Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 17:07:58 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqd_34024/04_2023/7yqd_34024.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqd_34024/04_2023/7yqd_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_34024/04_2023/7yqd_34024.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqd_34024/04_2023/7yqd_34024.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqd_34024/04_2023/7yqd_34024.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqd_34024/04_2023/7yqd_34024.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 5.59, per 1000 atoms: 0.54 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: 4.25 Conformation dependent library (CDL) restraints added in 1.5 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: 0.24 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: 2.93 Time building geometry restraints manager: 4.59 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.090 Check model and map are aligned: 0.160 Set scattering table: 0.090 Process input model: 28.080 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.590 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 1.259 Fit side-chains outliers start: 81 outliers final: 40 residues processed: 425 average time/residue: 0.2498 time to fit residues: 143.4226 Evaluate side-chains 355 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 315 time to evaluate : 1.284 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 4 residues processed: 40 average time/residue: 0.0981 time to fit residues: 9.1001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 55 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 120 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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** A 238 ASN 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3402 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= 0.229 Angle : 0.544 8.714 14119 Z= 0.300 Chirality : 0.035 0.123 1778 Planarity : 0.004 0.049 1722 Dihedral : 3.922 16.794 1421 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 4.24 % 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: 5.47 (0.20), residues: 1288 helix: 4.22 (0.12), residues: 1092 sheet: None (None), residues: 0 loop : -0.65 (0.29), residues: 196 *********************** 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 373 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 328 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 22 residues processed: 349 average time/residue: 0.2389 time to fit residues: 113.7556 Evaluate side-chains 317 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 295 time to evaluate : 1.306 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 4 residues processed: 22 average time/residue: 0.1004 time to fit residues: 5.6746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 67 optimal weight: 0.0030 chunk 37 optimal weight: 6.9990 chunk 100 optimal weight: 0.0770 chunk 82 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 119 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 overall best weight: 0.4548 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN ** A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 ASN ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 ASN C 112 ASN C 178 GLN ** D 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 10423 Z= 0.168 Angle : 0.466 6.346 14119 Z= 0.256 Chirality : 0.034 0.131 1778 Planarity : 0.003 0.029 1722 Dihedral : 3.618 14.273 1421 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 2.45 % 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: 5.28 (0.20), residues: 1288 helix: 4.06 (0.13), residues: 1092 sheet: None (None), residues: 0 loop : -0.44 (0.31), residues: 196 *********************** 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 354 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 328 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 14 residues processed: 339 average time/residue: 0.2354 time to fit residues: 111.6495 Evaluate side-chains 298 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 284 time to evaluate : 1.313 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 4 residues processed: 14 average time/residue: 0.1197 time to fit residues: 4.6583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 119 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 62 optimal weight: 0.0670 chunk 13 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 81 optimal weight: 0.0970 chunk 121 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 115 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 ASN B 112 ASN B 114 GLN B 178 GLN B 238 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 114 GLN ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.4770 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= 0.165 Angle : 0.459 7.924 14119 Z= 0.247 Chirality : 0.034 0.129 1778 Planarity : 0.003 0.029 1722 Dihedral : 3.534 13.766 1421 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Rotamer Outliers : 1.79 % 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: 5.16 (0.20), residues: 1288 helix: 3.95 (0.13), residues: 1092 sheet: None (None), residues: 0 loop : -0.35 (0.30), residues: 196 *********************** 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 308 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 289 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 13 residues processed: 301 average time/residue: 0.2104 time to fit residues: 88.3460 Evaluate side-chains 293 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 280 time to evaluate : 1.185 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 4 residues processed: 13 average time/residue: 0.1343 time to fit residues: 4.4289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 53 optimal weight: 0.7980 chunk 109 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN B 9 GLN ** 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 178 GLN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.4894 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= 0.178 Angle : 0.471 7.487 14119 Z= 0.253 Chirality : 0.035 0.153 1778 Planarity : 0.004 0.030 1722 Dihedral : 3.530 15.739 1421 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer Outliers : 1.51 % 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: 5.01 (0.21), residues: 1288 helix: 3.87 (0.14), residues: 1092 sheet: None (None), residues: 0 loop : -0.50 (0.30), residues: 196 *********************** 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 305 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 289 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 12 residues processed: 292 average time/residue: 0.2324 time to fit residues: 94.0873 Evaluate side-chains 289 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 277 time to evaluate : 1.382 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 4 residues processed: 12 average time/residue: 0.1048 time to fit residues: 4.0934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 43 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 128 optimal weight: 0.6980 chunk 106 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 112 ASN B 178 GLN ** 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 238 ASN F 178 GLN ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.4998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 10423 Z= 0.185 Angle : 0.487 6.648 14119 Z= 0.262 Chirality : 0.035 0.157 1778 Planarity : 0.004 0.039 1722 Dihedral : 3.603 19.729 1421 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer Outliers : 1.23 % 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: 4.91 (0.21), residues: 1288 helix: 3.80 (0.14), residues: 1092 sheet: None (None), residues: 0 loop : -0.51 (0.30), residues: 196 *********************** 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 302 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 289 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 11 residues processed: 295 average time/residue: 0.2323 time to fit residues: 94.4812 Evaluate side-chains 285 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 274 time to evaluate : 1.231 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 4 residues processed: 11 average time/residue: 0.0947 time to fit residues: 3.8203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 124 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 108 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 128 optimal weight: 0.0670 chunk 80 optimal weight: 0.3980 chunk 78 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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 226 ASN B 238 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 178 GLN F 63 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: 0.8094 moved from start: 0.5293 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= 0.167 Angle : 0.482 6.373 14119 Z= 0.260 Chirality : 0.035 0.158 1778 Planarity : 0.004 0.041 1722 Dihedral : 3.555 20.661 1421 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer Outliers : 1.23 % 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: 4.84 (0.21), residues: 1288 helix: 3.75 (0.14), residues: 1092 sheet: None (None), residues: 0 loop : -0.56 (0.31), residues: 196 *********************** 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 299 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 286 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 290 average time/residue: 0.2259 time to fit residues: 91.7495 Evaluate side-chains 279 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 270 time to evaluate : 1.312 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 4 residues processed: 9 average time/residue: 0.0994 time to fit residues: 3.3309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 79 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 76 optimal weight: 0.0000 chunk 38 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 63 optimal weight: 0.0970 chunk 11 optimal weight: 1.9990 chunk 100 optimal weight: 0.0040 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 GLN C 178 GLN C 238 ASN ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 238 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** G 226 ASN G 238 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.5582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 10423 Z= 0.162 Angle : 0.514 14.988 14119 Z= 0.269 Chirality : 0.035 0.165 1778 Planarity : 0.004 0.045 1722 Dihedral : 3.535 20.913 1421 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer Outliers : 1.04 % 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: 4.92 (0.21), residues: 1288 helix: 3.83 (0.14), residues: 1078 sheet: None (None), residues: 0 loop : -0.37 (0.31), residues: 210 *********************** 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 309 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 298 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 9 residues processed: 301 average time/residue: 0.2109 time to fit residues: 90.2084 Evaluate side-chains 283 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 274 time to evaluate : 1.164 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 4 residues processed: 9 average time/residue: 0.1073 time to fit residues: 3.3652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 116 optimal weight: 0.6980 chunk 122 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 119 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 126 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 178 GLN E 178 GLN ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.5422 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= 0.197 Angle : 0.545 13.388 14119 Z= 0.281 Chirality : 0.036 0.158 1778 Planarity : 0.004 0.037 1722 Dihedral : 3.552 19.560 1421 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer Outliers : 0.94 % 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: 4.58 (0.21), residues: 1288 helix: 3.60 (0.14), residues: 1092 sheet: None (None), residues: 0 loop : -0.82 (0.31), residues: 196 *********************** 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 291 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 281 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 284 average time/residue: 0.2311 time to fit residues: 91.5058 Evaluate side-chains 274 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 267 time to evaluate : 1.404 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 7 average time/residue: 0.1043 time to fit residues: 3.1678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 121 optimal weight: 0.5980 chunk 105 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 81 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 112 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN B 178 GLN C 178 GLN ** C 226 ASN ** 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 227 GLN ** F 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.5491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 10423 Z= 0.189 Angle : 0.547 13.896 14119 Z= 0.285 Chirality : 0.036 0.145 1778 Planarity : 0.004 0.035 1722 Dihedral : 3.574 20.713 1421 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer Outliers : 1.23 % 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: 4.53 (0.21), residues: 1288 helix: 3.58 (0.14), residues: 1092 sheet: None (None), residues: 0 loop : -0.91 (0.31), residues: 196 ********************** 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 293 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 280 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 286 average time/residue: 0.2337 time to fit residues: 92.8156 Evaluate side-chains 281 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 274 time to evaluate : 1.334 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 7 average time/residue: 0.1235 time to fit residues: 3.7254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 32 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 105 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 6 optimal weight: 0.0060 overall best weight: 0.6996 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 ASN ** 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 178 GLN E 227 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.115038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.093652 restraints weight = 18358.436| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.66 r_work: 0.3043 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.5519 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= 0.185 Angle : 0.546 13.659 14119 Z= 0.284 Chirality : 0.036 0.143 1778 Planarity : 0.004 0.034 1722 Dihedral : 3.563 20.155 1421 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer Outliers : 1.23 % 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: 4.51 (0.21), residues: 1288 helix: 3.57 (0.14), residues: 1092 sheet: None (None), residues: 0 loop : -0.97 (0.32), residues: 196 =============================================================================== Job complete usr+sys time: 2384.17 seconds wall clock time: 43 minutes 42.71 seconds (2622.71 seconds total)