Starting phenix.real_space_refine (version: 1.21rc1) on Tue Apr 25 19:36:33 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tqu_26072/04_2023/7tqu_26072_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tqu_26072/04_2023/7tqu_26072.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tqu_26072/04_2023/7tqu_26072.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tqu_26072/04_2023/7tqu_26072.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tqu_26072/04_2023/7tqu_26072_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tqu_26072/04_2023/7tqu_26072_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 127 5.16 5 C 13211 2.51 5 N 3554 2.21 5 O 3999 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "a TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 20891 Number of models: 1 Model: "" Number of chains: 17 Chain: "H" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 560 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 112} Link IDs: {'TRANS': 111} Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 336 Unresolved non-hydrogen dihedrals: 112 Planarities with less than four sites: {'UNK:plan-1': 112} Unresolved non-hydrogen planarities: 112 Chain: "L" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 510 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'TRANS': 101} Unresolved non-hydrogen bonds: 204 Unresolved non-hydrogen angles: 306 Unresolved non-hydrogen dihedrals: 102 Planarities with less than four sites: {'UNK:plan-1': 102} Unresolved non-hydrogen planarities: 102 Chain: "a" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2226 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 20, 'TRANS': 262} Chain: "b" Number of atoms: 2043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2043 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 16, 'TRANS': 246} Chain breaks: 1 Chain: "c" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1801 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 20, 'TRANS': 212} Chain: "d" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 512 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "e" Number of atoms: 2219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2219 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 20, 'TRANS': 261} Chain: "f" Number of atoms: 2057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2057 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 16, 'TRANS': 248} Chain: "g" Number of atoms: 1810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1810 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 20, 'TRANS': 213} Chain: "h" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 512 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "i" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2226 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 20, 'TRANS': 262} Chain: "j" Number of atoms: 2029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2029 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 16, 'TRANS': 244} Chain breaks: 1 Chain: "k" Number of atoms: 1826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1826 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 20, 'TRANS': 215} Chain: "l" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 512 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "a" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.68, per 1000 atoms: 0.51 Number of scatterers: 20891 At special positions: 0 Unit cell: (166.155, 166.155, 165.11, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 127 16.00 O 3999 8.00 N 3554 7.00 C 13211 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: 8.21 Conformation dependent library (CDL) restraints added in 2.9 seconds 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5204 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 64 helices and 37 sheets defined 11.7% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'H' and resid 52 through 54 No H-bonds generated for 'chain 'H' and resid 52 through 54' Processing helix chain 'L' and resid 25 through 27 No H-bonds generated for 'chain 'L' and resid 25 through 27' Processing helix chain 'a' and resid 52 through 54 No H-bonds generated for 'chain 'a' and resid 52 through 54' Processing helix chain 'a' and resid 72 through 76 Processing helix chain 'a' and resid 93 through 98 removed outlier: 5.072A pdb=" N LYS a 97 " --> pdb=" O GLY a 94 " (cutoff:3.500A) Processing helix chain 'a' and resid 111 through 119 removed outlier: 3.665A pdb=" N PHE a 119 " --> pdb=" O ARG a 115 " (cutoff:3.500A) Processing helix chain 'a' and resid 168 through 171 Processing helix chain 'a' and resid 226 through 228 No H-bonds generated for 'chain 'a' and resid 226 through 228' Processing helix chain 'a' and resid 283 through 285 No H-bonds generated for 'chain 'a' and resid 283 through 285' Processing helix chain 'b' and resid 34 through 36 No H-bonds generated for 'chain 'b' and resid 34 through 36' Processing helix chain 'b' and resid 82 through 85 No H-bonds generated for 'chain 'b' and resid 82 through 85' Processing helix chain 'b' and resid 90 through 98 Processing helix chain 'b' and resid 151 through 153 No H-bonds generated for 'chain 'b' and resid 151 through 153' Processing helix chain 'b' and resid 187 through 192 removed outlier: 4.295A pdb=" N PHE b 191 " --> pdb=" O GLY b 188 " (cutoff:3.500A) Processing helix chain 'c' and resid 43 through 47 Processing helix chain 'c' and resid 65 through 68 Processing helix chain 'c' and resid 94 through 96 No H-bonds generated for 'chain 'c' and resid 94 through 96' Processing helix chain 'c' and resid 98 through 105 removed outlier: 4.062A pdb=" N TYR c 105 " --> pdb=" O GLU c 101 " (cutoff:3.500A) Processing helix chain 'c' and resid 144 through 148 Processing helix chain 'c' and resid 182 through 184 No H-bonds generated for 'chain 'c' and resid 182 through 184' Processing helix chain 'd' and resid 36 through 38 No H-bonds generated for 'chain 'd' and resid 36 through 38' Processing helix chain 'd' and resid 50 through 54 removed outlier: 3.579A pdb=" N THR d 54 " --> pdb=" O SER d 51 " (cutoff:3.500A) Processing helix chain 'e' and resid 42 through 44 No H-bonds generated for 'chain 'e' and resid 42 through 44' Processing helix chain 'e' and resid 52 through 54 No H-bonds generated for 'chain 'e' and resid 52 through 54' Processing helix chain 'e' and resid 72 through 75 No H-bonds generated for 'chain 'e' and resid 72 through 75' Processing helix chain 'e' and resid 93 through 98 removed outlier: 4.649A pdb=" N LYS e 97 " --> pdb=" O GLY e 94 " (cutoff:3.500A) Processing helix chain 'e' and resid 111 through 119 removed outlier: 3.549A pdb=" N PHE e 119 " --> pdb=" O ARG e 115 " (cutoff:3.500A) Processing helix chain 'e' and resid 168 through 171 Processing helix chain 'e' and resid 226 through 229 No H-bonds generated for 'chain 'e' and resid 226 through 229' Processing helix chain 'e' and resid 283 through 285 No H-bonds generated for 'chain 'e' and resid 283 through 285' Processing helix chain 'f' and resid 34 through 36 No H-bonds generated for 'chain 'f' and resid 34 through 36' Processing helix chain 'f' and resid 44 through 46 No H-bonds generated for 'chain 'f' and resid 44 through 46' Processing helix chain 'f' and resid 82 through 86 removed outlier: 3.733A pdb=" N LEU f 86 " --> pdb=" O LEU f 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 82 through 86' Processing helix chain 'f' and resid 90 through 98 Processing helix chain 'f' and resid 145 through 148 No H-bonds generated for 'chain 'f' and resid 145 through 148' Processing helix chain 'f' and resid 151 through 153 No H-bonds generated for 'chain 'f' and resid 151 through 153' Processing helix chain 'f' and resid 170 through 172 No H-bonds generated for 'chain 'f' and resid 170 through 172' Processing helix chain 'f' and resid 187 through 192 removed outlier: 4.397A pdb=" N PHE f 191 " --> pdb=" O GLY f 188 " (cutoff:3.500A) Processing helix chain 'g' and resid 43 through 47 Processing helix chain 'g' and resid 65 through 68 Processing helix chain 'g' and resid 98 through 105 removed outlier: 3.837A pdb=" N TYR g 105 " --> pdb=" O GLU g 101 " (cutoff:3.500A) Processing helix chain 'g' and resid 144 through 149 removed outlier: 4.249A pdb=" N LEU g 149 " --> pdb=" O LYS g 145 " (cutoff:3.500A) Processing helix chain 'h' and resid 36 through 38 No H-bonds generated for 'chain 'h' and resid 36 through 38' Processing helix chain 'h' and resid 50 through 54 Processing helix chain 'i' and resid 52 through 54 No H-bonds generated for 'chain 'i' and resid 52 through 54' Processing helix chain 'i' and resid 72 through 75 No H-bonds generated for 'chain 'i' and resid 72 through 75' Processing helix chain 'i' and resid 93 through 98 removed outlier: 4.763A pdb=" N LYS i 97 " --> pdb=" O GLY i 94 " (cutoff:3.500A) Processing helix chain 'i' and resid 112 through 119 removed outlier: 3.887A pdb=" N LYS i 116 " --> pdb=" O GLN i 112 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE i 119 " --> pdb=" O ARG i 115 " (cutoff:3.500A) Processing helix chain 'i' and resid 168 through 171 Processing helix chain 'i' and resid 226 through 228 No H-bonds generated for 'chain 'i' and resid 226 through 228' Processing helix chain 'j' and resid 34 through 36 No H-bonds generated for 'chain 'j' and resid 34 through 36' Processing helix chain 'j' and resid 44 through 46 No H-bonds generated for 'chain 'j' and resid 44 through 46' Processing helix chain 'j' and resid 57 through 59 No H-bonds generated for 'chain 'j' and resid 57 through 59' Processing helix chain 'j' and resid 82 through 85 No H-bonds generated for 'chain 'j' and resid 82 through 85' Processing helix chain 'j' and resid 90 through 98 Processing helix chain 'j' and resid 151 through 153 No H-bonds generated for 'chain 'j' and resid 151 through 153' Processing helix chain 'j' and resid 187 through 192 removed outlier: 4.244A pdb=" N PHE j 191 " --> pdb=" O GLY j 188 " (cutoff:3.500A) Processing helix chain 'k' and resid 43 through 48 removed outlier: 3.739A pdb=" N GLU k 48 " --> pdb=" O MET k 44 " (cutoff:3.500A) Processing helix chain 'k' and resid 65 through 68 Processing helix chain 'k' and resid 98 through 105 removed outlier: 3.791A pdb=" N TYR k 105 " --> pdb=" O GLU k 101 " (cutoff:3.500A) Processing helix chain 'k' and resid 144 through 149 removed outlier: 4.710A pdb=" N LEU k 149 " --> pdb=" O LYS k 145 " (cutoff:3.500A) Processing helix chain 'l' and resid 14 through 17 removed outlier: 4.704A pdb=" N ASN l 17 " --> pdb=" O GLU l 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 14 through 17' Processing helix chain 'l' and resid 36 through 38 No H-bonds generated for 'chain 'l' and resid 36 through 38' Processing helix chain 'l' and resid 50 through 54 Processing sheet with id= A, first strand: chain 'H' and resid 18 through 23 Processing sheet with id= B, first strand: chain 'H' and resid 33 through 35 removed outlier: 3.514A pdb=" N UNK H 106 " --> pdb=" O UNK H 94 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'H' and resid 47 through 49 Processing sheet with id= D, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.209A pdb=" N UNK L 100 " --> pdb=" O UNK L 10 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'L' and resid 18 through 21 Processing sheet with id= F, first strand: chain 'L' and resid 82 through 86 Processing sheet with id= G, first strand: chain 'a' and resid 100 through 104 Processing sheet with id= H, first strand: chain 'a' and resid 122 through 124 Processing sheet with id= I, first strand: chain 'a' and resid 188 through 191 removed outlier: 6.161A pdb=" N MET a 256 " --> pdb=" O CYS a 81 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N CYS a 81 " --> pdb=" O MET a 256 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'b' and resid 14 through 18 Processing sheet with id= K, first strand: chain 'b' and resid 63 through 65 Processing sheet with id= L, first strand: chain 'b' and resid 69 through 71 Processing sheet with id= M, first strand: chain 'b' and resid 78 through 81 removed outlier: 6.263A pdb=" N ALA b 121 " --> pdb=" O LEU b 234 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'b' and resid 101 through 103 Processing sheet with id= O, first strand: chain 'c' and resid 70 through 73 Processing sheet with id= P, first strand: chain 'c' and resid 151 through 156 removed outlier: 4.363A pdb=" N LYS c 128 " --> pdb=" O GLN c 194 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE c 82 " --> pdb=" O CYS c 191 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N TYR c 193 " --> pdb=" O PRO c 80 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'd' and resid 4 through 7 Processing sheet with id= R, first strand: chain 'e' and resid 100 through 104 Processing sheet with id= S, first strand: chain 'e' and resid 187 through 191 removed outlier: 6.094A pdb=" N MET e 256 " --> pdb=" O CYS e 81 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N CYS e 81 " --> pdb=" O MET e 256 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'f' and resid 14 through 18 Processing sheet with id= U, first strand: chain 'f' and resid 63 through 65 Processing sheet with id= V, first strand: chain 'f' and resid 69 through 72 Processing sheet with id= W, first strand: chain 'f' and resid 78 through 81 removed outlier: 6.163A pdb=" N ALA f 121 " --> pdb=" O LEU f 234 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'f' and resid 101 through 103 Processing sheet with id= Y, first strand: chain 'g' and resid 70 through 73 Processing sheet with id= Z, first strand: chain 'g' and resid 82 through 85 removed outlier: 4.174A pdb=" N PHE g 82 " --> pdb=" O CYS g 191 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N CYS g 191 " --> pdb=" O PHE g 82 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLY g 127 " --> pdb=" O LEU g 157 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'h' and resid 4 through 7 Processing sheet with id= AB, first strand: chain 'i' and resid 100 through 104 Processing sheet with id= AC, first strand: chain 'i' and resid 188 through 191 removed outlier: 5.990A pdb=" N MET i 256 " --> pdb=" O CYS i 81 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N CYS i 81 " --> pdb=" O MET i 256 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'j' and resid 14 through 18 Processing sheet with id= AE, first strand: chain 'j' and resid 63 through 65 Processing sheet with id= AF, first strand: chain 'j' and resid 69 through 71 Processing sheet with id= AG, first strand: chain 'j' and resid 78 through 81 removed outlier: 6.157A pdb=" N ALA j 121 " --> pdb=" O LEU j 234 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'j' and resid 101 through 103 Processing sheet with id= AI, first strand: chain 'k' and resid 70 through 73 Processing sheet with id= AJ, first strand: chain 'k' and resid 82 through 85 removed outlier: 3.511A pdb=" N PHE k 82 " --> pdb=" O CYS k 191 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'l' and resid 4 through 7 458 hydrogen bonds defined for protein. 1125 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.44 Time building geometry restraints manager: 8.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4147 1.31 - 1.45: 7272 1.45 - 1.59: 9767 1.59 - 1.73: 23 1.73 - 1.87: 200 Bond restraints: 21409 Sorted by residual: bond pdb=" CB ILE k 236 " pdb=" CG1 ILE k 236 " ideal model delta sigma weight residual 1.530 1.676 -0.146 2.00e-02 2.50e+03 5.35e+01 bond pdb=" CA PRO i 268 " pdb=" CB PRO i 268 " ideal model delta sigma weight residual 1.539 1.483 0.057 9.30e-03 1.16e+04 3.72e+01 bond pdb=" CB HIS f 224 " pdb=" CG HIS f 224 " ideal model delta sigma weight residual 1.497 1.413 0.084 1.40e-02 5.10e+03 3.58e+01 bond pdb=" CA VAL k 221 " pdb=" C VAL k 221 " ideal model delta sigma weight residual 1.520 1.580 -0.060 1.00e-02 1.00e+04 3.56e+01 bond pdb=" CB HIS b 224 " pdb=" CG HIS b 224 " ideal model delta sigma weight residual 1.497 1.417 0.080 1.40e-02 5.10e+03 3.27e+01 ... (remaining 21404 not shown) Histogram of bond angle deviations from ideal: 92.67 - 100.99: 21 100.99 - 109.32: 4193 109.32 - 117.65: 11883 117.65 - 125.98: 12811 125.98 - 134.31: 315 Bond angle restraints: 29223 Sorted by residual: angle pdb=" N VAL k 221 " pdb=" CA VAL k 221 " pdb=" C VAL k 221 " ideal model delta sigma weight residual 113.20 124.52 -11.32 9.60e-01 1.09e+00 1.39e+02 angle pdb=" C PRO k 135 " pdb=" N PRO k 136 " pdb=" CA PRO k 136 " ideal model delta sigma weight residual 120.21 129.27 -9.06 9.60e-01 1.09e+00 8.90e+01 angle pdb=" N TRP e 264 " pdb=" CA TRP e 264 " pdb=" C TRP e 264 " ideal model delta sigma weight residual 112.59 123.35 -10.76 1.22e+00 6.72e-01 7.77e+01 angle pdb=" C ARG k 222 " pdb=" CA ARG k 222 " pdb=" CB ARG k 222 " ideal model delta sigma weight residual 116.54 106.57 9.97 1.15e+00 7.56e-01 7.52e+01 angle pdb=" N LEU b 234 " pdb=" CA LEU b 234 " pdb=" C LEU b 234 " ideal model delta sigma weight residual 113.88 103.35 10.53 1.23e+00 6.61e-01 7.33e+01 ... (remaining 29218 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 12371 17.81 - 35.63: 288 35.63 - 53.44: 67 53.44 - 71.26: 26 71.26 - 89.07: 10 Dihedral angle restraints: 12762 sinusoidal: 4702 harmonic: 8060 Sorted by residual: dihedral pdb=" C LEU f 82 " pdb=" N LEU f 82 " pdb=" CA LEU f 82 " pdb=" CB LEU f 82 " ideal model delta harmonic sigma weight residual -122.60 -132.84 10.24 0 2.50e+00 1.60e-01 1.68e+01 dihedral pdb=" C LEU b 82 " pdb=" N LEU b 82 " pdb=" CA LEU b 82 " pdb=" CB LEU b 82 " ideal model delta harmonic sigma weight residual -122.60 -132.15 9.55 0 2.50e+00 1.60e-01 1.46e+01 dihedral pdb=" CA ALA g 138 " pdb=" C ALA g 138 " pdb=" N LYS g 139 " pdb=" CA LYS g 139 " ideal model delta harmonic sigma weight residual 180.00 162.65 17.35 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 12759 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 2446 0.102 - 0.204: 720 0.204 - 0.306: 117 0.306 - 0.408: 11 0.408 - 0.510: 6 Chirality restraints: 3300 Sorted by residual: chirality pdb=" CA TRP e 264 " pdb=" N TRP e 264 " pdb=" C TRP e 264 " pdb=" CB TRP e 264 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.50e+00 chirality pdb=" CB VAL i 16 " pdb=" CA VAL i 16 " pdb=" CG1 VAL i 16 " pdb=" CG2 VAL i 16 " both_signs ideal model delta sigma weight residual False -2.63 -3.12 0.49 2.00e-01 2.50e+01 6.01e+00 chirality pdb=" CA LEU f 82 " pdb=" N LEU f 82 " pdb=" C LEU f 82 " pdb=" CB LEU f 82 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.00e+00 ... (remaining 3297 not shown) Planarity restraints: 3804 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP b 79 " 0.079 2.00e-02 2.50e+03 3.85e-02 3.71e+01 pdb=" CG TRP b 79 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 TRP b 79 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP b 79 " -0.033 2.00e-02 2.50e+03 pdb=" NE1 TRP b 79 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TRP b 79 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP b 79 " -0.051 2.00e-02 2.50e+03 pdb=" CZ2 TRP b 79 " 0.042 2.00e-02 2.50e+03 pdb=" CZ3 TRP b 79 " -0.017 2.00e-02 2.50e+03 pdb=" CH2 TRP b 79 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR b 142 " -0.068 2.00e-02 2.50e+03 3.59e-02 2.57e+01 pdb=" CG TYR b 142 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR b 142 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR b 142 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR b 142 " 0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR b 142 " 0.015 2.00e-02 2.50e+03 pdb=" CZ TYR b 142 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR b 142 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR a 137 " -0.049 2.00e-02 2.50e+03 2.64e-02 1.39e+01 pdb=" CG TYR a 137 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR a 137 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR a 137 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 TYR a 137 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR a 137 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR a 137 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR a 137 " -0.041 2.00e-02 2.50e+03 ... (remaining 3801 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 8345 2.88 - 3.39: 19250 3.39 - 3.89: 36036 3.89 - 4.40: 43086 4.40 - 4.90: 68611 Nonbonded interactions: 175328 Sorted by model distance: nonbonded pdb=" N VAL i 42 " pdb=" N GLU i 43 " model vdw 2.375 2.560 nonbonded pdb=" N VAL a 42 " pdb=" N GLU a 43 " model vdw 2.384 2.560 nonbonded pdb=" N GLN c 194 " pdb=" O GLN c 194 " model vdw 2.401 2.496 nonbonded pdb=" NZ LYS c 139 " pdb=" OD2 ASP c 146 " model vdw 2.418 2.520 nonbonded pdb=" N LEU b 234 " pdb=" N ALA b 235 " model vdw 2.418 2.560 ... (remaining 175323 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 'H' and resid 13 through 114) selection = chain 'L' } ncs_group { reference = (chain 'a' and (resid 17 through 298 or resid 300)) selection = chain 'e' selection = (chain 'i' and (resid 17 through 298 or resid 300)) } ncs_group { reference = (chain 'b' and (resid 8 through 164 or resid 169 through 272)) selection = (chain 'f' and (resid 8 through 164 or resid 169 through 272)) selection = chain 'j' } ncs_group { reference = chain 'c' selection = (chain 'g' and resid 1 through 233) selection = (chain 'k' and resid 1 through 233) } ncs_group { reference = chain 'd' selection = chain 'h' selection = chain 'l' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.550 Check model and map are aligned: 0.320 Set scattering table: 0.180 Process input model: 49.870 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 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 : 0.021 0.147 21409 Z= 1.358 Angle : 1.812 14.251 29223 Z= 1.226 Chirality : 0.096 0.510 3300 Planarity : 0.009 0.058 3804 Dihedral : 9.740 89.070 7558 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 0.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.16), residues: 2516 helix: -2.76 (0.27), residues: 210 sheet: 1.53 (0.20), residues: 608 loop : 0.62 (0.14), residues: 1698 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 789 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 789 time to evaluate : 2.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 789 average time/residue: 0.3565 time to fit residues: 426.8049 Evaluate side-chains 502 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 502 time to evaluate : 2.411 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 227 optimal weight: 2.9990 chunk 204 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 211 optimal weight: 6.9990 chunk 81 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 157 optimal weight: 5.9990 chunk 245 optimal weight: 7.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 63 ASN a 112 GLN a 148 GLN b 61 ASN b 111 GLN b 162 ASN b 196 GLN b 203 ASN c 11 ASN c 75 ASN c 96 HIS c 104 ASN d 4 GLN d 21 ASN e 49 GLN e 99 HIS e 112 GLN ** f 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 162 ASN ** f 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 69 GLN g 73 ASN g 104 ASN i 34 GLN i 49 GLN i 89 ASN i 148 GLN i 198 ASN i 230 ASN ** k 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 96 HIS k 108 HIS ** k 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 229 HIS ** l 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 21409 Z= 0.243 Angle : 0.655 8.140 29223 Z= 0.347 Chirality : 0.046 0.183 3300 Planarity : 0.004 0.044 3804 Dihedral : 5.764 44.139 3000 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer Outliers : 2.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.16), residues: 2516 helix: -2.11 (0.32), residues: 192 sheet: 1.23 (0.20), residues: 646 loop : 0.41 (0.15), residues: 1678 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 569 time to evaluate : 2.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 36 residues processed: 599 average time/residue: 0.3282 time to fit residues: 299.5358 Evaluate side-chains 519 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 483 time to evaluate : 2.330 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.2023 time to fit residues: 16.1686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 136 optimal weight: 9.9990 chunk 76 optimal weight: 10.0000 chunk 204 optimal weight: 0.2980 chunk 166 optimal weight: 9.9990 chunk 67 optimal weight: 0.9990 chunk 245 optimal weight: 9.9990 chunk 265 optimal weight: 20.0000 chunk 218 optimal weight: 2.9990 chunk 243 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 197 optimal weight: 10.0000 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 34 GLN d 4 GLN d 21 ASN e 49 GLN ** f 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 56 ASN g 69 GLN i 49 GLN ** i 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 230 ASN ** k 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 21409 Z= 0.284 Angle : 0.601 8.244 29223 Z= 0.312 Chirality : 0.045 0.204 3300 Planarity : 0.004 0.037 3804 Dihedral : 5.482 54.278 3000 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer Outliers : 3.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.16), residues: 2516 helix: -1.77 (0.34), residues: 194 sheet: 0.89 (0.19), residues: 670 loop : 0.20 (0.15), residues: 1652 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 506 time to evaluate : 2.336 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 72 outliers final: 43 residues processed: 537 average time/residue: 0.3372 time to fit residues: 275.1709 Evaluate side-chains 509 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 466 time to evaluate : 2.160 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.1939 time to fit residues: 18.6902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 242 optimal weight: 1.9990 chunk 184 optimal weight: 8.9990 chunk 127 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 117 optimal weight: 9.9990 chunk 164 optimal weight: 10.0000 chunk 246 optimal weight: 9.9990 chunk 260 optimal weight: 10.0000 chunk 128 optimal weight: 0.9980 chunk 233 optimal weight: 0.9990 chunk 70 optimal weight: 8.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 63 ASN ** b 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 11 ASN e 34 GLN e 112 GLN ** e 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 69 GLN i 32 ASN ** i 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 230 ASN j 261 ASN k 75 ASN ** k 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 21409 Z= 0.319 Angle : 0.604 8.214 29223 Z= 0.311 Chirality : 0.046 0.183 3300 Planarity : 0.004 0.036 3804 Dihedral : 5.487 52.294 3000 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer Outliers : 2.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.16), residues: 2516 helix: -1.69 (0.34), residues: 208 sheet: 0.60 (0.20), residues: 652 loop : -0.06 (0.15), residues: 1656 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 481 time to evaluate : 2.482 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 36 residues processed: 510 average time/residue: 0.3434 time to fit residues: 267.3642 Evaluate side-chains 476 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 440 time to evaluate : 2.333 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.2011 time to fit residues: 16.4052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 217 optimal weight: 8.9990 chunk 148 optimal weight: 10.0000 chunk 3 optimal weight: 30.0000 chunk 194 optimal weight: 20.0000 chunk 107 optimal weight: 9.9990 chunk 222 optimal weight: 4.9990 chunk 180 optimal weight: 9.9990 chunk 0 optimal weight: 40.0000 chunk 133 optimal weight: 10.0000 chunk 234 optimal weight: 5.9990 chunk 65 optimal weight: 20.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 113 ASN e 34 GLN ** e 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 56 ASN ** g 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 69 GLN i 32 ASN ** i 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 152 HIS ** k 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.4321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.085 21409 Z= 0.546 Angle : 0.712 10.119 29223 Z= 0.367 Chirality : 0.049 0.195 3300 Planarity : 0.005 0.040 3804 Dihedral : 5.879 52.742 3000 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer Outliers : 3.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.16), residues: 2516 helix: -1.97 (0.31), residues: 226 sheet: 0.21 (0.20), residues: 650 loop : -0.42 (0.15), residues: 1640 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 468 time to evaluate : 2.361 Fit side-chains revert: symmetry clash outliers start: 70 outliers final: 48 residues processed: 499 average time/residue: 0.3407 time to fit residues: 259.6631 Evaluate side-chains 484 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 436 time to evaluate : 2.313 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 0 residues processed: 48 average time/residue: 0.2082 time to fit residues: 21.2602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 87 optimal weight: 10.0000 chunk 235 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 153 optimal weight: 5.9990 chunk 64 optimal weight: 9.9990 chunk 261 optimal weight: 1.9990 chunk 216 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 137 optimal weight: 6.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 63 ASN b 30 ASN e 34 GLN ** e 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 69 GLN i 32 ASN ** i 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 230 ASN ** k 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 26 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.4495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 21409 Z= 0.208 Angle : 0.567 8.912 29223 Z= 0.288 Chirality : 0.044 0.176 3300 Planarity : 0.004 0.037 3804 Dihedral : 5.440 54.889 3000 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer Outliers : 1.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.16), residues: 2516 helix: -1.78 (0.33), residues: 221 sheet: 0.31 (0.20), residues: 649 loop : -0.26 (0.15), residues: 1646 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 488 time to evaluate : 2.328 Fit side-chains revert: symmetry clash outliers start: 31 outliers final: 18 residues processed: 501 average time/residue: 0.3592 time to fit residues: 277.6144 Evaluate side-chains 456 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 438 time to evaluate : 2.308 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2084 time to fit residues: 10.0553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 251 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 148 optimal weight: 9.9990 chunk 190 optimal weight: 0.4980 chunk 147 optimal weight: 9.9990 chunk 219 optimal weight: 0.0070 chunk 145 optimal weight: 10.0000 chunk 260 optimal weight: 7.9990 chunk 162 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 120 optimal weight: 10.0000 overall best weight: 1.9004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 63 ASN e 34 GLN e 89 ASN ** e 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 111 GLN ** f 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 69 GLN ** h 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 26 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.4624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 21409 Z= 0.198 Angle : 0.558 9.237 29223 Z= 0.281 Chirality : 0.044 0.211 3300 Planarity : 0.004 0.038 3804 Dihedral : 5.328 59.348 3000 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer Outliers : 1.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.16), residues: 2516 helix: -1.70 (0.33), residues: 220 sheet: 0.42 (0.20), residues: 643 loop : -0.20 (0.15), residues: 1653 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 464 time to evaluate : 2.306 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 15 residues processed: 479 average time/residue: 0.3377 time to fit residues: 246.6903 Evaluate side-chains 454 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 439 time to evaluate : 2.080 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1796 time to fit residues: 7.9091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 160 optimal weight: 0.0470 chunk 103 optimal weight: 9.9990 chunk 155 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 165 optimal weight: 7.9990 chunk 177 optimal weight: 5.9990 chunk 128 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 204 optimal weight: 0.0170 overall best weight: 2.2122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 63 ASN ** e 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 69 GLN ** h 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 230 ASN ** j 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 26 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.4740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 21409 Z= 0.207 Angle : 0.555 9.071 29223 Z= 0.279 Chirality : 0.044 0.161 3300 Planarity : 0.004 0.038 3804 Dihedral : 5.244 58.391 3000 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer Outliers : 1.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.16), residues: 2516 helix: -1.78 (0.32), residues: 227 sheet: 0.48 (0.20), residues: 642 loop : -0.23 (0.15), residues: 1647 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 452 time to evaluate : 2.185 Fit side-chains outliers start: 27 outliers final: 21 residues processed: 462 average time/residue: 0.3401 time to fit residues: 241.5962 Evaluate side-chains 456 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 435 time to evaluate : 2.325 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1968 time to fit residues: 10.7197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 236 optimal weight: 3.9990 chunk 249 optimal weight: 8.9990 chunk 227 optimal weight: 10.0000 chunk 242 optimal weight: 5.9990 chunk 145 optimal weight: 9.9990 chunk 105 optimal weight: 20.0000 chunk 190 optimal weight: 9.9990 chunk 74 optimal weight: 4.9990 chunk 219 optimal weight: 0.0470 chunk 229 optimal weight: 10.0000 chunk 241 optimal weight: 1.9990 overall best weight: 3.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 34 GLN ** e 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 69 GLN ** h 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 26 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.4819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 21409 Z= 0.268 Angle : 0.576 10.827 29223 Z= 0.290 Chirality : 0.044 0.162 3300 Planarity : 0.004 0.038 3804 Dihedral : 5.339 53.978 3000 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.16), residues: 2516 helix: -1.73 (0.32), residues: 226 sheet: 0.44 (0.20), residues: 629 loop : -0.27 (0.15), residues: 1661 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 449 time to evaluate : 2.362 Fit side-chains outliers start: 16 outliers final: 12 residues processed: 455 average time/residue: 0.3393 time to fit residues: 235.7471 Evaluate side-chains 445 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 433 time to evaluate : 2.175 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1943 time to fit residues: 7.2937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 159 optimal weight: 7.9990 chunk 256 optimal weight: 10.0000 chunk 156 optimal weight: 10.0000 chunk 121 optimal weight: 4.9990 chunk 178 optimal weight: 5.9990 chunk 268 optimal weight: 2.9990 chunk 247 optimal weight: 10.0000 chunk 214 optimal weight: 9.9990 chunk 22 optimal weight: 20.0000 chunk 165 optimal weight: 6.9990 chunk 131 optimal weight: 0.9980 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 63 ASN d 26 ASN ** e 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 69 GLN ** h 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 26 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.4907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.054 21409 Z= 0.322 Angle : 0.601 12.592 29223 Z= 0.303 Chirality : 0.045 0.155 3300 Planarity : 0.004 0.037 3804 Dihedral : 5.473 57.818 3000 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.16), residues: 2516 helix: -1.79 (0.32), residues: 226 sheet: 0.31 (0.20), residues: 629 loop : -0.34 (0.15), residues: 1661 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 450 time to evaluate : 2.246 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 455 average time/residue: 0.3295 time to fit residues: 229.9615 Evaluate side-chains 444 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 435 time to evaluate : 2.214 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1927 time to fit residues: 6.1805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 170 optimal weight: 2.9990 chunk 228 optimal weight: 9.9990 chunk 65 optimal weight: 8.9990 chunk 197 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 214 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 220 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 26 GLN d 16 GLN e 171 GLN ** e 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 69 GLN ** h 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 34 GLN ** i 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 26 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.113458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.102212 restraints weight = 39431.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.104535 restraints weight = 19323.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.106053 restraints weight = 11691.705| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.5009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 21409 Z= 0.311 Angle : 0.600 11.284 29223 Z= 0.304 Chirality : 0.045 0.157 3300 Planarity : 0.004 0.038 3804 Dihedral : 5.519 56.473 3000 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.16), residues: 2516 helix: -1.75 (0.32), residues: 224 sheet: 0.15 (0.20), residues: 633 loop : -0.44 (0.15), residues: 1659 =============================================================================== Job complete usr+sys time: 4919.77 seconds wall clock time: 89 minutes 55.04 seconds (5395.04 seconds total)