Starting phenix.real_space_refine (version: dev) on Mon Jun 6 02:37:31 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpp_14860/06_2022/7zpp_14860.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpp_14860/06_2022/7zpp_14860.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpp_14860/06_2022/7zpp_14860.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpp_14860/06_2022/7zpp_14860.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpp_14860/06_2022/7zpp_14860.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpp_14860/06_2022/7zpp_14860.pdb" } resolution = 4.5 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= 0.001 sd= 0.026 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4617/modules/chem_data/mon_lib" Total number of atoms: 33171 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 2201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2201 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 14, 'TRANS': 260} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 2075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2075 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 10, 'TRANS': 244, 'PCIS': 1} Chain breaks: 1 Chain: "C" Number of atoms: 2123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2123 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 249, 'PCIS': 1} Chain breaks: 1 Chain: "D" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1729 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 11, 'TRANS': 204} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "E" Number of atoms: 2090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2090 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 246, 'PCIS': 1} Chain breaks: 1 Chain: "F" Number of atoms: 2148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2148 Classifications: {'peptide': 266} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 252, 'PCIS': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 1657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1657 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 8, 'TRANS': 196} Chain breaks: 1 Chain: "H" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1761 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 10, 'TRANS': 205, 'PCIS': 1} Chain: "I" Number of atoms: 2201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2201 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 14, 'TRANS': 260} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "J" Number of atoms: 2075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2075 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 10, 'TRANS': 244, 'PCIS': 1} Chain breaks: 1 Chain: "K" Number of atoms: 2123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2123 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 249, 'PCIS': 1} Chain breaks: 1 Chain: "L" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1729 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 11, 'TRANS': 204} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "M" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2076 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 9, 'TRANS': 245, 'PCIS': 1} Chain breaks: 1 Chain: "N" Number of atoms: 2131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2131 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 250, 'PCIS': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "O" Number of atoms: 1657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1657 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 8, 'TRANS': 196} Chain breaks: 1 Chain: "P" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1761 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 10, 'TRANS': 205, 'PCIS': 1} Chain: "Q" Number of atoms: 428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 428 Classifications: {'DNA': 21} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 20} Chain: "R" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 389 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "S" Number of atoms: 428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 428 Classifications: {'DNA': 21} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 20} Chain: "T" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 389 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Time building chain proxies: 18.18, per 1000 atoms: 0.55 Number of scatterers: 33171 At special positions: 0 Unit cell: (161.59, 210.21, 92.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 122 16.00 P 78 15.00 O 6288 8.00 N 5806 7.00 C 20877 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: 14.48 Conformation dependent library (CDL) restraints added in 4.5 seconds 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7254 Finding SS restraints... Secondary structure from input PDB file: 161 helices and 62 sheets defined 52.2% alpha, 18.3% beta 20 base pairs and 62 stacking pairs defined. Time for finding SS restraints: 10.04 Creating SS restraints... Processing helix chain 'A' and resid 4 through 16 Processing helix chain 'A' and resid 18 through 27 removed outlier: 3.652A pdb=" N LEU A 22 " --> pdb=" O ASP A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 40 Processing helix chain 'A' and resid 41 through 47 Processing helix chain 'A' and resid 95 through 110 Processing helix chain 'A' and resid 120 through 125 Processing helix chain 'A' and resid 125 through 135 Processing helix chain 'A' and resid 146 through 149 Processing helix chain 'A' and resid 150 through 168 Processing helix chain 'A' and resid 169 through 171 No H-bonds generated for 'chain 'A' and resid 169 through 171' Processing helix chain 'A' and resid 173 through 187 Processing helix chain 'A' and resid 196 through 209 Processing helix chain 'A' and resid 209 through 216 removed outlier: 4.211A pdb=" N GLN A 213 " --> pdb=" O ARG A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'A' and resid 267 through 269 No H-bonds generated for 'chain 'A' and resid 267 through 269' Processing helix chain 'B' and resid 4 through 16 Processing helix chain 'B' and resid 18 through 27 Processing helix chain 'B' and resid 29 through 40 Processing helix chain 'B' and resid 95 through 110 Processing helix chain 'B' and resid 120 through 125 Processing helix chain 'B' and resid 125 through 136 Processing helix chain 'B' and resid 146 through 168 removed outlier: 3.714A pdb=" N LEU B 152 " --> pdb=" O GLN B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 171 No H-bonds generated for 'chain 'B' and resid 169 through 171' Processing helix chain 'B' and resid 173 through 187 Processing helix chain 'B' and resid 196 through 216 Processing helix chain 'C' and resid 3 through 16 removed outlier: 4.118A pdb=" N LEU C 7 " --> pdb=" O GLU C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 27 Processing helix chain 'C' and resid 29 through 40 Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 95 through 110 Processing helix chain 'C' and resid 120 through 125 Processing helix chain 'C' and resid 125 through 136 Processing helix chain 'C' and resid 146 through 168 removed outlier: 3.774A pdb=" N LEU C 152 " --> pdb=" O GLN C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 187 Processing helix chain 'C' and resid 196 through 219 removed outlier: 3.684A pdb=" N ILE C 210 " --> pdb=" O GLU C 206 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N LYS C 217 " --> pdb=" O GLN C 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 110 Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'D' and resid 125 through 135 Processing helix chain 'D' and resid 146 through 168 Processing helix chain 'D' and resid 173 through 187 Processing helix chain 'D' and resid 196 through 219 Processing helix chain 'E' and resid 1 through 3 No H-bonds generated for 'chain 'E' and resid 1 through 3' Processing helix chain 'E' and resid 4 through 16 Processing helix chain 'E' and resid 18 through 27 Processing helix chain 'E' and resid 29 through 40 Processing helix chain 'E' and resid 95 through 110 Processing helix chain 'E' and resid 120 through 125 Processing helix chain 'E' and resid 125 through 136 Processing helix chain 'E' and resid 146 through 168 Processing helix chain 'E' and resid 173 through 187 Processing helix chain 'E' and resid 196 through 219 Processing helix chain 'E' and resid 267 through 269 No H-bonds generated for 'chain 'E' and resid 267 through 269' Processing helix chain 'F' and resid 5 through 16 Processing helix chain 'F' and resid 18 through 27 Processing helix chain 'F' and resid 29 through 40 Processing helix chain 'F' and resid 40 through 46 removed outlier: 3.562A pdb=" N GLN F 44 " --> pdb=" O CYS F 40 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN F 46 " --> pdb=" O VAL F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 109 Processing helix chain 'F' and resid 120 through 125 Processing helix chain 'F' and resid 125 through 136 Processing helix chain 'F' and resid 146 through 168 Processing helix chain 'F' and resid 169 through 171 No H-bonds generated for 'chain 'F' and resid 169 through 171' Processing helix chain 'F' and resid 173 through 187 Processing helix chain 'F' and resid 196 through 218 Processing helix chain 'F' and resid 267 through 269 No H-bonds generated for 'chain 'F' and resid 267 through 269' Processing helix chain 'G' and resid 5 through 16 Processing helix chain 'G' and resid 18 through 27 Processing helix chain 'G' and resid 29 through 40 Processing helix chain 'G' and resid 40 through 46 Processing helix chain 'G' and resid 95 through 110 Processing helix chain 'G' and resid 120 through 125 Processing helix chain 'G' and resid 125 through 136 Processing helix chain 'G' and resid 146 through 168 removed outlier: 3.658A pdb=" N LEU G 152 " --> pdb=" O GLN G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 187 Processing helix chain 'G' and resid 196 through 219 removed outlier: 3.722A pdb=" N ILE G 210 " --> pdb=" O GLU G 206 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN G 211 " --> pdb=" O GLN G 207 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER G 214 " --> pdb=" O ILE G 210 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER G 216 " --> pdb=" O GLN G 212 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N LYS G 217 " --> pdb=" O GLN G 213 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 110 Processing helix chain 'H' and resid 120 through 125 Processing helix chain 'H' and resid 125 through 136 Processing helix chain 'H' and resid 146 through 168 removed outlier: 4.286A pdb=" N LEU H 152 " --> pdb=" O GLN H 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 173 through 187 Processing helix chain 'H' and resid 196 through 208 Processing helix chain 'H' and resid 209 through 219 removed outlier: 4.444A pdb=" N GLN H 213 " --> pdb=" O ARG H 209 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 16 Processing helix chain 'I' and resid 18 through 27 removed outlier: 3.652A pdb=" N LEU I 22 " --> pdb=" O ASP I 18 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 40 Processing helix chain 'I' and resid 41 through 47 Processing helix chain 'I' and resid 95 through 110 Processing helix chain 'I' and resid 120 through 125 Processing helix chain 'I' and resid 125 through 135 Processing helix chain 'I' and resid 146 through 149 Processing helix chain 'I' and resid 150 through 168 Processing helix chain 'I' and resid 169 through 171 No H-bonds generated for 'chain 'I' and resid 169 through 171' Processing helix chain 'I' and resid 173 through 187 Processing helix chain 'I' and resid 196 through 209 Processing helix chain 'I' and resid 209 through 216 removed outlier: 4.211A pdb=" N GLN I 213 " --> pdb=" O ARG I 209 " (cutoff:3.500A) Processing helix chain 'I' and resid 217 through 219 No H-bonds generated for 'chain 'I' and resid 217 through 219' Processing helix chain 'I' and resid 267 through 269 No H-bonds generated for 'chain 'I' and resid 267 through 269' Processing helix chain 'J' and resid 4 through 16 Processing helix chain 'J' and resid 18 through 27 Processing helix chain 'J' and resid 29 through 40 Processing helix chain 'J' and resid 95 through 110 Processing helix chain 'J' and resid 120 through 125 Processing helix chain 'J' and resid 125 through 136 Processing helix chain 'J' and resid 146 through 168 removed outlier: 3.714A pdb=" N LEU J 152 " --> pdb=" O GLN J 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 169 through 171 No H-bonds generated for 'chain 'J' and resid 169 through 171' Processing helix chain 'J' and resid 173 through 187 Processing helix chain 'J' and resid 196 through 216 Processing helix chain 'K' and resid 3 through 16 removed outlier: 4.118A pdb=" N LEU K 7 " --> pdb=" O GLU K 3 " (cutoff:3.500A) Processing helix chain 'K' and resid 18 through 27 Processing helix chain 'K' and resid 29 through 40 Processing helix chain 'K' and resid 40 through 46 Processing helix chain 'K' and resid 95 through 110 Processing helix chain 'K' and resid 120 through 125 Processing helix chain 'K' and resid 125 through 136 Processing helix chain 'K' and resid 146 through 168 removed outlier: 3.775A pdb=" N LEU K 152 " --> pdb=" O GLN K 148 " (cutoff:3.500A) Processing helix chain 'K' and resid 173 through 187 Processing helix chain 'K' and resid 196 through 219 removed outlier: 3.682A pdb=" N ILE K 210 " --> pdb=" O GLU K 206 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LYS K 217 " --> pdb=" O GLN K 213 " (cutoff:3.500A) Processing helix chain 'L' and resid 95 through 110 Processing helix chain 'L' and resid 120 through 125 Processing helix chain 'L' and resid 125 through 135 Processing helix chain 'L' and resid 146 through 168 Processing helix chain 'L' and resid 173 through 187 Processing helix chain 'L' and resid 196 through 219 Processing helix chain 'M' and resid 4 through 16 Processing helix chain 'M' and resid 18 through 27 Processing helix chain 'M' and resid 29 through 40 Processing helix chain 'M' and resid 95 through 110 Processing helix chain 'M' and resid 120 through 125 Processing helix chain 'M' and resid 125 through 136 Processing helix chain 'M' and resid 146 through 168 Processing helix chain 'M' and resid 173 through 187 Processing helix chain 'M' and resid 196 through 219 Processing helix chain 'M' and resid 267 through 269 No H-bonds generated for 'chain 'M' and resid 267 through 269' Processing helix chain 'N' and resid 5 through 16 Processing helix chain 'N' and resid 18 through 27 Processing helix chain 'N' and resid 29 through 40 Processing helix chain 'N' and resid 40 through 46 removed outlier: 3.562A pdb=" N GLN N 44 " --> pdb=" O CYS N 40 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN N 46 " --> pdb=" O VAL N 42 " (cutoff:3.500A) Processing helix chain 'N' and resid 95 through 109 Processing helix chain 'N' and resid 120 through 125 Processing helix chain 'N' and resid 125 through 136 Processing helix chain 'N' and resid 146 through 168 Processing helix chain 'N' and resid 169 through 171 No H-bonds generated for 'chain 'N' and resid 169 through 171' Processing helix chain 'N' and resid 173 through 187 Processing helix chain 'N' and resid 196 through 218 Processing helix chain 'N' and resid 267 through 269 No H-bonds generated for 'chain 'N' and resid 267 through 269' Processing helix chain 'O' and resid 5 through 16 Processing helix chain 'O' and resid 18 through 27 Processing helix chain 'O' and resid 29 through 40 Processing helix chain 'O' and resid 40 through 46 Processing helix chain 'O' and resid 95 through 110 Processing helix chain 'O' and resid 120 through 125 Processing helix chain 'O' and resid 125 through 136 Processing helix chain 'O' and resid 146 through 168 removed outlier: 3.658A pdb=" N LEU O 152 " --> pdb=" O GLN O 148 " (cutoff:3.500A) Processing helix chain 'O' and resid 173 through 187 Processing helix chain 'O' and resid 196 through 219 removed outlier: 3.722A pdb=" N ILE O 210 " --> pdb=" O GLU O 206 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN O 211 " --> pdb=" O GLN O 207 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER O 214 " --> pdb=" O ILE O 210 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER O 216 " --> pdb=" O GLN O 212 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N LYS O 217 " --> pdb=" O GLN O 213 " (cutoff:3.500A) Processing helix chain 'P' and resid 95 through 110 Processing helix chain 'P' and resid 120 through 125 Processing helix chain 'P' and resid 125 through 136 Processing helix chain 'P' and resid 146 through 168 removed outlier: 4.286A pdb=" N LEU P 152 " --> pdb=" O GLN P 148 " (cutoff:3.500A) Processing helix chain 'P' and resid 173 through 187 Processing helix chain 'P' and resid 196 through 208 Processing helix chain 'P' and resid 209 through 219 removed outlier: 4.444A pdb=" N GLN P 213 " --> pdb=" O ARG P 209 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 90 removed outlier: 3.756A pdb=" N VAL A 77 " --> pdb=" O ASP A 66 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASP A 66 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL A 79 " --> pdb=" O GLN A 64 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN A 64 " --> pdb=" O VAL A 79 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N TRP A 63 " --> pdb=" O GLN A 116 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 222 through 224 removed outlier: 4.581A pdb=" N ARG A 222 " --> pdb=" O VAL A 243 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 229 through 230 Processing sheet with id=AA4, first strand: chain 'A' and resid 245 through 246 removed outlier: 3.827A pdb=" N TRP A 245 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE A 264 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG A 260 " --> pdb=" O ASP A 255 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 86 through 90 removed outlier: 3.546A pdb=" N GLU B 89 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE B 75 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR B 68 " --> pdb=" O ILE B 75 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N TRP B 63 " --> pdb=" O GLN B 116 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 238 through 243 removed outlier: 5.058A pdb=" N GLY B 239 " --> pdb=" O TYR B 226 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N TYR B 226 " --> pdb=" O GLY B 239 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ARG B 222 " --> pdb=" O VAL B 243 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N PHE B 223 " --> pdb=" O ILE B 272 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 245 through 246 removed outlier: 3.775A pdb=" N TRP B 245 " --> pdb=" O VAL B 252 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL B 253 " --> pdb=" O LEU B 262 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG B 260 " --> pdb=" O ASP B 255 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 86 through 91 removed outlier: 3.804A pdb=" N ILE C 74 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL C 77 " --> pdb=" O ASP C 66 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TRP C 63 " --> pdb=" O GLN C 116 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR C 140 " --> pdb=" O LEU C 115 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 238 through 242 removed outlier: 6.365A pdb=" N CYS C 224 " --> pdb=" O PRO C 240 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE C 223 " --> pdb=" O ILE C 272 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 229 through 230 Processing sheet with id=AB2, first strand: chain 'C' and resid 245 through 246 removed outlier: 3.605A pdb=" N TRP C 245 " --> pdb=" O VAL C 252 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 86 through 87 removed outlier: 3.522A pdb=" N ILE D 74 " --> pdb=" O VAL D 91 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 86 through 87 removed outlier: 3.855A pdb=" N VAL D 77 " --> pdb=" O ASP D 66 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N TRP D 63 " --> pdb=" O GLN D 116 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 241 through 242 removed outlier: 3.544A pdb=" N PHE D 223 " --> pdb=" O ILE D 272 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 245 through 246 removed outlier: 4.241A pdb=" N TRP D 245 " --> pdb=" O VAL D 252 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL D 252 " --> pdb=" O TRP D 245 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 68 through 69 removed outlier: 3.512A pdb=" N THR E 68 " --> pdb=" O ILE E 75 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 68 through 69 removed outlier: 3.512A pdb=" N THR E 68 " --> pdb=" O ILE E 75 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N TRP E 63 " --> pdb=" O GLN E 116 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 238 through 242 removed outlier: 6.109A pdb=" N CYS E 224 " --> pdb=" O PRO E 240 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N PHE E 223 " --> pdb=" O ILE E 272 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 229 through 230 Processing sheet with id=AC2, first strand: chain 'E' and resid 245 through 246 removed outlier: 4.235A pdb=" N TRP E 245 " --> pdb=" O VAL E 252 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 68 through 70 removed outlier: 3.753A pdb=" N ILE F 74 " --> pdb=" O VAL F 91 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 68 through 70 removed outlier: 6.081A pdb=" N TRP F 63 " --> pdb=" O GLN F 116 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 260 through 265 removed outlier: 3.800A pdb=" N ARG F 260 " --> pdb=" O ASP F 255 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE F 264 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE F 251 " --> pdb=" O ILE F 264 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N LYS F 254 " --> pdb=" O VAL F 243 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N VAL F 243 " --> pdb=" O LYS F 254 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR F 226 " --> pdb=" O GLN F 238 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N CYS F 224 " --> pdb=" O PRO F 240 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 229 through 230 Processing sheet with id=AC7, first strand: chain 'G' and resid 86 through 87 removed outlier: 3.522A pdb=" N TYR G 87 " --> pdb=" O TRP G 78 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE G 74 " --> pdb=" O VAL G 91 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 86 through 87 removed outlier: 3.522A pdb=" N TYR G 87 " --> pdb=" O TRP G 78 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR G 68 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL G 77 " --> pdb=" O ASP G 66 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP G 66 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N TRP G 63 " --> pdb=" O GLN G 116 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 86 through 87 removed outlier: 3.556A pdb=" N ILE H 74 " --> pdb=" O VAL H 91 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 86 through 87 removed outlier: 3.766A pdb=" N THR H 68 " --> pdb=" O ILE H 75 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL H 77 " --> pdb=" O ASP H 66 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASP H 66 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N TRP H 63 " --> pdb=" O GLN H 116 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU H 115 " --> pdb=" O GLU H 138 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR H 140 " --> pdb=" O LEU H 115 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 238 through 242 removed outlier: 6.237A pdb=" N CYS H 224 " --> pdb=" O PRO H 240 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS H 270 " --> pdb=" O TYR H 225 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 229 through 230 Processing sheet with id=AD4, first strand: chain 'H' and resid 245 through 246 removed outlier: 3.883A pdb=" N TRP H 245 " --> pdb=" O VAL H 252 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL H 252 " --> pdb=" O TRP H 245 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 86 through 90 removed outlier: 3.757A pdb=" N VAL I 77 " --> pdb=" O ASP I 66 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASP I 66 " --> pdb=" O VAL I 77 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL I 79 " --> pdb=" O GLN I 64 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN I 64 " --> pdb=" O VAL I 79 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N TRP I 63 " --> pdb=" O GLN I 116 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 222 through 224 removed outlier: 4.581A pdb=" N ARG I 222 " --> pdb=" O VAL I 243 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 229 through 230 Processing sheet with id=AD8, first strand: chain 'I' and resid 245 through 246 removed outlier: 3.826A pdb=" N TRP I 245 " --> pdb=" O VAL I 252 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE I 264 " --> pdb=" O ILE I 251 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG I 260 " --> pdb=" O ASP I 255 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 86 through 90 removed outlier: 3.547A pdb=" N GLU J 89 " --> pdb=" O LEU J 76 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE J 75 " --> pdb=" O THR J 68 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR J 68 " --> pdb=" O ILE J 75 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N TRP J 63 " --> pdb=" O GLN J 116 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 238 through 243 removed outlier: 5.059A pdb=" N GLY J 239 " --> pdb=" O TYR J 226 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N TYR J 226 " --> pdb=" O GLY J 239 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ARG J 222 " --> pdb=" O VAL J 243 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N PHE J 223 " --> pdb=" O ILE J 272 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 245 through 246 removed outlier: 3.775A pdb=" N TRP J 245 " --> pdb=" O VAL J 252 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL J 253 " --> pdb=" O LEU J 262 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG J 260 " --> pdb=" O ASP J 255 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 86 through 91 removed outlier: 3.802A pdb=" N ILE K 74 " --> pdb=" O VAL K 91 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL K 77 " --> pdb=" O ASP K 66 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TRP K 63 " --> pdb=" O GLN K 116 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR K 140 " --> pdb=" O LEU K 115 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 238 through 242 removed outlier: 6.365A pdb=" N CYS K 224 " --> pdb=" O PRO K 240 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE K 223 " --> pdb=" O ILE K 272 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 229 through 230 Processing sheet with id=AE6, first strand: chain 'K' and resid 245 through 246 removed outlier: 3.605A pdb=" N TRP K 245 " --> pdb=" O VAL K 252 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 86 through 87 removed outlier: 3.522A pdb=" N ILE L 74 " --> pdb=" O VAL L 91 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 86 through 87 removed outlier: 3.854A pdb=" N VAL L 77 " --> pdb=" O ASP L 66 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N TRP L 63 " --> pdb=" O GLN L 116 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 241 through 242 removed outlier: 3.545A pdb=" N PHE L 223 " --> pdb=" O ILE L 272 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 245 through 246 removed outlier: 4.241A pdb=" N TRP L 245 " --> pdb=" O VAL L 252 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL L 252 " --> pdb=" O TRP L 245 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 68 through 69 removed outlier: 3.512A pdb=" N THR M 68 " --> pdb=" O ILE M 75 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 68 through 69 removed outlier: 3.512A pdb=" N THR M 68 " --> pdb=" O ILE M 75 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N TRP M 63 " --> pdb=" O GLN M 116 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'M' and resid 238 through 242 removed outlier: 6.109A pdb=" N CYS M 224 " --> pdb=" O PRO M 240 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N PHE M 223 " --> pdb=" O ILE M 272 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 229 through 230 Processing sheet with id=AF6, first strand: chain 'M' and resid 245 through 246 removed outlier: 4.235A pdb=" N TRP M 245 " --> pdb=" O VAL M 252 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'N' and resid 68 through 70 removed outlier: 3.752A pdb=" N ILE N 74 " --> pdb=" O VAL N 91 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'N' and resid 68 through 70 removed outlier: 6.081A pdb=" N TRP N 63 " --> pdb=" O GLN N 116 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'N' and resid 260 through 265 removed outlier: 3.800A pdb=" N ARG N 260 " --> pdb=" O ASP N 255 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE N 264 " --> pdb=" O ILE N 251 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE N 251 " --> pdb=" O ILE N 264 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N LYS N 254 " --> pdb=" O VAL N 243 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N VAL N 243 " --> pdb=" O LYS N 254 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR N 226 " --> pdb=" O GLN N 238 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N CYS N 224 " --> pdb=" O PRO N 240 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'N' and resid 229 through 230 Processing sheet with id=AG2, first strand: chain 'O' and resid 86 through 87 removed outlier: 3.522A pdb=" N TYR O 87 " --> pdb=" O TRP O 78 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE O 74 " --> pdb=" O VAL O 91 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'O' and resid 86 through 87 removed outlier: 3.522A pdb=" N TYR O 87 " --> pdb=" O TRP O 78 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR O 68 " --> pdb=" O ILE O 75 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL O 77 " --> pdb=" O ASP O 66 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP O 66 " --> pdb=" O VAL O 77 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N TRP O 63 " --> pdb=" O GLN O 116 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'P' and resid 86 through 87 removed outlier: 3.556A pdb=" N ILE P 74 " --> pdb=" O VAL P 91 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'P' and resid 86 through 87 removed outlier: 3.766A pdb=" N THR P 68 " --> pdb=" O ILE P 75 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL P 77 " --> pdb=" O ASP P 66 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASP P 66 " --> pdb=" O VAL P 77 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N TRP P 63 " --> pdb=" O GLN P 116 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU P 115 " --> pdb=" O GLU P 138 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR P 140 " --> pdb=" O LEU P 115 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'P' and resid 238 through 242 removed outlier: 6.237A pdb=" N CYS P 224 " --> pdb=" O PRO P 240 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS P 270 " --> pdb=" O TYR P 225 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'P' and resid 229 through 230 Processing sheet with id=AG8, first strand: chain 'P' and resid 245 through 246 removed outlier: 3.882A pdb=" N TRP P 245 " --> pdb=" O VAL P 252 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL P 252 " --> pdb=" O TRP P 245 " (cutoff:3.500A) 1714 hydrogen bonds defined for protein. 5010 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 52 hydrogen bonds 104 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 62 stacking parallelities Total time for adding SS restraints: 12.39 Time building geometry restraints manager: 15.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9808 1.34 - 1.46: 5962 1.46 - 1.57: 17989 1.57 - 1.69: 154 1.69 - 1.81: 206 Bond restraints: 34119 Sorted by residual: bond pdb=" CA PRO L 273 " pdb=" C PRO L 273 " ideal model delta sigma weight residual 1.514 1.525 -0.011 5.50e-03 3.31e+04 3.87e+00 bond pdb=" CA PRO D 273 " pdb=" C PRO D 273 " ideal model delta sigma weight residual 1.514 1.525 -0.011 5.50e-03 3.31e+04 3.81e+00 bond pdb=" N GLU E 219 " pdb=" CA GLU E 219 " ideal model delta sigma weight residual 1.456 1.483 -0.027 1.44e-02 4.82e+03 3.51e+00 bond pdb=" N GLU M 219 " pdb=" CA GLU M 219 " ideal model delta sigma weight residual 1.456 1.483 -0.027 1.44e-02 4.82e+03 3.41e+00 bond pdb=" CA PRO F 273 " pdb=" C PRO F 273 " ideal model delta sigma weight residual 1.514 1.506 0.009 5.50e-03 3.31e+04 2.46e+00 ... (remaining 34114 not shown) Histogram of bond angle deviations from ideal: 97.45 - 105.45: 1008 105.45 - 113.46: 18832 113.46 - 121.46: 18222 121.46 - 129.47: 8055 129.47 - 137.47: 398 Bond angle restraints: 46515 Sorted by residual: angle pdb=" C GLN E 218 " pdb=" N GLU E 219 " pdb=" CA GLU E 219 " ideal model delta sigma weight residual 122.55 110.04 12.51 2.03e+00 2.43e-01 3.80e+01 angle pdb=" C GLN M 218 " pdb=" N GLU M 219 " pdb=" CA GLU M 219 " ideal model delta sigma weight residual 122.55 110.09 12.46 2.03e+00 2.43e-01 3.77e+01 angle pdb=" CB ARG O 189 " pdb=" CG ARG O 189 " pdb=" CD ARG O 189 " ideal model delta sigma weight residual 111.30 121.95 -10.65 2.30e+00 1.89e-01 2.14e+01 angle pdb=" CB ARG G 189 " pdb=" CG ARG G 189 " pdb=" CD ARG G 189 " ideal model delta sigma weight residual 111.30 121.93 -10.63 2.30e+00 1.89e-01 2.13e+01 angle pdb=" C THR O 103 " pdb=" N MET O 104 " pdb=" CA MET O 104 " ideal model delta sigma weight residual 121.14 113.07 8.07 1.75e+00 3.27e-01 2.13e+01 ... (remaining 46510 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.44: 19508 34.44 - 68.88: 491 68.88 - 103.31: 62 103.31 - 137.75: 0 137.75 - 172.19: 4 Dihedral angle restraints: 20065 sinusoidal: 8812 harmonic: 11253 Sorted by residual: dihedral pdb=" CA ILE D 187 " pdb=" C ILE D 187 " pdb=" N LYS D 188 " pdb=" CA LYS D 188 " ideal model delta harmonic sigma weight residual -180.00 -157.35 -22.65 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA ILE L 187 " pdb=" C ILE L 187 " pdb=" N LYS L 188 " pdb=" CA LYS L 188 " ideal model delta harmonic sigma weight residual -180.00 -157.37 -22.63 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA TYR B 70 " pdb=" C TYR B 70 " pdb=" N GLU B 71 " pdb=" CA GLU B 71 " ideal model delta harmonic sigma weight residual -180.00 -157.53 -22.47 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 20062 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 3513 0.038 - 0.075: 960 0.075 - 0.113: 415 0.113 - 0.151: 105 0.151 - 0.188: 13 Chirality restraints: 5006 Sorted by residual: chirality pdb=" CB ILE B 221 " pdb=" CA ILE B 221 " pdb=" CG1 ILE B 221 " pdb=" CG2 ILE B 221 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.86e-01 chirality pdb=" CB VAL F 153 " pdb=" CA VAL F 153 " pdb=" CG1 VAL F 153 " pdb=" CG2 VAL F 153 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.18 2.00e-01 2.50e+01 8.49e-01 chirality pdb=" CB ILE J 221 " pdb=" CA ILE J 221 " pdb=" CG1 ILE J 221 " pdb=" CG2 ILE J 221 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.40e-01 ... (remaining 5003 not shown) Planarity restraints: 5714 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 28 " 0.037 5.00e-02 4.00e+02 5.60e-02 5.02e+00 pdb=" N PRO A 29 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 29 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 29 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE I 28 " 0.037 5.00e-02 4.00e+02 5.59e-02 5.00e+00 pdb=" N PRO I 29 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO I 29 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO I 29 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 272 " -0.031 5.00e-02 4.00e+02 4.78e-02 3.66e+00 pdb=" N PRO D 273 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO D 273 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 273 " -0.026 5.00e-02 4.00e+02 ... (remaining 5711 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 1270 2.71 - 3.26: 33763 3.26 - 3.81: 56135 3.81 - 4.35: 67169 4.35 - 4.90: 108427 Nonbonded interactions: 266764 Sorted by model distance: nonbonded pdb=" OG1 THR I 95 " pdb=" OE1 GLU I 98 " model vdw 2.166 2.440 nonbonded pdb=" OG1 THR A 95 " pdb=" OE1 GLU A 98 " model vdw 2.167 2.440 nonbonded pdb=" O ASP G 18 " pdb=" OG SER G 21 " model vdw 2.170 2.440 nonbonded pdb=" O ASP O 18 " pdb=" OG SER O 21 " model vdw 2.170 2.440 nonbonded pdb=" ND1 HIS M 23 " pdb=" O ILE M 28 " model vdw 2.195 2.520 ... (remaining 266759 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 44 or resid 60 through 212 or (resid 213 and (na \ me N or name CA or name C or name O or name CB )) or resid 214 or (resid 215 and \ (name N or name CA or name C or name O or name CB )) or resid 216 or (resid 217 \ and (name N or name CA or name C or name O or name CB )) or resid 218 through 2 \ 72)) selection = (chain 'B' and (resid 4 through 212 or (resid 213 and (name N or name CA or name \ C or name O or name CB )) or resid 214 or (resid 215 and (name N or name CA or \ name C or name O or name CB )) or resid 216 or (resid 217 and (name N or name CA \ or name C or name O or name CB )) or resid 218 through 272)) selection = (chain 'C' and (resid 4 through 44 or resid 60 through 212 or (resid 213 and (na \ me N or name CA or name C or name O or name CB )) or resid 214 or (resid 215 and \ (name N or name CA or name C or name O or name CB )) or resid 216 or (resid 217 \ and (name N or name CA or name C or name O or name CB )) or resid 218 through 2 \ 72)) selection = (chain 'E' and (resid 4 through 212 or (resid 213 and (name N or name CA or name \ C or name O or name CB )) or resid 214 or (resid 215 and (name N or name CA or \ name C or name O or name CB )) or resid 216 or (resid 217 and (name N or name CA \ or name C or name O or name CB )) or resid 218 through 272)) selection = (chain 'F' and (resid 4 through 44 or resid 60 through 216 or (resid 217 and (na \ me N or name CA or name C or name O or name CB )) or resid 218 through 272)) selection = (chain 'I' and (resid 4 through 44 or resid 60 through 212 or (resid 213 and (na \ me N or name CA or name C or name O or name CB )) or resid 214 or (resid 215 and \ (name N or name CA or name C or name O or name CB )) or resid 216 or (resid 217 \ and (name N or name CA or name C or name O or name CB )) or resid 218 through 2 \ 72)) selection = (chain 'J' and (resid 4 through 212 or (resid 213 and (name N or name CA or name \ C or name O or name CB )) or resid 214 or (resid 215 and (name N or name CA or \ name C or name O or name CB )) or resid 216 or (resid 217 and (name N or name CA \ or name C or name O or name CB )) or resid 218 through 272)) selection = (chain 'K' and (resid 4 through 44 or resid 60 through 212 or (resid 213 and (na \ me N or name CA or name C or name O or name CB )) or resid 214 or (resid 215 and \ (name N or name CA or name C or name O or name CB )) or resid 216 or (resid 217 \ and (name N or name CA or name C or name O or name CB )) or resid 218 through 2 \ 72)) selection = (chain 'M' and (resid 4 through 212 or (resid 213 and (name N or name CA or name \ C or name O or name CB )) or resid 214 or (resid 215 and (name N or name CA or \ name C or name O or name CB )) or resid 216 or (resid 217 and (name N or name CA \ or name C or name O or name CB )) or resid 218 through 272)) selection = (chain 'N' and (resid 4 through 44 or resid 60 through 212 or (resid 213 and (na \ me N or name CA or name C or name O or name CB )) or resid 214 through 272)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 60 through 227 or (resid 228 through 231 and (name N or na \ me CA or name C or name O or name CB )) or resid 232 or (resid 233 and (name N o \ r name CA or name C or name O or name CB )) or resid 234 through 275)) selection = chain 'L' selection = (chain 'P' and (resid 60 through 227 or (resid 228 through 231 and (name N or na \ me CA or name C or name O or name CB )) or resid 232 or (resid 233 and (name N o \ r name CA or name C or name O or name CB )) or resid 234 through 275)) } ncs_group { reference = chain 'G' selection = chain 'O' } ncs_group { reference = chain 'Q' selection = chain 'S' } ncs_group { reference = chain 'R' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 78 5.49 5 S 122 5.16 5 C 20877 2.51 5 N 5806 2.21 5 O 6288 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 8.800 Check model and map are aligned: 0.470 Convert atoms to be neutral: 0.290 Process input model: 92.270 Find NCS groups from input model: 2.430 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Set scattering table: 0.010 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: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5274 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 : 0.003 0.043 34119 Z= 0.169 Angle : 0.640 13.062 46515 Z= 0.346 Chirality : 0.044 0.188 5006 Planarity : 0.004 0.056 5714 Dihedral : 15.264 172.189 12811 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.82 % Favored : 96.08 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % 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: 0.57 (0.14), residues: 3851 helix: 1.52 (0.12), residues: 1868 sheet: -0.21 (0.18), residues: 850 loop : -1.00 (0.18), residues: 1133 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1225 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1225 time to evaluate : 3.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 1225 average time/residue: 0.4827 time to fit residues: 923.0092 Evaluate side-chains 1022 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1022 time to evaluate : 3.645 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.5154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 327 optimal weight: 0.0270 chunk 294 optimal weight: 6.9990 chunk 163 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 198 optimal weight: 3.9990 chunk 157 optimal weight: 8.9990 chunk 304 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 184 optimal weight: 3.9990 chunk 226 optimal weight: 0.7980 chunk 352 optimal weight: 8.9990 overall best weight: 1.9644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 ASN B 16 HIS ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 GLN ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 GLN C 129 GLN C 186 ASN ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 ASN E 23 HIS E 102 GLN ** E 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 69 HIS G 148 GLN G 208 GLN G 211 GLN ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 157 HIS H 242 GLN ** I 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 139 HIS I 146 ASN J 16 HIS J 62 HIS J 139 HIS ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 186 ASN J 208 GLN ** J 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 242 GLN ** K 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 44 GLN ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 129 GLN ** K 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 23 HIS M 102 GLN M 204 ASN N 213 GLN O 69 HIS O 102 GLN O 208 GLN ** P 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 242 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5698 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.116 34119 Z= 0.402 Angle : 0.816 14.590 46515 Z= 0.437 Chirality : 0.051 0.348 5006 Planarity : 0.006 0.082 5714 Dihedral : 14.518 174.802 4959 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 22.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.39 % Favored : 95.51 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % 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: -0.25 (0.13), residues: 3851 helix: 1.01 (0.12), residues: 1866 sheet: -0.64 (0.17), residues: 866 loop : -1.69 (0.17), residues: 1119 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1208 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 1195 time to evaluate : 3.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 3 residues processed: 1200 average time/residue: 0.4949 time to fit residues: 933.9104 Evaluate side-chains 1090 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1087 time to evaluate : 3.515 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3321 time to fit residues: 6.9776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 195 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 293 optimal weight: 0.7980 chunk 239 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 352 optimal weight: 1.9990 chunk 381 optimal weight: 4.9990 chunk 314 optimal weight: 3.9990 chunk 350 optimal weight: 0.8980 chunk 120 optimal weight: 0.9980 chunk 283 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 GLN ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 GLN ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 16 HIS C 44 GLN C 129 GLN C 186 ASN ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 ASN ** E 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 23 HIS ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 208 GLN ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 157 HIS ** H 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 139 HIS I 146 ASN ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 208 GLN ** J 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 116 GLN ** K 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 242 GLN ** L 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 208 GLN O 211 GLN ** P 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5657 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 34119 Z= 0.237 Angle : 0.668 13.124 46515 Z= 0.356 Chirality : 0.047 0.277 5006 Planarity : 0.005 0.081 5714 Dihedral : 14.504 173.942 4959 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.34 % Favored : 95.56 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % 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: -0.17 (0.13), residues: 3851 helix: 1.10 (0.12), residues: 1871 sheet: -0.58 (0.17), residues: 814 loop : -1.68 (0.16), residues: 1166 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1199 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1191 time to evaluate : 3.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 0 residues processed: 1191 average time/residue: 0.4727 time to fit residues: 877.3056 Evaluate side-chains 1080 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1080 time to evaluate : 3.481 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.9469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 348 optimal weight: 5.9990 chunk 265 optimal weight: 2.9990 chunk 183 optimal weight: 0.0170 chunk 39 optimal weight: 6.9990 chunk 168 optimal weight: 2.9990 chunk 237 optimal weight: 0.8980 chunk 354 optimal weight: 0.8980 chunk 375 optimal weight: 0.0030 chunk 185 optimal weight: 0.5980 chunk 335 optimal weight: 0.8980 chunk 101 optimal weight: 0.3980 overall best weight: 0.3828 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 ASN ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 212 GLN E 16 HIS ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 150 GLN ** F 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 208 GLN H 69 HIS H 102 GLN H 157 HIS H 207 GLN H 242 GLN H 266 ASN ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 242 GLN J 62 HIS J 157 HIS ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 208 GLN ** J 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 242 GLN ** L 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 212 GLN L 266 ASN M 69 HIS ** M 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 213 GLN O 102 GLN O 208 GLN ** P 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 242 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5606 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.100 34119 Z= 0.210 Angle : 0.676 16.611 46515 Z= 0.354 Chirality : 0.047 0.227 5006 Planarity : 0.005 0.085 5714 Dihedral : 14.506 174.113 4959 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.28 % Favored : 95.61 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % 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: -0.06 (0.13), residues: 3851 helix: 1.16 (0.12), residues: 1865 sheet: -0.48 (0.17), residues: 830 loop : -1.60 (0.17), residues: 1156 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1182 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1177 time to evaluate : 3.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 1179 average time/residue: 0.4822 time to fit residues: 891.3509 Evaluate side-chains 1080 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1078 time to evaluate : 3.799 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3958 time to fit residues: 7.4487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 312 optimal weight: 0.0870 chunk 212 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 279 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 320 optimal weight: 0.9990 chunk 259 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 chunk 336 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 overall best weight: 0.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 ASN ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN D 116 GLN ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 16 HIS ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 GLN G 208 GLN G 211 GLN H 157 HIS H 242 GLN ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 146 ASN ** J 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 208 GLN ** J 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 116 GLN ** L 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 69 HIS ** M 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 148 GLN ** N 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 207 GLN O 208 GLN P 157 HIS ** P 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5698 moved from start: 0.4754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 34119 Z= 0.242 Angle : 0.696 14.361 46515 Z= 0.368 Chirality : 0.048 0.243 5006 Planarity : 0.005 0.090 5714 Dihedral : 14.605 174.373 4959 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.88 % Favored : 95.01 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % 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: -0.20 (0.13), residues: 3851 helix: 1.06 (0.12), residues: 1878 sheet: -0.49 (0.18), residues: 792 loop : -1.75 (0.16), residues: 1181 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1197 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1194 time to evaluate : 3.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 1195 average time/residue: 0.4722 time to fit residues: 884.3346 Evaluate side-chains 1097 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1094 time to evaluate : 3.595 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3243 time to fit residues: 6.4007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 126 optimal weight: 0.6980 chunk 337 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 220 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 375 optimal weight: 0.4980 chunk 311 optimal weight: 0.0970 chunk 173 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 197 optimal weight: 0.8980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 ASN ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 208 GLN ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 208 GLN H 157 HIS H 266 ASN J 62 HIS J 157 HIS ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 208 GLN ** J 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 162 ASN M 69 HIS ** M 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 207 GLN O 208 GLN O 211 GLN P 157 HIS P 207 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5659 moved from start: 0.5021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.107 34119 Z= 0.209 Angle : 0.696 14.254 46515 Z= 0.366 Chirality : 0.048 0.223 5006 Planarity : 0.005 0.088 5714 Dihedral : 14.571 174.321 4959 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.52 % Favored : 95.38 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % 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: -0.18 (0.13), residues: 3851 helix: 1.05 (0.12), residues: 1877 sheet: -0.49 (0.17), residues: 829 loop : -1.72 (0.17), residues: 1145 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1189 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1184 time to evaluate : 3.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 1186 average time/residue: 0.4740 time to fit residues: 878.5917 Evaluate side-chains 1102 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1098 time to evaluate : 3.982 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3432 time to fit residues: 7.6731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 361 optimal weight: 8.9990 chunk 42 optimal weight: 0.8980 chunk 213 optimal weight: 0.9980 chunk 274 optimal weight: 0.9990 chunk 212 optimal weight: 1.9990 chunk 316 optimal weight: 4.9990 chunk 209 optimal weight: 0.0370 chunk 373 optimal weight: 0.0270 chunk 234 optimal weight: 3.9990 chunk 227 optimal weight: 0.5980 chunk 172 optimal weight: 0.3980 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 HIS ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 GLN B 242 GLN C 186 ASN ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 16 HIS ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 208 GLN ** H 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 157 HIS I 146 ASN I 207 GLN ** I 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 13 ASN ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 ASN ** L 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 69 HIS ** M 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 148 GLN ** N 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 62 HIS O 208 GLN P 157 HIS P 242 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5647 moved from start: 0.5255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.090 34119 Z= 0.199 Angle : 0.717 13.798 46515 Z= 0.380 Chirality : 0.049 0.271 5006 Planarity : 0.005 0.143 5714 Dihedral : 14.580 174.364 4959 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.65 % Favored : 95.25 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % 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: -0.27 (0.13), residues: 3851 helix: 0.97 (0.12), residues: 1874 sheet: -0.52 (0.18), residues: 793 loop : -1.73 (0.16), residues: 1184 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1181 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1180 time to evaluate : 3.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1181 average time/residue: 0.4807 time to fit residues: 887.8170 Evaluate side-chains 1080 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1079 time to evaluate : 3.531 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3236 time to fit residues: 5.3107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 231 optimal weight: 0.9990 chunk 149 optimal weight: 0.8980 chunk 223 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 73 optimal weight: 7.9990 chunk 72 optimal weight: 9.9990 chunk 237 optimal weight: 0.9980 chunk 254 optimal weight: 9.9990 chunk 184 optimal weight: 2.9990 chunk 34 optimal weight: 0.0060 chunk 293 optimal weight: 1.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 HIS ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 ASN ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 16 HIS ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 ASN ** F 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 208 GLN H 148 GLN H 157 HIS H 242 GLN ** I 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 13 ASN J 157 HIS ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 207 GLN ** J 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 213 GLN ** M 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 69 HIS ** M 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 218 GLN ** N 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 208 GLN ** P 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 157 HIS ** P 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5719 moved from start: 0.5588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.319 34119 Z= 0.269 Angle : 0.746 16.222 46515 Z= 0.399 Chirality : 0.050 0.297 5006 Planarity : 0.005 0.151 5714 Dihedral : 14.593 175.104 4959 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 18.13 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.01 % Favored : 94.88 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % 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: -0.35 (0.13), residues: 3851 helix: 0.89 (0.12), residues: 1861 sheet: -0.50 (0.18), residues: 802 loop : -1.76 (0.16), residues: 1188 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1180 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1180 time to evaluate : 3.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 1180 average time/residue: 0.4812 time to fit residues: 890.5469 Evaluate side-chains 1076 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1076 time to evaluate : 3.978 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.6466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 340 optimal weight: 1.9990 chunk 358 optimal weight: 0.0980 chunk 326 optimal weight: 6.9990 chunk 348 optimal weight: 9.9990 chunk 209 optimal weight: 0.8980 chunk 151 optimal weight: 0.9980 chunk 273 optimal weight: 7.9990 chunk 106 optimal weight: 4.9990 chunk 314 optimal weight: 4.9990 chunk 329 optimal weight: 0.6980 chunk 347 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 129 GLN B 62 HIS ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 ASN ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 GLN C 186 ASN ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 ASN ** F 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 208 GLN H 157 HIS H 207 GLN H 242 GLN I 207 GLN ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 97 GLN ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 162 ASN ** K 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 158 GLN ** L 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 69 HIS ** M 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 148 GLN O 208 GLN O 211 GLN ** P 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 148 GLN ** P 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5737 moved from start: 0.5869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.092 34119 Z= 0.235 Angle : 0.765 14.572 46515 Z= 0.409 Chirality : 0.051 0.322 5006 Planarity : 0.005 0.127 5714 Dihedral : 14.612 175.476 4959 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 18.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.04 % Favored : 94.86 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % 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: -0.45 (0.13), residues: 3851 helix: 0.76 (0.12), residues: 1862 sheet: -0.52 (0.18), residues: 769 loop : -1.71 (0.16), residues: 1220 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1203 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1203 time to evaluate : 3.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 1203 average time/residue: 0.4645 time to fit residues: 877.5960 Evaluate side-chains 1091 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1091 time to evaluate : 3.598 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.2484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 228 optimal weight: 0.0470 chunk 368 optimal weight: 0.9990 chunk 224 optimal weight: 0.0040 chunk 174 optimal weight: 4.9990 chunk 256 optimal weight: 2.9990 chunk 386 optimal weight: 2.9990 chunk 355 optimal weight: 0.7980 chunk 307 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 237 optimal weight: 2.9990 chunk 188 optimal weight: 3.9990 overall best weight: 0.5292 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 HIS ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 ASN ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 16 HIS ** E 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 ASN H 157 HIS ** I 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 157 HIS ** P 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5725 moved from start: 0.6043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.155 34119 Z= 0.247 Angle : 0.786 15.061 46515 Z= 0.420 Chirality : 0.051 0.308 5006 Planarity : 0.005 0.114 5714 Dihedral : 14.603 175.817 4959 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.83 % Favored : 95.01 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % 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: -0.54 (0.13), residues: 3851 helix: 0.65 (0.12), residues: 1864 sheet: -0.54 (0.17), residues: 831 loop : -1.76 (0.16), residues: 1156 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1185 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1185 time to evaluate : 3.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 1185 average time/residue: 0.4784 time to fit residues: 891.2441 Evaluate side-chains 1074 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1074 time to evaluate : 3.824 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 244 optimal weight: 0.8980 chunk 327 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 283 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 85 optimal weight: 4.9990 chunk 308 optimal weight: 0.7980 chunk 129 optimal weight: 0.9980 chunk 316 optimal weight: 0.5980 chunk 39 optimal weight: 0.0670 chunk 56 optimal weight: 0.0170 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 129 GLN ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 ASN B 157 HIS ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 16 HIS ** E 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 ASN ** H 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 GLN H 157 HIS H 242 GLN I 242 GLN J 157 HIS ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 12 HIS ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 116 GLN ** K 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.194443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.148979 restraints weight = 71721.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.154707 restraints weight = 43491.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.158652 restraints weight = 29790.350| |-----------------------------------------------------------------------------| r_work (final): 0.4001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6589 moved from start: 0.6190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.092 34119 Z= 0.236 Angle : 0.788 13.908 46515 Z= 0.420 Chirality : 0.051 0.327 5006 Planarity : 0.005 0.069 5714 Dihedral : 14.608 176.209 4959 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.86 % Favored : 95.04 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % 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: -0.59 (0.13), residues: 3851 helix: 0.60 (0.12), residues: 1867 sheet: -0.53 (0.18), residues: 798 loop : -1.78 (0.16), residues: 1186 =============================================================================== Job complete usr+sys time: 12034.80 seconds wall clock time: 215 minutes 46.90 seconds (12946.90 seconds total)