET cc_start: 0.6133 (ttt) cc_final: 0.5309 (mtt) REVERT: I 23 ILE cc_start: 0.8792 (mm) cc_final: 0.8379 (mt) REVERT: K 71 LYS cc_start: 0.6081 (tttp) cc_final: 0.5380 (mptt) outliers start: 56 outliers final: 29 residues processed: 335 average time/residue: 0.2070 time to fit residues: 105.1195 Evaluate side-chains 320 residues out of total 1439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 284 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 113 ASN Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 182 GLU Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 87 LEU Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain K residue 72 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 87 optimal weight: 9.9990 chunk 2 optimal weight: 0.7980 chunk 114 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 78 optimal weight: 0.6980 chunk 137 optimal weight: 1.9990 chunk 38 optimal weight: 0.0010 chunk 51 optimal weight: 0.9990 overall best weight: 0.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13117 Z= 0.218 Angle : 0.725 14.704 17871 Z= 0.351 Chirality : 0.043 0.222 2288 Planarity : 0.006 0.083 2149 Dihedral : 6.027 58.508 1723 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.54 % Favored : 92.34 % Rotamer: Outliers : 3.54 % Allowed : 22.03 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.12 % Twisted General : 0.06 % 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: 0.36 (0.22), residues: 1645 helix: 1.24 (0.15), residues: 1309 sheet: None (None), residues: 0 loop : -3.93 (0.29), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP I 68 HIS 0.002 0.002 HIS F 147 PHE 0.019 0.002 PHE C 154 TYR 0.007 0.001 TYR C 120 ARG 0.004 0.000 ARG C 111 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 293 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.7915 (mtt) cc_final: 0.7582 (mtt) REVERT: A 139 LYS cc_start: 0.8354 (ttmt) cc_final: 0.7910 (tttm) REVERT: A 220 ILE cc_start: 0.8558 (tt) cc_final: 0.8350 (tt) REVERT: B 70 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.7841 (ptp-170) REVERT: B 247 PHE cc_start: 0.7802 (OUTLIER) cc_final: 0.7546 (m-80) REVERT: C 69 THR cc_start: 0.9424 (p) cc_final: 0.9180 (m) REVERT: C 192 MET cc_start: 0.7787 (OUTLIER) cc_final: 0.7181 (mpp) REVERT: D 109 PHE cc_start: 0.7745 (m-80) cc_final: 0.7387 (m-80) REVERT: D 209 MET cc_start: 0.8021 (mmm) cc_final: 0.7804 (mmm) REVERT: D 211 MET cc_start: 0.7184 (mmm) cc_final: 0.6549 (mtm) REVERT: D 229 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7853 (mm) REVERT: E 105 MET cc_start: 0.7250 (mmm) cc_final: 0.6408 (mmm) REVERT: E 182 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.6582 (mp0) REVERT: E 209 MET cc_start: 0.4692 (ppp) cc_final: 0.3606 (tpp) REVERT: F 43 ARG cc_start: 0.7489 (mtm-85) cc_final: 0.7256 (ttp80) REVERT: F 94 MET cc_start: 0.8462 (mpp) cc_final: 0.8221 (mpp) REVERT: F 187 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8162 (mm) REVERT: H 37 MET cc_start: 0.6288 (ttt) cc_final: 0.5610 (mtt) REVERT: I 23 ILE cc_start: 0.8774 (mm) cc_final: 0.8360 (mt) outliers start: 51 outliers final: 30 residues processed: 324 average time/residue: 0.2178 time to fit residues: 108.7957 Evaluate side-chains 319 residues out of total 1439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 283 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 182 GLU Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain F residue 257 MET Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 74 MET Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 87 LEU Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain K residue 79 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 0.9990 chunk 30 optimal weight: 7.9990 chunk 90 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 12 optimal weight: 0.4980 chunk 50 optimal weight: 0.0070 chunk 80 optimal weight: 0.8980 chunk 148 optimal weight: 8.9990 overall best weight: 0.6802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 188 GLN F 104 GLN F 109 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13117 Z= 0.200 Angle : 0.720 12.739 17871 Z= 0.347 Chirality : 0.042 0.218 2288 Planarity : 0.006 0.082 2149 Dihedral : 5.879 58.537 1723 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.72 % Favored : 92.16 % Rotamer: Outliers : 3.68 % Allowed : 23.77 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.12 % Twisted General : 0.06 % 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: 0.58 (0.22), residues: 1645 helix: 1.45 (0.15), residues: 1289 sheet: None (None), residues: 0 loop : -3.81 (0.28), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 68 HIS 0.002 0.001 HIS F 97 PHE 0.018 0.001 PHE C 154 TYR 0.007 0.001 TYR C 120 ARG 0.004 0.000 ARG C 111 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 302 time to evaluate : 1.506 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.7915 (mtt) cc_final: 0.7548 (mtt) REVERT: A 84 LEU cc_start: 0.4143 (OUTLIER) cc_final: 0.3239 (mm) REVERT: A 139 LYS cc_start: 0.8353 (ttmt) cc_final: 0.7910 (tttm) REVERT: A 220 ILE cc_start: 0.8438 (tt) cc_final: 0.8220 (tt) REVERT: B 70 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.7854 (ptp-170) REVERT: C 69 THR cc_start: 0.9400 (p) cc_final: 0.9139 (m) REVERT: C 192 MET cc_start: 0.7782 (OUTLIER) cc_final: 0.7175 (mpp) REVERT: D 100 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.7988 (tt) REVERT: D 109 PHE cc_start: 0.7720 (m-80) cc_final: 0.7355 (m-80) REVERT: D 139 LYS cc_start: 0.8034 (ttpt) cc_final: 0.7660 (ttmm) REVERT: D 229 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7810 (mm) REVERT: E 105 MET cc_start: 0.7179 (mmm) cc_final: 0.6453 (mmm) REVERT: E 182 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.6582 (mp0) REVERT: E 209 MET cc_start: 0.4868 (ppp) cc_final: 0.3681 (tpp) REVERT: F 33 MET cc_start: 0.7552 (ttt) cc_final: 0.7011 (ttt) REVERT: F 43 ARG cc_start: 0.7453 (mtm-85) cc_final: 0.7215 (ttp80) REVERT: F 187 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8151 (mm) REVERT: F 244 GLN cc_start: 0.7989 (mm-40) cc_final: 0.7788 (mm-40) REVERT: H 37 MET cc_start: 0.6203 (ttt) cc_final: 0.5660 (mtt) REVERT: I 23 ILE cc_start: 0.8777 (mm) cc_final: 0.8342 (mt) outliers start: 53 outliers final: 27 residues processed: 337 average time/residue: 0.2177 time to fit residues: 112.3251 Evaluate side-chains 319 residues out of total 1439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 285 time to evaluate : 1.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 182 GLU Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain F residue 257 MET Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 74 MET Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 87 LEU Chi-restraints excluded: chain J residue 62 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 17 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 153 optimal weight: 8.9990 chunk 95 optimal weight: 0.2980 chunk 93 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13117 Z= 0.217 Angle : 0.746 15.365 17871 Z= 0.357 Chirality : 0.043 0.226 2288 Planarity : 0.006 0.084 2149 Dihedral : 5.850 58.205 1723 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.54 % Favored : 92.40 % Rotamer: Outliers : 3.34 % Allowed : 23.84 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.12 % Twisted General : 0.06 % 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: 0.67 (0.22), residues: 1645 helix: 1.51 (0.15), residues: 1289 sheet: None (None), residues: 0 loop : -3.71 (0.29), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP I 68 HIS 0.002 0.001 HIS F 97 PHE 0.020 0.001 PHE B 247 TYR 0.006 0.001 TYR C 120 ARG 0.005 0.000 ARG B 70 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 295 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.3934 (OUTLIER) cc_final: 0.3279 (mm) REVERT: A 139 LYS cc_start: 0.8345 (ttmt) cc_final: 0.7921 (tttm) REVERT: B 70 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.7860 (ptp-170) REVERT: C 69 THR cc_start: 0.9410 (p) cc_final: 0.9144 (m) REVERT: C 192 MET cc_start: 0.7772 (OUTLIER) cc_final: 0.7143 (mpp) REVERT: D 100 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8043 (tt) REVERT: D 109 PHE cc_start: 0.7771 (m-80) cc_final: 0.7370 (m-80) REVERT: D 139 LYS cc_start: 0.8160 (ttpt) cc_final: 0.7659 (ttmm) REVERT: D 201 ASP cc_start: 0.8060 (t0) cc_final: 0.7811 (t0) REVERT: D 211 MET cc_start: 0.6955 (mmm) cc_final: 0.6470 (mtm) REVERT: D 229 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7823 (mm) REVERT: E 105 MET cc_start: 0.7174 (mmm) cc_final: 0.6385 (mmm) REVERT: E 209 MET cc_start: 0.5161 (ppp) cc_final: 0.4118 (tpp) REVERT: F 33 MET cc_start: 0.7495 (ttt) cc_final: 0.6911 (ttt) REVERT: H 37 MET cc_start: 0.6178 (ttt) cc_final: 0.5730 (mtt) REVERT: I 23 ILE cc_start: 0.8788 (mm) cc_final: 0.8398 (mt) REVERT: J 23 ILE cc_start: 0.9013 (mm) cc_final: 0.8792 (mm) outliers start: 48 outliers final: 32 residues processed: 326 average time/residue: 0.2150 time to fit residues: 106.1169 Evaluate side-chains 325 residues out of total 1439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 288 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain F residue 217 PHE Chi-restraints excluded: chain F residue 257 MET Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 68 TRP Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 74 MET Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 87 LEU Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain K residue 72 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 91 optimal weight: 0.7980 chunk 46 optimal weight: 0.0970 chunk 30 optimal weight: 0.0470 chunk 29 optimal weight: 1.9990 chunk 97 optimal weight: 0.3980 chunk 104 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13117 Z= 0.186 Angle : 0.737 14.842 17871 Z= 0.352 Chirality : 0.042 0.219 2288 Planarity : 0.006 0.081 2149 Dihedral : 5.683 57.832 1723 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.05 % Favored : 92.83 % Rotamer: Outliers : 2.36 % Allowed : 24.81 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.12 % Twisted General : 0.06 % 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: 0.84 (0.22), residues: 1645 helix: 1.61 (0.15), residues: 1292 sheet: None (None), residues: 0 loop : -3.61 (0.29), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 68 HIS 0.001 0.001 HIS F 97 PHE 0.018 0.001 PHE B 247 TYR 0.005 0.001 TYR C 120 ARG 0.004 0.000 ARG C 111 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 296 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.3779 (OUTLIER) cc_final: 0.3061 (mm) REVERT: A 139 LYS cc_start: 0.8335 (ttmt) cc_final: 0.7937 (tttm) REVERT: B 70 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.7853 (ptp-170) REVERT: B 80 GLN cc_start: 0.7808 (mt0) cc_final: 0.7603 (mt0) REVERT: C 69 THR cc_start: 0.9395 (p) cc_final: 0.9156 (m) REVERT: C 192 MET cc_start: 0.7716 (OUTLIER) cc_final: 0.7090 (mpp) REVERT: D 100 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8017 (tt) REVERT: D 109 PHE cc_start: 0.7661 (m-80) cc_final: 0.7307 (m-80) REVERT: D 139 LYS cc_start: 0.8143 (ttpt) cc_final: 0.7735 (ttmm) REVERT: D 211 MET cc_start: 0.6802 (mmm) cc_final: 0.6544 (mtm) REVERT: E 105 MET cc_start: 0.7103 (mmm) cc_final: 0.6422 (mmm) REVERT: E 209 MET cc_start: 0.5271 (ppp) cc_final: 0.4373 (tpp) REVERT: F 33 MET cc_start: 0.7397 (ttt) cc_final: 0.6786 (ttt) REVERT: F 217 PHE cc_start: 0.7759 (OUTLIER) cc_final: 0.7019 (t80) REVERT: H 37 MET cc_start: 0.6146 (ttt) cc_final: 0.5786 (mtt) REVERT: I 23 ILE cc_start: 0.8787 (mm) cc_final: 0.8359 (mt) REVERT: J 23 ILE cc_start: 0.8975 (mm) cc_final: 0.8760 (mm) outliers start: 34 outliers final: 23 residues processed: 318 average time/residue: 0.2064 time to fit residues: 99.9039 Evaluate side-chains 312 residues out of total 1439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 284 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain F residue 217 PHE Chi-restraints excluded: chain F residue 257 MET Chi-restraints excluded: chain G residue 68 TRP Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 17 THR Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain K residue 72 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 0.8980 chunk 142 optimal weight: 0.2980 chunk 146 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 129 optimal weight: 0.9990 chunk 135 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 151 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 109 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13117 Z= 0.210 Angle : 0.761 15.554 17871 Z= 0.362 Chirality : 0.043 0.224 2288 Planarity : 0.006 0.082 2149 Dihedral : 5.672 56.455 1723 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.42 % Favored : 92.52 % Rotamer: Outliers : 2.64 % Allowed : 25.99 % Favored : 71.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.12 % Twisted General : 0.06 % 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: 0.83 (0.22), residues: 1645 helix: 1.61 (0.15), residues: 1291 sheet: None (None), residues: 0 loop : -3.63 (0.28), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 68 HIS 0.002 0.001 HIS F 97 PHE 0.028 0.002 PHE A 191 TYR 0.007 0.001 TYR G 81 ARG 0.004 0.000 ARG B 70 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 288 time to evaluate : 1.523 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.3695 (OUTLIER) cc_final: 0.3102 (mm) REVERT: A 139 LYS cc_start: 0.8330 (ttmt) cc_final: 0.7925 (tttm) REVERT: A 182 GLU cc_start: 0.7663 (tp30) cc_final: 0.7457 (tp30) REVERT: A 192 MET cc_start: 0.7605 (mtp) cc_final: 0.7392 (mtp) REVERT: B 70 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.7932 (ptp-170) REVERT: C 69 THR cc_start: 0.9388 (p) cc_final: 0.9174 (m) REVERT: C 192 MET cc_start: 0.7849 (OUTLIER) cc_final: 0.7220 (mpp) REVERT: D 100 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8020 (tt) REVERT: D 109 PHE cc_start: 0.7600 (m-10) cc_final: 0.7237 (m-80) REVERT: D 139 LYS cc_start: 0.8194 (ttpt) cc_final: 0.7805 (ttmm) REVERT: D 229 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7773 (mm) REVERT: E 105 MET cc_start: 0.7141 (mmm) cc_final: 0.6467 (mmm) REVERT: E 209 MET cc_start: 0.5580 (ppp) cc_final: 0.4917 (tpp) REVERT: E 247 PHE cc_start: 0.8260 (t80) cc_final: 0.7922 (t80) REVERT: F 33 MET cc_start: 0.7473 (ttt) cc_final: 0.6904 (ttt) REVERT: F 43 ARG cc_start: 0.7455 (mtm-85) cc_final: 0.7210 (mtm110) REVERT: F 217 PHE cc_start: 0.7779 (OUTLIER) cc_final: 0.7080 (t80) REVERT: H 37 MET cc_start: 0.6143 (ttt) cc_final: 0.5844 (mtt) REVERT: I 23 ILE cc_start: 0.8803 (mm) cc_final: 0.8399 (mt) REVERT: J 23 ILE cc_start: 0.8958 (mm) cc_final: 0.8745 (mm) outliers start: 38 outliers final: 23 residues processed: 312 average time/residue: 0.2080 time to fit residues: 99.0001 Evaluate side-chains 312 residues out of total 1439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 283 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain F residue 217 PHE Chi-restraints excluded: chain G residue 68 TRP Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 17 THR Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain J residue 62 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 104 optimal weight: 0.9990 chunk 158 optimal weight: 0.0050 chunk 145 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 100 optimal weight: 0.0050 chunk 134 optimal weight: 1.9990 overall best weight: 0.5208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13117 Z= 0.192 Angle : 0.737 14.205 17871 Z= 0.354 Chirality : 0.042 0.224 2288 Planarity : 0.006 0.081 2149 Dihedral : 5.554 54.981 1723 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.42 % Favored : 92.46 % Rotamer: Outliers : 2.29 % Allowed : 26.89 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.12 % 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: 0.98 (0.22), residues: 1645 helix: 1.70 (0.15), residues: 1293 sheet: None (None), residues: 0 loop : -3.53 (0.29), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 68 HIS 0.002 0.001 HIS F 97 PHE 0.042 0.001 PHE A 191 TYR 0.010 0.001 TYR G 81 ARG 0.004 0.000 ARG C 111 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 287 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.3574 (OUTLIER) cc_final: 0.2976 (mm) REVERT: A 139 LYS cc_start: 0.8327 (ttmt) cc_final: 0.7924 (tttm) REVERT: A 192 MET cc_start: 0.7584 (mtp) cc_final: 0.7314 (mtp) REVERT: B 70 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.7917 (ptp-170) REVERT: C 91 GLN cc_start: 0.6649 (pt0) cc_final: 0.6380 (tp-100) REVERT: C 192 MET cc_start: 0.7770 (OUTLIER) cc_final: 0.7183 (mpp) REVERT: D 100 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8005 (tt) REVERT: D 109 PHE cc_start: 0.7586 (m-10) cc_final: 0.7231 (m-80) REVERT: D 139 LYS cc_start: 0.8147 (ttpt) cc_final: 0.7750 (ttmm) REVERT: D 173 ILE cc_start: 0.7521 (tt) cc_final: 0.6892 (mt) REVERT: D 229 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7767 (mm) REVERT: E 105 MET cc_start: 0.7060 (mmm) cc_final: 0.6436 (mmm) REVERT: E 209 MET cc_start: 0.5590 (ppp) cc_final: 0.5049 (tpp) REVERT: E 247 PHE cc_start: 0.8217 (t80) cc_final: 0.7843 (t80) REVERT: F 33 MET cc_start: 0.7410 (ttt) cc_final: 0.6792 (ttt) REVERT: F 43 ARG cc_start: 0.7415 (mtm-85) cc_final: 0.7173 (mtm110) REVERT: F 217 PHE cc_start: 0.7699 (OUTLIER) cc_final: 0.7087 (t80) REVERT: H 37 MET cc_start: 0.6129 (ttt) cc_final: 0.5873 (mtt) REVERT: I 23 ILE cc_start: 0.8777 (mm) cc_final: 0.8399 (mt) outliers start: 33 outliers final: 24 residues processed: 309 average time/residue: 0.2274 time to fit residues: 107.9469 Evaluate side-chains 310 residues out of total 1439 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 280 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain C residue 65 MET Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain F residue 217 PHE Chi-restraints excluded: chain G residue 68 TRP Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 17 THR Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 87 LEU Chi-restraints excluded: chain J residue 62 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 38 optimal weight: 0.0980 chunk 116 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 126 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 110 optimal weight: 0.2980 chunk 7 optimal weight: 9.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 ASN H 45 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.174723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.149910 restraints weight = 15313.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.152793 restraints weight = 10261.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.154644 restraints weight = 7876.286| |-----------------------------------------------------------------------------| r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13117 Z= 0.218 Angle : 0.749 15.197 17871 Z= 0.358 Chirality : 0.043 0.229 2288 Planarity : 0.006 0.082 2149 Dihedral : 5.543 55.944 1723 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.36 % Favored : 92.58 % Rotamer: Outliers : 2.36 % Allowed : 26.82 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.12 % 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: 0.99 (0.22), residues: 1645 helix: 1.70 (0.15), residues: 1292 sheet: None (None), residues: 0 loop : -3.47 (0.29), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 68 HIS 0.002 0.001 HIS F 97 PHE 0.038 0.002 PHE A 191 TYR 0.013 0.001 TYR G 81 ARG 0.004 0.000 ARG C 111 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2744.23 seconds wall clock time: 50 minutes 41.42 seconds (3041.42 seconds total)