Starting phenix.real_space_refine on Fri Mar 15 01:22:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqd_34024/03_2024/7yqd_34024.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqd_34024/03_2024/7yqd_34024.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqd_34024/03_2024/7yqd_34024.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqd_34024/03_2024/7yqd_34024.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqd_34024/03_2024/7yqd_34024.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqd_34024/03_2024/7yqd_34024.pdb" } resolution = 3.4 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= 0.022 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 28 5.16 5 C 6671 2.51 5 N 1771 2.21 5 O 1820 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 120": "OE1" <-> "OE2" Residue "A GLU 125": "OE1" <-> "OE2" Residue "A ASP 201": "OD1" <-> "OD2" Residue "A GLU 208": "OE1" <-> "OE2" Residue "A TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 120": "OE1" <-> "OE2" Residue "B GLU 125": "OE1" <-> "OE2" Residue "B ASP 201": "OD1" <-> "OD2" Residue "B GLU 208": "OE1" <-> "OE2" Residue "B TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 120": "OE1" <-> "OE2" Residue "C GLU 125": "OE1" <-> "OE2" Residue "C ASP 201": "OD1" <-> "OD2" Residue "C GLU 208": "OE1" <-> "OE2" Residue "C TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 120": "OE1" <-> "OE2" Residue "D GLU 125": "OE1" <-> "OE2" Residue "D ASP 201": "OD1" <-> "OD2" Residue "D GLU 208": "OE1" <-> "OE2" Residue "D TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 120": "OE1" <-> "OE2" Residue "E GLU 125": "OE1" <-> "OE2" Residue "E ASP 201": "OD1" <-> "OD2" Residue "E GLU 208": "OE1" <-> "OE2" Residue "E TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 120": "OE1" <-> "OE2" Residue "F GLU 125": "OE1" <-> "OE2" Residue "F ASP 201": "OD1" <-> "OD2" Residue "F GLU 208": "OE1" <-> "OE2" Residue "F TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 120": "OE1" <-> "OE2" Residue "G GLU 125": "OE1" <-> "OE2" Residue "G ASP 201": "OD1" <-> "OD2" Residue "G GLU 208": "OE1" <-> "OE2" Residue "G TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10290 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1470 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 5, 'TRANS': 184} Chain breaks: 2 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 69 Chain: "B" Number of atoms: 1470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1470 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 5, 'TRANS': 184} Chain breaks: 2 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 69 Chain: "C" Number of atoms: 1470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1470 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 5, 'TRANS': 184} Chain breaks: 2 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 69 Chain: "D" Number of atoms: 1470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1470 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 5, 'TRANS': 184} Chain breaks: 2 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 69 Chain: "E" Number of atoms: 1470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1470 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 5, 'TRANS': 184} Chain breaks: 2 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 69 Chain: "F" Number of atoms: 1470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1470 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 5, 'TRANS': 184} Chain breaks: 2 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 69 Chain: "G" Number of atoms: 1470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1470 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 5, 'TRANS': 184} Chain breaks: 2 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 69 Time building chain proxies: 5.89, per 1000 atoms: 0.57 Number of scatterers: 10290 At special positions: 0 Unit cell: (110.24, 112.32, 78, 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 28 16.00 O 1820 8.00 N 1771 7.00 C 6671 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: 4.21 Conformation dependent library (CDL) restraints added in 1.8 seconds 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2646 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 0 sheets defined 87.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 8 through 32 Processing helix chain 'A' and resid 32 through 47 Processing helix chain 'A' and resid 48 through 52 removed outlier: 4.074A pdb=" N ILE A 52 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 143 Proline residue: A 124 - end of helix removed outlier: 3.598A pdb=" N THR A 135 " --> pdb=" O GLU A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 196 removed outlier: 3.542A pdb=" N TYR A 183 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA A 194 " --> pdb=" O VAL A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 244 removed outlier: 4.113A pdb=" N ARG A 203 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR A 207 " --> pdb=" O ARG A 203 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS A 241 " --> pdb=" O LYS A 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 32 Processing helix chain 'B' and resid 32 through 47 Processing helix chain 'B' and resid 48 through 52 removed outlier: 4.074A pdb=" N ILE B 52 " --> pdb=" O ILE B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 143 Proline residue: B 124 - end of helix removed outlier: 3.598A pdb=" N THR B 135 " --> pdb=" O GLU B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 196 removed outlier: 3.542A pdb=" N TYR B 183 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA B 194 " --> pdb=" O VAL B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 244 removed outlier: 4.112A pdb=" N ARG B 203 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR B 207 " --> pdb=" O ARG B 203 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU B 240 " --> pdb=" O LEU B 236 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS B 241 " --> pdb=" O LYS B 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 32 Processing helix chain 'C' and resid 32 through 47 Processing helix chain 'C' and resid 48 through 52 removed outlier: 4.074A pdb=" N ILE C 52 " --> pdb=" O ILE C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 143 Proline residue: C 124 - end of helix removed outlier: 3.598A pdb=" N THR C 135 " --> pdb=" O GLU C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 196 removed outlier: 3.542A pdb=" N TYR C 183 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA C 194 " --> pdb=" O VAL C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 244 removed outlier: 4.112A pdb=" N ARG C 203 " --> pdb=" O VAL C 199 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR C 207 " --> pdb=" O ARG C 203 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU C 240 " --> pdb=" O LEU C 236 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS C 241 " --> pdb=" O LYS C 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 32 Processing helix chain 'D' and resid 32 through 47 Processing helix chain 'D' and resid 48 through 52 removed outlier: 4.075A pdb=" N ILE D 52 " --> pdb=" O ILE D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 143 Proline residue: D 124 - end of helix removed outlier: 3.598A pdb=" N THR D 135 " --> pdb=" O GLU D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 196 removed outlier: 3.542A pdb=" N TYR D 183 " --> pdb=" O ILE D 179 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA D 194 " --> pdb=" O VAL D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 244 removed outlier: 4.112A pdb=" N ARG D 203 " --> pdb=" O VAL D 199 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR D 207 " --> pdb=" O ARG D 203 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU D 240 " --> pdb=" O LEU D 236 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS D 241 " --> pdb=" O LYS D 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 32 Processing helix chain 'E' and resid 32 through 47 Processing helix chain 'E' and resid 48 through 52 removed outlier: 4.074A pdb=" N ILE E 52 " --> pdb=" O ILE E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 143 Proline residue: E 124 - end of helix removed outlier: 3.598A pdb=" N THR E 135 " --> pdb=" O GLU E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 196 removed outlier: 3.542A pdb=" N TYR E 183 " --> pdb=" O ILE E 179 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA E 194 " --> pdb=" O VAL E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 244 removed outlier: 4.113A pdb=" N ARG E 203 " --> pdb=" O VAL E 199 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR E 207 " --> pdb=" O ARG E 203 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU E 240 " --> pdb=" O LEU E 236 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS E 241 " --> pdb=" O LYS E 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 32 Processing helix chain 'F' and resid 32 through 47 Processing helix chain 'F' and resid 48 through 52 removed outlier: 4.074A pdb=" N ILE F 52 " --> pdb=" O ILE F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 143 Proline residue: F 124 - end of helix removed outlier: 3.598A pdb=" N THR F 135 " --> pdb=" O GLU F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 196 removed outlier: 3.542A pdb=" N TYR F 183 " --> pdb=" O ILE F 179 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA F 194 " --> pdb=" O VAL F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 244 removed outlier: 4.112A pdb=" N ARG F 203 " --> pdb=" O VAL F 199 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR F 207 " --> pdb=" O ARG F 203 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU F 240 " --> pdb=" O LEU F 236 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS F 241 " --> pdb=" O LYS F 237 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 32 Processing helix chain 'G' and resid 32 through 47 Processing helix chain 'G' and resid 48 through 52 removed outlier: 4.074A pdb=" N ILE G 52 " --> pdb=" O ILE G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 143 Proline residue: G 124 - end of helix removed outlier: 3.599A pdb=" N THR G 135 " --> pdb=" O GLU G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 154 through 196 removed outlier: 3.543A pdb=" N TYR G 183 " --> pdb=" O ILE G 179 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA G 194 " --> pdb=" O VAL G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 199 through 244 removed outlier: 4.112A pdb=" N ARG G 203 " --> pdb=" O VAL G 199 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR G 207 " --> pdb=" O ARG G 203 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU G 240 " --> pdb=" O LEU G 236 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS G 241 " --> pdb=" O LYS G 237 " (cutoff:3.500A) 931 hydrogen bonds defined for protein. 2772 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: 3.13 Time building geometry restraints manager: 4.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1938 1.33 - 1.45: 2164 1.45 - 1.57: 6272 1.57 - 1.69: 0 1.69 - 1.81: 49 Bond restraints: 10423 Sorted by residual: bond pdb=" N ILE F 144 " pdb=" CA ILE F 144 " ideal model delta sigma weight residual 1.461 1.494 -0.033 9.10e-03 1.21e+04 1.32e+01 bond pdb=" N ILE C 144 " pdb=" CA ILE C 144 " ideal model delta sigma weight residual 1.461 1.494 -0.033 9.10e-03 1.21e+04 1.32e+01 bond pdb=" N ILE B 144 " pdb=" CA ILE B 144 " ideal model delta sigma weight residual 1.461 1.493 -0.033 9.10e-03 1.21e+04 1.29e+01 bond pdb=" N ILE D 144 " pdb=" CA ILE D 144 " ideal model delta sigma weight residual 1.461 1.493 -0.033 9.10e-03 1.21e+04 1.28e+01 bond pdb=" N ILE E 144 " pdb=" CA ILE E 144 " ideal model delta sigma weight residual 1.461 1.493 -0.033 9.10e-03 1.21e+04 1.28e+01 ... (remaining 10418 not shown) Histogram of bond angle deviations from ideal: 100.30 - 107.07: 224 107.07 - 113.85: 6256 113.85 - 120.63: 4849 120.63 - 127.40: 2729 127.40 - 134.18: 61 Bond angle restraints: 14119 Sorted by residual: angle pdb=" CA ILE D 144 " pdb=" C ILE D 144 " pdb=" N PRO D 145 " ideal model delta sigma weight residual 119.30 122.49 -3.19 8.10e-01 1.52e+00 1.55e+01 angle pdb=" CA ILE G 144 " pdb=" C ILE G 144 " pdb=" N PRO G 145 " ideal model delta sigma weight residual 119.30 122.48 -3.18 8.10e-01 1.52e+00 1.54e+01 angle pdb=" CA ILE A 144 " pdb=" C ILE A 144 " pdb=" N PRO A 145 " ideal model delta sigma weight residual 119.30 122.47 -3.17 8.10e-01 1.52e+00 1.53e+01 angle pdb=" CA ILE E 144 " pdb=" C ILE E 144 " pdb=" N PRO E 145 " ideal model delta sigma weight residual 119.30 122.46 -3.16 8.10e-01 1.52e+00 1.52e+01 angle pdb=" CA ILE F 144 " pdb=" C ILE F 144 " pdb=" N PRO F 145 " ideal model delta sigma weight residual 119.30 122.45 -3.15 8.10e-01 1.52e+00 1.52e+01 ... (remaining 14114 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.67: 5559 11.67 - 23.35: 566 23.35 - 35.02: 189 35.02 - 46.69: 105 46.69 - 58.36: 53 Dihedral angle restraints: 6472 sinusoidal: 2468 harmonic: 4004 Sorted by residual: dihedral pdb=" C GLN A 178 " pdb=" N GLN A 178 " pdb=" CA GLN A 178 " pdb=" CB GLN A 178 " ideal model delta harmonic sigma weight residual -122.60 -133.35 10.75 0 2.50e+00 1.60e-01 1.85e+01 dihedral pdb=" C GLN E 178 " pdb=" N GLN E 178 " pdb=" CA GLN E 178 " pdb=" CB GLN E 178 " ideal model delta harmonic sigma weight residual -122.60 -133.32 10.72 0 2.50e+00 1.60e-01 1.84e+01 dihedral pdb=" C GLN B 178 " pdb=" N GLN B 178 " pdb=" CA GLN B 178 " pdb=" CB GLN B 178 " ideal model delta harmonic sigma weight residual -122.60 -133.31 10.71 0 2.50e+00 1.60e-01 1.84e+01 ... (remaining 6469 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 684 0.067 - 0.134: 761 0.134 - 0.201: 277 0.201 - 0.268: 49 0.268 - 0.335: 7 Chirality restraints: 1778 Sorted by residual: chirality pdb=" CA GLN A 178 " pdb=" N GLN A 178 " pdb=" C GLN A 178 " pdb=" CB GLN A 178 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" CA GLN D 178 " pdb=" N GLN D 178 " pdb=" C GLN D 178 " pdb=" CB GLN D 178 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" CA GLN E 178 " pdb=" N GLN E 178 " pdb=" C GLN E 178 " pdb=" CB GLN E 178 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.78e+00 ... (remaining 1775 not shown) Planarity restraints: 1722 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 120 " 0.007 2.00e-02 2.50e+03 1.37e-02 1.87e+00 pdb=" C GLU A 120 " -0.024 2.00e-02 2.50e+03 pdb=" O GLU A 120 " 0.009 2.00e-02 2.50e+03 pdb=" N LYS A 121 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU G 120 " -0.007 2.00e-02 2.50e+03 1.34e-02 1.80e+00 pdb=" C GLU G 120 " 0.023 2.00e-02 2.50e+03 pdb=" O GLU G 120 " -0.009 2.00e-02 2.50e+03 pdb=" N LYS G 121 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 120 " 0.007 2.00e-02 2.50e+03 1.34e-02 1.79e+00 pdb=" C GLU C 120 " -0.023 2.00e-02 2.50e+03 pdb=" O GLU C 120 " 0.009 2.00e-02 2.50e+03 pdb=" N LYS C 121 " 0.008 2.00e-02 2.50e+03 ... (remaining 1719 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 3223 2.85 - 3.36: 11277 3.36 - 3.87: 15518 3.87 - 4.39: 18213 4.39 - 4.90: 30412 Nonbonded interactions: 78643 Sorted by model distance: nonbonded pdb=" CB ASN F 226 " pdb=" CE MET G 138 " model vdw 2.335 3.860 nonbonded pdb=" CB ASN A 226 " pdb=" CE MET C 138 " model vdw 2.343 3.860 nonbonded pdb=" CB ASN C 226 " pdb=" CE MET D 138 " model vdw 2.349 3.860 nonbonded pdb=" CB ASN D 226 " pdb=" CE MET E 138 " model vdw 2.349 3.860 nonbonded pdb=" CE MET B 138 " pdb=" CB ASN G 226 " model vdw 2.352 3.860 ... (remaining 78638 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' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 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: 3.450 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 30.180 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.038 10423 Z= 0.762 Angle : 1.460 5.669 14119 Z= 1.214 Chirality : 0.104 0.335 1778 Planarity : 0.005 0.022 1722 Dihedral : 13.648 58.363 3826 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 7.63 % Allowed : 7.92 % Favored : 84.45 % Cbeta Deviations : 0.53 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 6.20 (0.18), residues: 1288 helix: 4.77 (0.11), residues: 1092 sheet: None (None), residues: 0 loop : -0.71 (0.26), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 139 HIS 0.003 0.001 HIS E 232 PHE 0.006 0.001 PHE G 44 TYR 0.010 0.002 TYR G 183 ARG 0.002 0.001 ARG F 204 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 372 time to evaluate : 1.014 Fit side-chains REVERT: A 54 ASP cc_start: 0.8387 (t0) cc_final: 0.7993 (t70) REVERT: A 238 ASN cc_start: 0.8511 (m-40) cc_final: 0.8253 (m-40) REVERT: B 37 LYS cc_start: 0.9461 (OUTLIER) cc_final: 0.9240 (mmtt) REVERT: B 54 ASP cc_start: 0.8484 (t0) cc_final: 0.7906 (t0) REVERT: B 201 ASP cc_start: 0.7901 (m-30) cc_final: 0.7485 (m-30) REVERT: C 54 ASP cc_start: 0.8467 (t0) cc_final: 0.8071 (t0) REVERT: C 234 MET cc_start: 0.9020 (ttm) cc_final: 0.8798 (ttm) REVERT: D 37 LYS cc_start: 0.9357 (OUTLIER) cc_final: 0.9150 (mmtt) REVERT: D 54 ASP cc_start: 0.8526 (t0) cc_final: 0.7974 (t0) REVERT: D 166 ARG cc_start: 0.8996 (ttp-170) cc_final: 0.8636 (mtt90) REVERT: E 54 ASP cc_start: 0.8478 (t0) cc_final: 0.8030 (t70) REVERT: F 54 ASP cc_start: 0.8476 (t0) cc_final: 0.8201 (t0) REVERT: G 54 ASP cc_start: 0.8449 (t0) cc_final: 0.8092 (t0) REVERT: G 117 ASP cc_start: 0.8424 (m-30) cc_final: 0.8016 (m-30) outliers start: 81 outliers final: 40 residues processed: 425 average time/residue: 0.2455 time to fit residues: 139.9466 Evaluate side-chains 359 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 317 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 37 LYS Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 198 HIS Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain D residue 37 LYS Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 198 HIS Chi-restraints excluded: chain D residue 226 ASN Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 198 HIS Chi-restraints excluded: chain E residue 226 ASN Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 198 HIS Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 239 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 120 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN A 112 ASN ** A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 ASN ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 ASN ** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 ASN G 178 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10423 Z= 0.226 Angle : 0.540 8.787 14119 Z= 0.296 Chirality : 0.036 0.129 1778 Planarity : 0.004 0.050 1722 Dihedral : 8.254 58.506 1502 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 6.22 % Allowed : 14.99 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.52 (0.19), residues: 1288 helix: 4.23 (0.12), residues: 1092 sheet: None (None), residues: 0 loop : -0.42 (0.28), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 139 HIS 0.003 0.001 HIS F 59 PHE 0.005 0.001 PHE E 18 TYR 0.018 0.001 TYR F 214 ARG 0.005 0.001 ARG D 21 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 330 time to evaluate : 1.293 Fit side-chains revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8332 (t0) cc_final: 0.8024 (t70) REVERT: B 37 LYS cc_start: 0.9247 (OUTLIER) cc_final: 0.9041 (mmtt) REVERT: B 54 ASP cc_start: 0.8352 (t0) cc_final: 0.7908 (t70) REVERT: B 128 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8273 (mm) REVERT: B 166 ARG cc_start: 0.8818 (OUTLIER) cc_final: 0.8369 (ttp-170) REVERT: C 54 ASP cc_start: 0.8324 (t0) cc_final: 0.7854 (t0) REVERT: C 166 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.8460 (ttp-170) REVERT: D 54 ASP cc_start: 0.8436 (t0) cc_final: 0.8156 (t0) REVERT: D 166 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.8529 (mtt90) REVERT: D 210 ASP cc_start: 0.8344 (m-30) cc_final: 0.8024 (m-30) REVERT: E 54 ASP cc_start: 0.8355 (t0) cc_final: 0.7937 (t0) REVERT: F 54 ASP cc_start: 0.8403 (t0) cc_final: 0.8033 (t0) REVERT: F 166 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.8567 (ttp-170) REVERT: F 203 ARG cc_start: 0.7231 (ttm110) cc_final: 0.7029 (mtp85) REVERT: G 54 ASP cc_start: 0.8391 (t0) cc_final: 0.7971 (t0) outliers start: 66 outliers final: 39 residues processed: 364 average time/residue: 0.2341 time to fit residues: 116.0602 Evaluate side-chains 348 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 303 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 37 LYS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 178 GLN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain D residue 37 LYS Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 166 ARG Chi-restraints excluded: chain D residue 178 GLN Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 166 ARG Chi-restraints excluded: chain F residue 178 GLN Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 114 GLN Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain G residue 239 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 67 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 GLN A 238 ASN B 112 ASN B 114 GLN B 178 GLN B 238 ASN C 112 ASN ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 ASN E 178 GLN F 112 ASN ** F 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 ASN F 238 ASN ** G 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 178 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10423 Z= 0.308 Angle : 0.546 6.885 14119 Z= 0.296 Chirality : 0.037 0.126 1778 Planarity : 0.004 0.031 1722 Dihedral : 6.046 56.239 1460 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 5.94 % Allowed : 17.53 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.71 (0.20), residues: 1288 helix: 3.70 (0.13), residues: 1092 sheet: None (None), residues: 0 loop : -0.81 (0.30), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 139 HIS 0.004 0.001 HIS F 59 PHE 0.006 0.001 PHE C 33 TYR 0.010 0.002 TYR A 214 ARG 0.007 0.001 ARG G 21 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 303 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8412 (t0) cc_final: 0.7759 (t0) REVERT: A 208 GLU cc_start: 0.8389 (tp30) cc_final: 0.8079 (tp30) REVERT: B 54 ASP cc_start: 0.8334 (t0) cc_final: 0.7836 (t70) REVERT: B 62 MET cc_start: 0.6878 (ttm) cc_final: 0.6587 (mtp) REVERT: B 166 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.8441 (ttp-170) REVERT: B 210 ASP cc_start: 0.8490 (m-30) cc_final: 0.8252 (m-30) REVERT: C 54 ASP cc_start: 0.8538 (t0) cc_final: 0.8111 (t70) REVERT: C 142 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8423 (mp) REVERT: C 166 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.8633 (ttp-170) REVERT: C 210 ASP cc_start: 0.8448 (m-30) cc_final: 0.8148 (m-30) REVERT: D 21 ARG cc_start: 0.7966 (ttp-110) cc_final: 0.7764 (ttp-110) REVERT: D 54 ASP cc_start: 0.8521 (t0) cc_final: 0.7926 (t0) REVERT: D 57 GLN cc_start: 0.8188 (mp10) cc_final: 0.7894 (mp10) REVERT: D 138 MET cc_start: 0.8361 (tpp) cc_final: 0.8155 (tpp) REVERT: D 166 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8634 (mtt90) REVERT: D 188 LYS cc_start: 0.8679 (tttt) cc_final: 0.8417 (ttmm) REVERT: D 208 GLU cc_start: 0.8444 (tp30) cc_final: 0.8143 (tp30) REVERT: D 210 ASP cc_start: 0.8344 (m-30) cc_final: 0.8131 (m-30) REVERT: E 54 ASP cc_start: 0.8314 (t0) cc_final: 0.7852 (t0) REVERT: E 57 GLN cc_start: 0.7999 (mp10) cc_final: 0.7768 (mp10) REVERT: F 54 ASP cc_start: 0.8341 (t0) cc_final: 0.8016 (t70) REVERT: G 54 ASP cc_start: 0.8418 (t0) cc_final: 0.7783 (t0) outliers start: 63 outliers final: 43 residues processed: 338 average time/residue: 0.2271 time to fit residues: 104.8063 Evaluate side-chains 346 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 299 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 178 GLN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 166 ARG Chi-restraints excluded: chain D residue 178 GLN Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain F residue 12 LYS Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 178 GLN Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 114 GLN Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 178 GLN Chi-restraints excluded: chain G residue 239 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 119 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 62 optimal weight: 0.0170 chunk 13 optimal weight: 0.8980 chunk 57 optimal weight: 9.9990 chunk 81 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 63 optimal weight: 0.0010 chunk 115 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.5024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN ** A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 ASN ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 ASN ** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 238 ASN F 112 ASN ** F 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10423 Z= 0.167 Angle : 0.454 6.299 14119 Z= 0.249 Chirality : 0.034 0.124 1778 Planarity : 0.004 0.028 1722 Dihedral : 5.568 51.626 1452 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Rotamer: Outliers : 5.09 % Allowed : 19.70 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.03 (0.21), residues: 1288 helix: 3.87 (0.13), residues: 1092 sheet: None (None), residues: 0 loop : -0.38 (0.30), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 139 HIS 0.001 0.000 HIS F 59 PHE 0.006 0.001 PHE E 18 TYR 0.009 0.001 TYR F 214 ARG 0.009 0.001 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 320 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8370 (t0) cc_final: 0.7938 (t0) REVERT: A 112 ASN cc_start: 0.8453 (OUTLIER) cc_final: 0.8182 (t0) REVERT: A 210 ASP cc_start: 0.8276 (m-30) cc_final: 0.8023 (m-30) REVERT: B 54 ASP cc_start: 0.8334 (t0) cc_final: 0.7651 (t70) REVERT: B 138 MET cc_start: 0.8158 (tpp) cc_final: 0.7955 (tpp) REVERT: B 210 ASP cc_start: 0.8368 (m-30) cc_final: 0.8024 (m-30) REVERT: C 54 ASP cc_start: 0.8465 (t0) cc_final: 0.8023 (t70) REVERT: D 54 ASP cc_start: 0.8443 (t0) cc_final: 0.8090 (t0) REVERT: D 142 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8660 (mp) REVERT: D 188 LYS cc_start: 0.8577 (tttt) cc_final: 0.8283 (ttmm) REVERT: D 208 GLU cc_start: 0.8390 (tp30) cc_final: 0.8040 (tp30) REVERT: E 54 ASP cc_start: 0.8254 (t0) cc_final: 0.7863 (t0) REVERT: E 57 GLN cc_start: 0.8060 (mp10) cc_final: 0.7839 (mp10) REVERT: F 54 ASP cc_start: 0.8316 (t0) cc_final: 0.8070 (t70) REVERT: F 166 ARG cc_start: 0.8564 (ttp-170) cc_final: 0.8230 (mtt90) REVERT: G 54 ASP cc_start: 0.8328 (t0) cc_final: 0.7541 (t0) REVERT: G 57 GLN cc_start: 0.8234 (mp10) cc_final: 0.7924 (mp10) outliers start: 54 outliers final: 31 residues processed: 352 average time/residue: 0.2353 time to fit residues: 112.5207 Evaluate side-chains 330 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 297 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ASN Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain C residue 112 ASN Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain C residue 201 ASP Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 178 GLN Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 112 ASN Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain F residue 12 LYS Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 178 GLN Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 178 GLN Chi-restraints excluded: chain G residue 239 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 107 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 95 optimal weight: 9.9990 chunk 53 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN A 178 GLN B 178 GLN C 112 ASN ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 ASN E 178 GLN E 238 ASN F 112 ASN ** F 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 238 ASN ** G 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 178 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10423 Z= 0.228 Angle : 0.492 7.521 14119 Z= 0.264 Chirality : 0.036 0.128 1778 Planarity : 0.004 0.037 1722 Dihedral : 5.276 49.169 1447 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 5.28 % Allowed : 19.32 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.79 (0.21), residues: 1288 helix: 3.71 (0.14), residues: 1092 sheet: None (None), residues: 0 loop : -0.52 (0.32), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 139 HIS 0.002 0.001 HIS D 59 PHE 0.006 0.001 PHE C 33 TYR 0.006 0.001 TYR E 228 ARG 0.010 0.001 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 303 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8462 (t0) cc_final: 0.7800 (t0) REVERT: A 112 ASN cc_start: 0.8576 (OUTLIER) cc_final: 0.8247 (t0) REVERT: A 138 MET cc_start: 0.7934 (tpp) cc_final: 0.7711 (tpp) REVERT: A 238 ASN cc_start: 0.8726 (m110) cc_final: 0.8499 (m110) REVERT: B 54 ASP cc_start: 0.8388 (t0) cc_final: 0.7765 (t70) REVERT: B 210 ASP cc_start: 0.8369 (m-30) cc_final: 0.8063 (m-30) REVERT: C 54 ASP cc_start: 0.8386 (t0) cc_final: 0.7869 (t0) REVERT: C 226 ASN cc_start: 0.9041 (m-40) cc_final: 0.8770 (m-40) REVERT: D 54 ASP cc_start: 0.8457 (t0) cc_final: 0.7821 (t0) REVERT: D 57 GLN cc_start: 0.8122 (mp10) cc_final: 0.7792 (mp10) REVERT: D 142 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8708 (mp) REVERT: D 188 LYS cc_start: 0.8611 (tttt) cc_final: 0.8312 (ttmm) REVERT: D 203 ARG cc_start: 0.7191 (mtp85) cc_final: 0.6989 (mtp85) REVERT: D 208 GLU cc_start: 0.8454 (tp30) cc_final: 0.8062 (tp30) REVERT: E 54 ASP cc_start: 0.8256 (t0) cc_final: 0.8001 (t0) REVERT: E 166 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.8214 (ttp-170) REVERT: E 226 ASN cc_start: 0.9148 (m-40) cc_final: 0.8751 (m-40) REVERT: F 54 ASP cc_start: 0.8357 (t0) cc_final: 0.8123 (t70) REVERT: G 54 ASP cc_start: 0.8430 (t0) cc_final: 0.7838 (t0) outliers start: 56 outliers final: 40 residues processed: 343 average time/residue: 0.2467 time to fit residues: 113.4776 Evaluate side-chains 335 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 292 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 112 ASN Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 178 GLN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 178 GLN Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 166 ARG Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 178 GLN Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 114 GLN Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 178 GLN Chi-restraints excluded: chain G residue 239 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 43 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 chunk 25 optimal weight: 0.0770 chunk 75 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 128 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 59 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 GLN A 178 GLN B 9 GLN B 178 GLN C 112 ASN ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 ASN E 178 GLN F 112 ASN ** F 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 238 ASN ** G 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 178 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.4669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10423 Z= 0.184 Angle : 0.475 6.788 14119 Z= 0.256 Chirality : 0.035 0.166 1778 Planarity : 0.004 0.041 1722 Dihedral : 5.117 47.794 1445 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 4.62 % Allowed : 20.64 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.82 (0.21), residues: 1288 helix: 3.72 (0.14), residues: 1092 sheet: None (None), residues: 0 loop : -0.46 (0.33), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 139 HIS 0.001 0.000 HIS D 59 PHE 0.006 0.001 PHE C 18 TYR 0.005 0.001 TYR D 183 ARG 0.013 0.001 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 296 time to evaluate : 0.999 Fit side-chains revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8501 (t0) cc_final: 0.7865 (t0) REVERT: A 138 MET cc_start: 0.7879 (tpp) cc_final: 0.7675 (tpp) REVERT: A 238 ASN cc_start: 0.8718 (m110) cc_final: 0.8497 (m110) REVERT: B 54 ASP cc_start: 0.8376 (t0) cc_final: 0.7827 (t70) REVERT: B 210 ASP cc_start: 0.8344 (m-30) cc_final: 0.8028 (m-30) REVERT: C 54 ASP cc_start: 0.8412 (t0) cc_final: 0.7917 (t0) REVERT: D 54 ASP cc_start: 0.8433 (t0) cc_final: 0.7806 (t0) REVERT: D 142 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8657 (mp) REVERT: D 188 LYS cc_start: 0.8577 (tttt) cc_final: 0.8271 (ttmm) REVERT: E 54 ASP cc_start: 0.8324 (t0) cc_final: 0.7826 (t0) REVERT: E 57 GLN cc_start: 0.8218 (mp10) cc_final: 0.7885 (mp10) REVERT: E 166 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.8214 (ttp-170) REVERT: E 226 ASN cc_start: 0.9133 (m-40) cc_final: 0.8649 (m-40) REVERT: F 54 ASP cc_start: 0.8328 (t0) cc_final: 0.7879 (t70) REVERT: G 54 ASP cc_start: 0.8365 (t0) cc_final: 0.7907 (t0) outliers start: 49 outliers final: 38 residues processed: 332 average time/residue: 0.2395 time to fit residues: 107.7274 Evaluate side-chains 331 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 291 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 178 GLN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain C residue 112 ASN Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain C residue 201 ASP Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 178 GLN Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain E residue 22 ILE Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 166 ARG Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 178 GLN Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 114 GLN Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 178 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 124 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 108 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 80 optimal weight: 0.0670 chunk 78 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN A 178 GLN B 112 ASN B 178 GLN ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 ASN E 112 ASN E 178 GLN E 238 ASN F 112 ASN ** F 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 178 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.4861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10423 Z= 0.176 Angle : 0.475 6.446 14119 Z= 0.256 Chirality : 0.035 0.163 1778 Planarity : 0.004 0.044 1722 Dihedral : 4.803 46.050 1441 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 4.05 % Allowed : 21.02 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.83 (0.21), residues: 1288 helix: 3.73 (0.14), residues: 1092 sheet: None (None), residues: 0 loop : -0.42 (0.34), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 139 HIS 0.001 0.000 HIS A 53 PHE 0.006 0.001 PHE C 18 TYR 0.004 0.001 TYR D 183 ARG 0.014 0.001 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 300 time to evaluate : 1.168 Fit side-chains revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8420 (t0) cc_final: 0.7651 (t0) REVERT: A 112 ASN cc_start: 0.8512 (OUTLIER) cc_final: 0.8268 (t0) REVERT: A 238 ASN cc_start: 0.8702 (m110) cc_final: 0.8480 (m110) REVERT: B 54 ASP cc_start: 0.8355 (t0) cc_final: 0.7847 (t70) REVERT: B 210 ASP cc_start: 0.8325 (m-30) cc_final: 0.8045 (m-30) REVERT: C 54 ASP cc_start: 0.8477 (t0) cc_final: 0.7750 (t0) REVERT: D 54 ASP cc_start: 0.8361 (t0) cc_final: 0.7700 (t0) REVERT: D 57 GLN cc_start: 0.8036 (mp10) cc_final: 0.7818 (mp10) REVERT: D 141 GLN cc_start: 0.8874 (tt0) cc_final: 0.8660 (tt0) REVERT: D 142 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8705 (mp) REVERT: D 188 LYS cc_start: 0.8549 (tttt) cc_final: 0.8245 (ttmm) REVERT: D 210 ASP cc_start: 0.8008 (m-30) cc_final: 0.7475 (m-30) REVERT: E 54 ASP cc_start: 0.8314 (t0) cc_final: 0.7774 (t0) REVERT: E 57 GLN cc_start: 0.8227 (mp10) cc_final: 0.7911 (mp10) REVERT: E 166 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.8190 (ttp-170) REVERT: E 226 ASN cc_start: 0.9107 (m-40) cc_final: 0.8623 (m-40) REVERT: F 54 ASP cc_start: 0.8318 (t0) cc_final: 0.8020 (t70) REVERT: G 54 ASP cc_start: 0.8399 (t0) cc_final: 0.7822 (t0) REVERT: G 57 GLN cc_start: 0.8210 (mp10) cc_final: 0.8001 (mp10) outliers start: 43 outliers final: 29 residues processed: 332 average time/residue: 0.2409 time to fit residues: 107.7973 Evaluate side-chains 319 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 287 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 112 ASN Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain C residue 201 ASP Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 178 GLN Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 166 ARG Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 178 GLN Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 155 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 79 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN A 226 ASN B 112 ASN C 112 ASN ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 ASN E 178 GLN F 112 ASN ** F 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 178 GLN G 226 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.4926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10423 Z= 0.199 Angle : 0.509 6.480 14119 Z= 0.272 Chirality : 0.036 0.180 1778 Planarity : 0.004 0.051 1722 Dihedral : 4.596 44.520 1437 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 3.86 % Allowed : 21.49 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.71 (0.21), residues: 1288 helix: 3.65 (0.14), residues: 1092 sheet: None (None), residues: 0 loop : -0.50 (0.34), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 139 HIS 0.001 0.000 HIS D 59 PHE 0.006 0.001 PHE C 18 TYR 0.005 0.001 TYR F 228 ARG 0.015 0.001 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 286 time to evaluate : 1.450 Fit side-chains revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8390 (t0) cc_final: 0.7883 (t0) REVERT: B 54 ASP cc_start: 0.8354 (t0) cc_final: 0.7566 (t70) REVERT: B 57 GLN cc_start: 0.8194 (mp10) cc_final: 0.7791 (mp10) REVERT: B 210 ASP cc_start: 0.8314 (m-30) cc_final: 0.8038 (m-30) REVERT: C 54 ASP cc_start: 0.8400 (t0) cc_final: 0.7946 (t0) REVERT: D 54 ASP cc_start: 0.8396 (t0) cc_final: 0.7682 (t0) REVERT: D 57 GLN cc_start: 0.8093 (mp10) cc_final: 0.7848 (mp10) REVERT: D 188 LYS cc_start: 0.8586 (tttt) cc_final: 0.8281 (ttmm) REVERT: E 54 ASP cc_start: 0.8354 (t0) cc_final: 0.7800 (t0) REVERT: E 57 GLN cc_start: 0.8250 (mp10) cc_final: 0.7947 (mp10) REVERT: E 166 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.8173 (ttp-170) REVERT: E 226 ASN cc_start: 0.9097 (m-40) cc_final: 0.8765 (m-40) REVERT: F 54 ASP cc_start: 0.8327 (t0) cc_final: 0.7793 (t70) REVERT: G 54 ASP cc_start: 0.8261 (t0) cc_final: 0.7766 (t0) REVERT: G 138 MET cc_start: 0.8940 (OUTLIER) cc_final: 0.8558 (tpp) outliers start: 41 outliers final: 31 residues processed: 317 average time/residue: 0.2347 time to fit residues: 102.0980 Evaluate side-chains 314 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 281 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain C residue 201 ASP Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 178 GLN Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 166 ARG Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 178 GLN Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 114 GLN Chi-restraints excluded: chain G residue 138 MET Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 155 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 116 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 119 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 126 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN A 178 GLN B 226 ASN C 112 ASN ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 ASN E 178 GLN F 112 ASN ** F 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 178 GLN G 238 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.5018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10423 Z= 0.193 Angle : 0.528 14.881 14119 Z= 0.275 Chirality : 0.036 0.157 1778 Planarity : 0.004 0.052 1722 Dihedral : 4.489 40.180 1437 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 3.86 % Allowed : 20.83 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.66 (0.21), residues: 1288 helix: 3.62 (0.14), residues: 1092 sheet: None (None), residues: 0 loop : -0.55 (0.33), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 139 HIS 0.001 0.000 HIS D 59 PHE 0.006 0.001 PHE E 18 TYR 0.005 0.001 TYR E 175 ARG 0.016 0.001 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 289 time to evaluate : 1.289 Fit side-chains revert: symmetry clash REVERT: A 12 LYS cc_start: 0.8106 (ttmm) cc_final: 0.7833 (ttpt) REVERT: A 54 ASP cc_start: 0.8380 (t0) cc_final: 0.7560 (t0) REVERT: A 57 GLN cc_start: 0.8132 (mp10) cc_final: 0.7861 (mp10) REVERT: A 112 ASN cc_start: 0.8448 (OUTLIER) cc_final: 0.8108 (t0) REVERT: B 54 ASP cc_start: 0.8341 (t0) cc_final: 0.7656 (t70) REVERT: B 57 GLN cc_start: 0.8229 (mp10) cc_final: 0.7850 (mp10) REVERT: B 210 ASP cc_start: 0.8452 (m-30) cc_final: 0.8236 (m-30) REVERT: C 54 ASP cc_start: 0.8382 (t0) cc_final: 0.8042 (t0) REVERT: D 54 ASP cc_start: 0.8368 (t0) cc_final: 0.7945 (t0) REVERT: D 138 MET cc_start: 0.9019 (tpt) cc_final: 0.8349 (tpt) REVERT: D 188 LYS cc_start: 0.8589 (tttt) cc_final: 0.8276 (ttmm) REVERT: D 210 ASP cc_start: 0.7901 (m-30) cc_final: 0.7580 (m-30) REVERT: E 54 ASP cc_start: 0.8358 (t0) cc_final: 0.7802 (t0) REVERT: E 57 GLN cc_start: 0.8241 (mp10) cc_final: 0.7944 (mp10) REVERT: E 166 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.8185 (ttp-170) REVERT: E 226 ASN cc_start: 0.8999 (m-40) cc_final: 0.8776 (m-40) REVERT: F 14 LYS cc_start: 0.8585 (mmmm) cc_final: 0.8371 (mttt) REVERT: G 211 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7806 (mm-30) outliers start: 41 outliers final: 32 residues processed: 319 average time/residue: 0.2271 time to fit residues: 99.0770 Evaluate side-chains 315 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 281 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 112 ASN Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain C residue 201 ASP Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 178 GLN Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 166 ARG Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 178 GLN Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 114 GLN Chi-restraints excluded: chain G residue 138 MET Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 155 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 112 optimal weight: 0.7980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN A 178 GLN B 112 ASN C 112 ASN ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 178 GLN E 178 GLN F 112 ASN ** F 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 178 GLN G 226 ASN G 238 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.4946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10423 Z= 0.240 Angle : 0.548 7.549 14119 Z= 0.291 Chirality : 0.037 0.210 1778 Planarity : 0.004 0.051 1722 Dihedral : 4.553 39.259 1437 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 3.58 % Allowed : 21.39 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.49 (0.21), residues: 1288 helix: 3.51 (0.14), residues: 1092 sheet: None (None), residues: 0 loop : -0.68 (0.34), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 139 HIS 0.002 0.001 HIS D 59 PHE 0.006 0.001 PHE D 33 TYR 0.007 0.001 TYR A 175 ARG 0.015 0.001 ARG B 21 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 278 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.8135 (ttmm) cc_final: 0.7862 (ttpt) REVERT: A 54 ASP cc_start: 0.8351 (t0) cc_final: 0.7575 (t0) REVERT: A 57 GLN cc_start: 0.8125 (mp10) cc_final: 0.7841 (mp10) REVERT: A 112 ASN cc_start: 0.8589 (OUTLIER) cc_final: 0.8276 (t0) REVERT: B 54 ASP cc_start: 0.8338 (t0) cc_final: 0.7610 (t70) REVERT: B 57 GLN cc_start: 0.8263 (mp10) cc_final: 0.7888 (mp10) REVERT: B 210 ASP cc_start: 0.8408 (m-30) cc_final: 0.8156 (m-30) REVERT: D 188 LYS cc_start: 0.8599 (tttt) cc_final: 0.8299 (ttmm) REVERT: E 54 ASP cc_start: 0.8388 (t0) cc_final: 0.7805 (t0) REVERT: E 57 GLN cc_start: 0.8244 (mp10) cc_final: 0.7934 (mp10) REVERT: E 166 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.8194 (ttp-170) REVERT: E 226 ASN cc_start: 0.9097 (m-40) cc_final: 0.8786 (m-40) outliers start: 38 outliers final: 28 residues processed: 308 average time/residue: 0.2369 time to fit residues: 98.9281 Evaluate side-chains 306 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 276 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 112 ASN Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 201 ASP Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 178 GLN Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 166 ARG Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 178 GLN Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 155 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 32 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 105 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 19 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN A 178 GLN B 112 ASN C 112 ASN ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 178 GLN F 112 ASN ** F 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 178 GLN ** G 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 238 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.111337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.089565 restraints weight = 18283.367| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.66 r_work: 0.2973 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.4963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10423 Z= 0.220 Angle : 0.567 11.895 14119 Z= 0.296 Chirality : 0.037 0.249 1778 Planarity : 0.004 0.051 1722 Dihedral : 4.461 38.518 1435 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 3.11 % Allowed : 22.53 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.42 (0.21), residues: 1288 helix: 3.47 (0.14), residues: 1092 sheet: None (None), residues: 0 loop : -0.70 (0.34), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 139 HIS 0.002 0.001 HIS D 53 PHE 0.006 0.001 PHE E 18 TYR 0.005 0.001 TYR E 183 ARG 0.015 0.001 ARG B 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2534.11 seconds wall clock time: 45 minutes 57.89 seconds (2757.89 seconds total)