Starting phenix.real_space_refine (version: 1.21rc1) on Sun Oct 8 16:57:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wxl_21961/10_2023/6wxl_21961.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wxl_21961/10_2023/6wxl_21961.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wxl_21961/10_2023/6wxl_21961.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wxl_21961/10_2023/6wxl_21961.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wxl_21961/10_2023/6wxl_21961.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wxl_21961/10_2023/6wxl_21961.pdb" } resolution = 2.76 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= 0.006 sd= 0.220 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 102 5.16 5 C 10593 2.51 5 N 2970 2.21 5 O 3351 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 231": "OD1" <-> "OD2" Residue "A TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 19": "OD1" <-> "OD2" Residue "B GLU 57": "OE1" <-> "OE2" Residue "B ASP 67": "OD1" <-> "OD2" Residue "B GLU 69": "OE1" <-> "OE2" Residue "B GLU 90": "OE1" <-> "OE2" Residue "B ASP 112": "OD1" <-> "OD2" Residue "B ASP 116": "OD1" <-> "OD2" Residue "B GLU 139": "OE1" <-> "OE2" Residue "B PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 146": "OD1" <-> "OD2" Residue "B ASP 158": "OD1" <-> "OD2" Residue "B GLU 165": "OE1" <-> "OE2" Residue "L ASP 1": "OD1" <-> "OD2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 10": "OE1" <-> "OE2" Residue "H TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 85": "OD1" <-> "OD2" Residue "H TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 19": "OD1" <-> "OD2" Residue "D GLU 57": "OE1" <-> "OE2" Residue "D ASP 67": "OD1" <-> "OD2" Residue "D GLU 69": "OE1" <-> "OE2" Residue "D GLU 90": "OE1" <-> "OE2" Residue "D ASP 112": "OD1" <-> "OD2" Residue "D ASP 116": "OD1" <-> "OD2" Residue "D GLU 139": "OE1" <-> "OE2" Residue "D PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 146": "OD1" <-> "OD2" Residue "D ASP 158": "OD1" <-> "OD2" Residue "D GLU 165": "OE1" <-> "OE2" Residue "E ASP 1": "OD1" <-> "OD2" Residue "E TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 10": "OE1" <-> "OE2" Residue "F TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 85": "OD1" <-> "OD2" Residue "F TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 19": "OD1" <-> "OD2" Residue "I GLU 57": "OE1" <-> "OE2" Residue "I ASP 67": "OD1" <-> "OD2" Residue "I GLU 69": "OE1" <-> "OE2" Residue "I GLU 90": "OE1" <-> "OE2" Residue "I ASP 112": "OD1" <-> "OD2" Residue "I ASP 116": "OD1" <-> "OD2" Residue "I GLU 139": "OE1" <-> "OE2" Residue "I PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 146": "OD1" <-> "OD2" Residue "I ASP 158": "OD1" <-> "OD2" Residue "I GLU 165": "OE1" <-> "OE2" Residue "J ASP 1": "OD1" <-> "OD2" Residue "J TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 10": "OE1" <-> "OE2" Residue "K TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 85": "OD1" <-> "OD2" Residue "K TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 231": "OD1" <-> "OD2" Residue "C TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 231": "OD1" <-> "OD2" Residue "G TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 17016 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2415 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 13, 'TRANS': 302} Chain: "B" Number of atoms: 1380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1380 Classifications: {'peptide': 170} Link IDs: {'TRANS': 169} Chain: "L" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 863 Classifications: {'peptide': 114} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 105} Chain: "H" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 972 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "D" Number of atoms: 1380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1380 Classifications: {'peptide': 170} Link IDs: {'TRANS': 169} Chain: "E" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 863 Classifications: {'peptide': 114} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 105} Chain: "F" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 972 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "I" Number of atoms: 1380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1380 Classifications: {'peptide': 170} Link IDs: {'TRANS': 169} Chain: "J" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 863 Classifications: {'peptide': 114} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 105} Chain: "K" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 972 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "C" Number of atoms: 2415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2415 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 13, 'TRANS': 302} Chain: "G" Number of atoms: 2415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2415 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 13, 'TRANS': 302} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 9.21, per 1000 atoms: 0.54 Number of scatterers: 17016 At special positions: 0 Unit cell: (129.96, 133.209, 148.371, 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 102 16.00 O 3351 8.00 N 2970 7.00 C 10593 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS B 137 " distance=2.07 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.04 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 137 " - pdb=" SG CYS C 14 " distance=2.07 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 137 " - pdb=" SG CYS G 14 " distance=2.07 Simple disulfide: pdb=" SG CYS I 144 " - pdb=" SG CYS I 148 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.04 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS G 52 " - pdb=" SG CYS G 277 " distance=2.04 Simple disulfide: pdb=" SG CYS G 64 " - pdb=" SG CYS G 76 " distance=2.03 Simple disulfide: pdb=" SG CYS G 97 " - pdb=" SG CYS G 139 " distance=2.03 Simple disulfide: pdb=" SG CYS G 281 " - pdb=" SG CYS G 305 " distance=2.03 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 Links applied NAG-ASN " NAG A 401 " - " ASN A 38 " " NAG B 301 " - " ASN B 82 " " NAG B 302 " - " ASN B 154 " " NAG C 401 " - " ASN C 38 " " NAG D 301 " - " ASN D 82 " " NAG D 302 " - " ASN D 154 " " NAG G 401 " - " ASN G 38 " " NAG I 301 " - " ASN I 82 " " NAG I 302 " - " ASN I 154 " Time building additional restraints: 6.22 Conformation dependent library (CDL) restraints added in 2.2 seconds 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3918 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 51 sheets defined 18.6% alpha, 30.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.03 Creating SS restraints... Processing helix chain 'A' and resid 67 through 72 removed outlier: 3.840A pdb=" N THR A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 77 removed outlier: 3.837A pdb=" N ASP A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 113 Processing helix chain 'A' and resid 187 through 196 removed outlier: 3.623A pdb=" N THR A 192 " --> pdb=" O THR A 188 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS A 193 " --> pdb=" O ALA A 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 54 removed outlier: 3.700A pdb=" N GLN B 47 " --> pdb=" O SER B 43 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE B 48 " --> pdb=" O ALA B 44 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY B 50 " --> pdb=" O ASP B 46 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG B 54 " --> pdb=" O GLY B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 126 removed outlier: 3.689A pdb=" N ASN B 82 " --> pdb=" O GLY B 78 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN B 105 " --> pdb=" O ALA B 101 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N MET B 115 " --> pdb=" O ALA B 111 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP B 116 " --> pdb=" O ASP B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 154 removed outlier: 3.576A pdb=" N ARG B 153 " --> pdb=" O MET B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 161 removed outlier: 3.507A pdb=" N LYS B 161 " --> pdb=" O ASP B 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 158 through 161' Processing helix chain 'B' and resid 162 through 172 removed outlier: 3.830A pdb=" N GLN B 168 " --> pdb=" O GLU B 164 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN B 169 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG B 170 " --> pdb=" O ALA B 166 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN B 172 " --> pdb=" O GLN B 168 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 100B through 100G Processing helix chain 'D' and resid 38 through 54 removed outlier: 3.700A pdb=" N GLN D 47 " --> pdb=" O SER D 43 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE D 48 " --> pdb=" O ALA D 44 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY D 50 " --> pdb=" O ASP D 46 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG D 54 " --> pdb=" O GLY D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 126 removed outlier: 3.689A pdb=" N ASN D 82 " --> pdb=" O GLY D 78 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN D 105 " --> pdb=" O ALA D 101 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N MET D 115 " --> pdb=" O ALA D 111 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP D 116 " --> pdb=" O ASP D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 154 removed outlier: 3.577A pdb=" N ARG D 153 " --> pdb=" O MET D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 161 removed outlier: 3.508A pdb=" N LYS D 161 " --> pdb=" O ASP D 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 158 through 161' Processing helix chain 'D' and resid 162 through 172 removed outlier: 3.830A pdb=" N GLN D 168 " --> pdb=" O GLU D 164 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN D 169 " --> pdb=" O GLU D 165 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG D 170 " --> pdb=" O ALA D 166 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN D 172 " --> pdb=" O GLN D 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'F' and resid 100B through 100G Processing helix chain 'I' and resid 38 through 54 removed outlier: 3.700A pdb=" N GLN I 47 " --> pdb=" O SER I 43 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE I 48 " --> pdb=" O ALA I 44 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY I 50 " --> pdb=" O ASP I 46 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG I 54 " --> pdb=" O GLY I 50 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 126 removed outlier: 3.689A pdb=" N ASN I 82 " --> pdb=" O GLY I 78 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN I 105 " --> pdb=" O ALA I 101 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N MET I 115 " --> pdb=" O ALA I 111 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP I 116 " --> pdb=" O ASP I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 154 removed outlier: 3.578A pdb=" N ARG I 153 " --> pdb=" O MET I 149 " (cutoff:3.500A) Processing helix chain 'I' and resid 158 through 161 removed outlier: 3.508A pdb=" N LYS I 161 " --> pdb=" O ASP I 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 158 through 161' Processing helix chain 'I' and resid 162 through 172 removed outlier: 3.830A pdb=" N GLN I 168 " --> pdb=" O GLU I 164 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN I 169 " --> pdb=" O GLU I 165 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG I 170 " --> pdb=" O ALA I 166 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN I 172 " --> pdb=" O GLN I 168 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'K' and resid 100B through 100G Processing helix chain 'C' and resid 67 through 72 removed outlier: 3.840A pdb=" N THR C 71 " --> pdb=" O LEU C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 77 removed outlier: 3.837A pdb=" N ASP C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 113 Processing helix chain 'C' and resid 187 through 196 removed outlier: 3.622A pdb=" N THR C 192 " --> pdb=" O THR C 188 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS C 193 " --> pdb=" O ALA C 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 72 removed outlier: 3.839A pdb=" N THR G 71 " --> pdb=" O LEU G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 77 removed outlier: 3.838A pdb=" N ASP G 77 " --> pdb=" O PRO G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 113 Processing helix chain 'G' and resid 187 through 196 removed outlier: 3.621A pdb=" N THR G 192 " --> pdb=" O THR G 188 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS G 193 " --> pdb=" O ALA G 189 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 31 through 37 removed outlier: 3.501A pdb=" N GLY B 33 " --> pdb=" O HIS B 26 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N TYR B 22 " --> pdb=" O ASP B 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 52 removed outlier: 5.655A pdb=" N ILE A 51 " --> pdb=" O ASP A 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 58 through 60 removed outlier: 6.847A pdb=" N VAL A 59 " --> pdb=" O ILE A 88 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 100 through 102 removed outlier: 6.778A pdb=" N LYS A 101 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N TRP A 234 " --> pdb=" O LYS A 101 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N VAL A 179 " --> pdb=" O ARG A 256 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ARG A 256 " --> pdb=" O VAL A 179 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 100 through 102 removed outlier: 6.778A pdb=" N LYS A 101 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N TRP A 234 " --> pdb=" O LYS A 101 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N VAL A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 136 through 140 removed outlier: 3.582A pdb=" N SER A 146 " --> pdb=" O THR A 136 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB2, first strand: chain 'A' and resid 286 through 287 removed outlier: 3.511A pdb=" N GLY A 286 " --> pdb=" O TYR A 283 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.721A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.514A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.605A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 4 through 6 removed outlier: 3.557A pdb=" N VAL H 5 " --> pdb=" O LYS H 23 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.638A pdb=" N LEU H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG H 50 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AB9, first strand: chain 'D' and resid 31 through 37 removed outlier: 3.501A pdb=" N GLY D 33 " --> pdb=" O HIS D 26 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N TYR D 22 " --> pdb=" O ASP D 37 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 5 through 7 removed outlier: 3.720A pdb=" N ASP E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.513A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 10 through 13 removed outlier: 3.605A pdb=" N THR E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 4 through 6 removed outlier: 3.555A pdb=" N VAL F 5 " --> pdb=" O LYS F 23 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.637A pdb=" N LEU F 34 " --> pdb=" O ARG F 50 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG F 50 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 10 through 12 Processing sheet with id=AC7, first strand: chain 'I' and resid 31 through 37 removed outlier: 3.501A pdb=" N GLY I 33 " --> pdb=" O HIS I 26 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N TYR I 22 " --> pdb=" O ASP I 37 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 5 through 7 removed outlier: 3.719A pdb=" N ASP J 70 " --> pdb=" O SER J 67 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.513A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.605A pdb=" N THR J 97 " --> pdb=" O GLN J 90 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 4 through 6 removed outlier: 3.557A pdb=" N VAL K 5 " --> pdb=" O LYS K 23 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.638A pdb=" N LEU K 34 " --> pdb=" O ARG K 50 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG K 50 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N TRP K 36 " --> pdb=" O MET K 48 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 10 through 12 Processing sheet with id=AD5, first strand: chain 'C' and resid 24 through 26 Processing sheet with id=AD6, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AD7, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AD8, first strand: chain 'C' and resid 51 through 52 removed outlier: 5.655A pdb=" N ILE C 51 " --> pdb=" O ASP C 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 58 through 60 removed outlier: 6.848A pdb=" N VAL C 59 " --> pdb=" O ILE C 88 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.779A pdb=" N LYS C 101 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N TRP C 234 " --> pdb=" O LYS C 101 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL C 179 " --> pdb=" O ARG C 256 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ARG C 256 " --> pdb=" O VAL C 179 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.779A pdb=" N LYS C 101 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N TRP C 234 " --> pdb=" O LYS C 101 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N VAL C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 136 through 140 removed outlier: 3.582A pdb=" N SER C 146 " --> pdb=" O THR C 136 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AE5, first strand: chain 'C' and resid 286 through 287 removed outlier: 3.512A pdb=" N GLY C 286 " --> pdb=" O TYR C 283 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 24 through 26 Processing sheet with id=AE7, first strand: chain 'G' and resid 39 through 41 Processing sheet with id=AE8, first strand: chain 'G' and resid 43 through 44 Processing sheet with id=AE9, first strand: chain 'G' and resid 51 through 52 removed outlier: 5.655A pdb=" N ILE G 51 " --> pdb=" O ASP G 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'G' and resid 58 through 60 removed outlier: 6.850A pdb=" N VAL G 59 " --> pdb=" O ILE G 88 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 100 through 102 removed outlier: 6.780A pdb=" N LYS G 101 " --> pdb=" O PHE G 232 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N TRP G 234 " --> pdb=" O LYS G 101 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N VAL G 179 " --> pdb=" O ARG G 256 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ARG G 256 " --> pdb=" O VAL G 179 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 100 through 102 removed outlier: 6.780A pdb=" N LYS G 101 " --> pdb=" O PHE G 232 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N TRP G 234 " --> pdb=" O LYS G 101 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N VAL G 179 " --> pdb=" O PRO G 254 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 136 through 140 removed outlier: 3.581A pdb=" N SER G 146 " --> pdb=" O THR G 136 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 164 through 169 Processing sheet with id=AF6, first strand: chain 'G' and resid 286 through 287 removed outlier: 3.511A pdb=" N GLY G 286 " --> pdb=" O TYR G 283 " (cutoff:3.500A) 663 hydrogen bonds defined for protein. 1728 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.98 Time building geometry restraints manager: 6.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 5683 1.35 - 1.47: 4309 1.47 - 1.60: 7204 1.60 - 1.72: 0 1.72 - 1.85: 156 Bond restraints: 17352 Sorted by residual: bond pdb=" C1 NAG I 301 " pdb=" O5 NAG I 301 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.60e+00 bond pdb=" C1 NAG B 301 " pdb=" O5 NAG B 301 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.39e+00 bond pdb=" C1 NAG D 301 " pdb=" O5 NAG D 301 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.33e+00 bond pdb=" C1 NAG C 401 " pdb=" O5 NAG C 401 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.09e+00 bond pdb=" C1 NAG D 302 " pdb=" O5 NAG D 302 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.06e+00 ... (remaining 17347 not shown) Histogram of bond angle deviations from ideal: 99.80 - 106.66: 432 106.66 - 113.52: 9341 113.52 - 120.39: 6343 120.39 - 127.25: 7186 127.25 - 134.11: 155 Bond angle restraints: 23457 Sorted by residual: angle pdb=" N THR J 94 " pdb=" CA THR J 94 " pdb=" C THR J 94 " ideal model delta sigma weight residual 109.81 118.18 -8.37 2.21e+00 2.05e-01 1.43e+01 angle pdb=" N THR L 94 " pdb=" CA THR L 94 " pdb=" C THR L 94 " ideal model delta sigma weight residual 109.81 118.17 -8.36 2.21e+00 2.05e-01 1.43e+01 angle pdb=" N THR E 94 " pdb=" CA THR E 94 " pdb=" C THR E 94 " ideal model delta sigma weight residual 109.81 118.15 -8.34 2.21e+00 2.05e-01 1.42e+01 angle pdb=" CA THR E 94 " pdb=" C THR E 94 " pdb=" N PRO E 95 " ideal model delta sigma weight residual 118.44 123.84 -5.40 1.59e+00 3.96e-01 1.15e+01 angle pdb=" CA THR L 94 " pdb=" C THR L 94 " pdb=" N PRO L 95 " ideal model delta sigma weight residual 118.44 123.73 -5.29 1.59e+00 3.96e-01 1.11e+01 ... (remaining 23452 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.73: 9223 16.73 - 33.47: 822 33.47 - 50.20: 185 50.20 - 66.94: 39 66.94 - 83.67: 30 Dihedral angle restraints: 10299 sinusoidal: 4122 harmonic: 6177 Sorted by residual: dihedral pdb=" CB CYS A 52 " pdb=" SG CYS A 52 " pdb=" SG CYS A 277 " pdb=" CB CYS A 277 " ideal model delta sinusoidal sigma weight residual -86.00 -10.81 -75.19 1 1.00e+01 1.00e-02 7.15e+01 dihedral pdb=" CB CYS C 52 " pdb=" SG CYS C 52 " pdb=" SG CYS C 277 " pdb=" CB CYS C 277 " ideal model delta sinusoidal sigma weight residual -86.00 -10.83 -75.17 1 1.00e+01 1.00e-02 7.14e+01 dihedral pdb=" CB CYS G 52 " pdb=" SG CYS G 52 " pdb=" SG CYS G 277 " pdb=" CB CYS G 277 " ideal model delta sinusoidal sigma weight residual -86.00 -10.85 -75.15 1 1.00e+01 1.00e-02 7.14e+01 ... (remaining 10296 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2039 0.060 - 0.119: 456 0.119 - 0.179: 55 0.179 - 0.239: 0 0.239 - 0.298: 6 Chirality restraints: 2556 Sorted by residual: chirality pdb=" CA THR L 94 " pdb=" N THR L 94 " pdb=" C THR L 94 " pdb=" CB THR L 94 " both_signs ideal model delta sigma weight residual False 2.53 2.23 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CA THR J 94 " pdb=" N THR J 94 " pdb=" C THR J 94 " pdb=" CB THR J 94 " both_signs ideal model delta sigma weight residual False 2.53 2.23 0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CA THR E 94 " pdb=" N THR E 94 " pdb=" C THR E 94 " pdb=" CB THR E 94 " both_signs ideal model delta sigma weight residual False 2.53 2.23 0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 2553 not shown) Planarity restraints: 3069 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO E 95 " -0.049 5.00e-02 4.00e+02 7.42e-02 8.80e+00 pdb=" N PRO E 95A" 0.128 5.00e-02 4.00e+02 pdb=" CA PRO E 95A" -0.037 5.00e-02 4.00e+02 pdb=" CD PRO E 95A" -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO L 95 " -0.049 5.00e-02 4.00e+02 7.38e-02 8.71e+00 pdb=" N PRO L 95A" 0.128 5.00e-02 4.00e+02 pdb=" CA PRO L 95A" -0.037 5.00e-02 4.00e+02 pdb=" CD PRO L 95A" -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO J 95 " -0.049 5.00e-02 4.00e+02 7.37e-02 8.70e+00 pdb=" N PRO J 95A" 0.128 5.00e-02 4.00e+02 pdb=" CA PRO J 95A" -0.037 5.00e-02 4.00e+02 pdb=" CD PRO J 95A" -0.042 5.00e-02 4.00e+02 ... (remaining 3066 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 4531 2.80 - 3.33: 12971 3.33 - 3.85: 28159 3.85 - 4.38: 33460 4.38 - 4.90: 58587 Nonbonded interactions: 137708 Sorted by model distance: nonbonded pdb=" OH TYR H 27 " pdb=" O LYS H 95 " model vdw 2.281 2.440 nonbonded pdb=" OH TYR F 27 " pdb=" O LYS F 95 " model vdw 2.281 2.440 nonbonded pdb=" OH TYR K 27 " pdb=" O LYS K 95 " model vdw 2.283 2.440 nonbonded pdb=" OH TYR K 100D" pdb=" OD2 ASP K 101 " model vdw 2.307 2.440 nonbonded pdb=" OH TYR F 100D" pdb=" OD2 ASP F 101 " model vdw 2.308 2.440 ... (remaining 137703 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 'C' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'K' } 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: 3.170 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: 14.860 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 45.280 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 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 : 0.005 0.050 17352 Z= 0.311 Angle : 0.708 9.995 23457 Z= 0.394 Chirality : 0.050 0.298 2556 Planarity : 0.006 0.074 3060 Dihedral : 14.131 83.674 6309 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.16 % Allowed : 3.99 % Favored : 95.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -3.74 (0.14), residues: 2151 helix: -4.18 (0.13), residues: 324 sheet: -1.45 (0.19), residues: 624 loop : -2.61 (0.13), residues: 1203 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 316 time to evaluate : 1.997 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 318 average time/residue: 1.5510 time to fit residues: 539.5968 Evaluate side-chains 214 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 2.050 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 179 optimal weight: 0.0970 chunk 161 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 108 optimal weight: 4.9990 chunk 86 optimal weight: 7.9990 chunk 166 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 193 optimal weight: 8.9990 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN A 211 GLN A 224 ASN B 60 ASN H 6 GLN H 35 HIS H 78 HIS D 47 GLN D 60 ASN D 155 ASN E 27 HIS F 6 GLN F 35 HIS F 78 HIS ** I 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 27 HIS K 3 GLN K 6 GLN K 35 HIS K 78 HIS C 208 ASN C 224 ASN G 208 ASN G 224 ASN G 240 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 17352 Z= 0.285 Angle : 0.595 11.026 23457 Z= 0.316 Chirality : 0.045 0.201 2556 Planarity : 0.005 0.069 3060 Dihedral : 4.698 21.012 2376 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.62 % Allowed : 11.48 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -2.68 (0.15), residues: 2151 helix: -1.29 (0.25), residues: 336 sheet: -1.48 (0.18), residues: 693 loop : -2.11 (0.14), residues: 1122 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 229 time to evaluate : 2.071 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 15 residues processed: 256 average time/residue: 1.4282 time to fit residues: 404.6866 Evaluate side-chains 214 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 199 time to evaluate : 1.970 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 9 residues processed: 6 average time/residue: 0.5364 time to fit residues: 6.7745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 107 optimal weight: 8.9990 chunk 60 optimal weight: 4.9990 chunk 160 optimal weight: 0.8980 chunk 131 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 193 optimal weight: 7.9990 chunk 209 optimal weight: 4.9990 chunk 172 optimal weight: 0.0470 chunk 192 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 155 optimal weight: 0.3980 overall best weight: 1.4682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN B 47 GLN B 60 ASN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 45 GLN H 6 GLN D 60 ASN D 155 ASN F 6 GLN I 27 GLN ** I 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN K 6 GLN C 208 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17352 Z= 0.264 Angle : 0.555 7.850 23457 Z= 0.293 Chirality : 0.044 0.203 2556 Planarity : 0.004 0.058 3060 Dihedral : 4.492 20.947 2376 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.17 % Allowed : 13.55 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -2.01 (0.16), residues: 2151 helix: -0.01 (0.28), residues: 336 sheet: -1.16 (0.19), residues: 681 loop : -1.86 (0.15), residues: 1134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 204 time to evaluate : 2.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 21 residues processed: 240 average time/residue: 1.2862 time to fit residues: 344.3477 Evaluate side-chains 210 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 189 time to evaluate : 1.838 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 14 residues processed: 7 average time/residue: 0.8858 time to fit residues: 10.0394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 191 optimal weight: 4.9990 chunk 145 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 130 optimal weight: 6.9990 chunk 194 optimal weight: 6.9990 chunk 205 optimal weight: 9.9990 chunk 101 optimal weight: 2.9990 chunk 184 optimal weight: 3.9990 chunk 55 optimal weight: 0.3980 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN A 224 ASN B 60 ASN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 ASN ** I 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN C 208 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 17352 Z= 0.407 Angle : 0.638 9.142 23457 Z= 0.334 Chirality : 0.048 0.241 2556 Planarity : 0.005 0.061 3060 Dihedral : 4.750 21.482 2376 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.72 % Allowed : 14.21 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.89 (0.17), residues: 2151 helix: 0.22 (0.29), residues: 327 sheet: -1.06 (0.20), residues: 693 loop : -1.83 (0.15), residues: 1131 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 197 time to evaluate : 1.924 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 35 residues processed: 247 average time/residue: 1.3682 time to fit residues: 375.8672 Evaluate side-chains 221 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 186 time to evaluate : 2.175 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 26 residues processed: 10 average time/residue: 0.8225 time to fit residues: 12.2873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 171 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 2 optimal weight: 0.2980 chunk 153 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 175 optimal weight: 5.9990 chunk 142 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 105 optimal weight: 0.0470 chunk 184 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN A 224 ASN B 60 ASN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 208 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 17352 Z= 0.144 Angle : 0.480 5.862 23457 Z= 0.256 Chirality : 0.042 0.167 2556 Planarity : 0.004 0.051 3060 Dihedral : 4.188 20.457 2376 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.46 % Allowed : 16.23 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.37 (0.17), residues: 2151 helix: 0.99 (0.29), residues: 336 sheet: -0.75 (0.20), residues: 711 loop : -1.62 (0.16), residues: 1104 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 199 time to evaluate : 2.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 26 residues processed: 232 average time/residue: 1.3463 time to fit residues: 347.7006 Evaluate side-chains 212 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 186 time to evaluate : 1.873 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 20 residues processed: 7 average time/residue: 0.3717 time to fit residues: 6.2503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 69 optimal weight: 3.9990 chunk 185 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 chunk 206 optimal weight: 6.9990 chunk 171 optimal weight: 0.4980 chunk 95 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 108 optimal weight: 0.7980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN B 60 ASN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 ASN ** I 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17352 Z= 0.232 Angle : 0.542 9.278 23457 Z= 0.283 Chirality : 0.044 0.190 2556 Planarity : 0.004 0.052 3060 Dihedral : 4.291 20.284 2376 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.06 % Allowed : 16.56 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.31 (0.17), residues: 2151 helix: 1.02 (0.30), residues: 327 sheet: -0.69 (0.20), residues: 711 loop : -1.57 (0.16), residues: 1113 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 191 time to evaluate : 1.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 34 residues processed: 235 average time/residue: 1.2620 time to fit residues: 331.6632 Evaluate side-chains 222 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 188 time to evaluate : 1.983 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 27 residues processed: 8 average time/residue: 0.3540 time to fit residues: 6.8860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 198 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 117 optimal weight: 8.9990 chunk 150 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 chunk 173 optimal weight: 0.8980 chunk 115 optimal weight: 0.5980 chunk 205 optimal weight: 0.9990 chunk 128 optimal weight: 7.9990 chunk 125 optimal weight: 2.9990 chunk 94 optimal weight: 0.0050 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 224 ASN B 60 ASN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 17352 Z= 0.163 Angle : 0.488 6.239 23457 Z= 0.257 Chirality : 0.042 0.173 2556 Planarity : 0.004 0.049 3060 Dihedral : 4.065 17.994 2376 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.30 % Allowed : 17.87 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.09 (0.17), residues: 2151 helix: 1.40 (0.30), residues: 327 sheet: -0.55 (0.20), residues: 711 loop : -1.50 (0.16), residues: 1113 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 195 time to evaluate : 2.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 26 residues processed: 226 average time/residue: 1.3293 time to fit residues: 335.0965 Evaluate side-chains 211 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 185 time to evaluate : 2.016 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 21 residues processed: 6 average time/residue: 0.4584 time to fit residues: 6.4008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 127 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 161 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN B 60 ASN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 HIS ** I 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 ASN K 43 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.073 17352 Z= 0.508 Angle : 0.694 11.314 23457 Z= 0.359 Chirality : 0.051 0.264 2556 Planarity : 0.005 0.062 3060 Dihedral : 4.736 25.079 2376 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.17 % Allowed : 17.43 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.50 (0.17), residues: 2151 helix: 0.60 (0.29), residues: 327 sheet: -0.76 (0.20), residues: 711 loop : -1.64 (0.16), residues: 1113 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 189 time to evaluate : 1.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 36 residues processed: 231 average time/residue: 1.3383 time to fit residues: 343.9522 Evaluate side-chains 223 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 187 time to evaluate : 1.875 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 26 residues processed: 11 average time/residue: 0.5078 time to fit residues: 9.5781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 186 optimal weight: 5.9990 chunk 196 optimal weight: 3.9990 chunk 179 optimal weight: 0.7980 chunk 191 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 150 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 172 optimal weight: 4.9990 chunk 180 optimal weight: 0.9980 chunk 190 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 208 ASN A 224 ASN B 60 ASN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 17352 Z= 0.196 Angle : 0.527 9.577 23457 Z= 0.277 Chirality : 0.043 0.182 2556 Planarity : 0.004 0.060 3060 Dihedral : 4.312 24.272 2376 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.91 % Allowed : 18.74 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.21 (0.17), residues: 2151 helix: 1.15 (0.30), residues: 327 sheet: -0.62 (0.20), residues: 711 loop : -1.53 (0.16), residues: 1113 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 194 time to evaluate : 2.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 28 residues processed: 223 average time/residue: 1.3453 time to fit residues: 335.1868 Evaluate side-chains 212 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 184 time to evaluate : 2.105 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 25 residues processed: 4 average time/residue: 0.1912 time to fit residues: 4.1109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 125 optimal weight: 0.4980 chunk 202 optimal weight: 0.9990 chunk 123 optimal weight: 4.9990 chunk 95 optimal weight: 0.0670 chunk 140 optimal weight: 8.9990 chunk 212 optimal weight: 3.9990 chunk 195 optimal weight: 8.9990 chunk 168 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.5124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN B 60 ASN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 17352 Z= 0.270 Angle : 0.563 9.711 23457 Z= 0.293 Chirality : 0.045 0.203 2556 Planarity : 0.004 0.066 3060 Dihedral : 4.388 23.797 2376 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.69 % Allowed : 19.34 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.25 (0.17), residues: 2151 helix: 1.08 (0.29), residues: 327 sheet: -0.65 (0.20), residues: 711 loop : -1.54 (0.16), residues: 1113 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 188 time to evaluate : 2.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 30 residues processed: 214 average time/residue: 1.3777 time to fit residues: 329.2398 Evaluate side-chains 215 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 185 time to evaluate : 2.252 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 27 residues processed: 5 average time/residue: 0.4137 time to fit residues: 5.4994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 134 optimal weight: 0.0040 chunk 180 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 155 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 169 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 173 optimal weight: 4.9990 chunk 21 optimal weight: 0.4980 chunk 31 optimal weight: 4.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN B 60 ASN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.113533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.095536 restraints weight = 23241.045| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.66 r_work: 0.3018 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 17352 Z= 0.150 Angle : 0.484 7.911 23457 Z= 0.255 Chirality : 0.042 0.172 2556 Planarity : 0.004 0.063 3060 Dihedral : 4.036 22.214 2376 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.53 % Allowed : 19.62 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.91 (0.18), residues: 2151 helix: 1.63 (0.30), residues: 327 sheet: -0.49 (0.20), residues: 693 loop : -1.35 (0.16), residues: 1131 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6426.29 seconds wall clock time: 114 minutes 55.69 seconds (6895.69 seconds total)