Starting phenix.real_space_refine on Mon Mar 18 12:32:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tqu_26072/03_2024/7tqu_26072_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tqu_26072/03_2024/7tqu_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_26072/03_2024/7tqu_26072.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tqu_26072/03_2024/7tqu_26072.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tqu_26072/03_2024/7tqu_26072_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tqu_26072/03_2024/7tqu_26072_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 10.87, per 1000 atoms: 0.52 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: 7.78 Conformation dependent library (CDL) restraints added in 3.4 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: 4.58 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: 5.81 Time building geometry restraints manager: 8.48 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: 1.050 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: 5.960 Check model and map are aligned: 0.290 Set scattering table: 0.170 Process input model: 53.950 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.140 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.690 ------------------------------------------------------------------------------- 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 % Allowed : 0.27 % Favored : 99.73 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.009 TRP b 79 HIS 0.012 0.002 HIS j 118 PHE 0.042 0.006 PHE j 117 TYR 0.068 0.007 TYR b 142 ARG 0.009 0.001 ARG c 93 *********************** 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 : 1.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 64 TYR cc_start: 0.8109 (m-80) cc_final: 0.7824 (m-10) REVERT: a 78 ARG cc_start: 0.8474 (mmt-90) cc_final: 0.6472 (mtm180) REVERT: a 97 LYS cc_start: 0.8917 (pttt) cc_final: 0.8699 (pttt) REVERT: a 109 ASP cc_start: 0.8370 (m-30) cc_final: 0.7890 (m-30) REVERT: a 122 TYR cc_start: 0.9106 (m-80) cc_final: 0.8829 (m-80) REVERT: a 127 LEU cc_start: 0.9449 (tp) cc_final: 0.9231 (tp) REVERT: a 169 THR cc_start: 0.9136 (p) cc_final: 0.8879 (t) REVERT: b 64 TYR cc_start: 0.9398 (m-80) cc_final: 0.8959 (m-80) REVERT: b 74 THR cc_start: 0.8918 (p) cc_final: 0.8718 (p) REVERT: b 193 TYR cc_start: 0.9133 (m-80) cc_final: 0.8928 (m-10) REVERT: b 214 ASN cc_start: 0.8991 (t0) cc_final: 0.8726 (m-40) REVERT: b 264 ARG cc_start: 0.7204 (ptt180) cc_final: 0.5248 (mmt90) REVERT: c 49 ILE cc_start: 0.8971 (mt) cc_final: 0.8735 (mt) REVERT: c 50 ASP cc_start: 0.7563 (m-30) cc_final: 0.7314 (m-30) REVERT: c 53 ILE cc_start: 0.9627 (mt) cc_final: 0.9335 (mt) REVERT: c 55 MET cc_start: 0.9132 (tpp) cc_final: 0.8896 (tpp) REVERT: c 74 ASP cc_start: 0.8256 (p0) cc_final: 0.7989 (p0) REVERT: c 156 ASP cc_start: 0.8992 (t0) cc_final: 0.8771 (t0) REVERT: d 24 THR cc_start: 0.8742 (p) cc_final: 0.8517 (t) REVERT: d 36 SER cc_start: 0.8096 (p) cc_final: 0.7717 (t) REVERT: d 61 MET cc_start: 0.7445 (ttm) cc_final: 0.7214 (ttp) REVERT: e 31 VAL cc_start: 0.9368 (t) cc_final: 0.8992 (p) REVERT: e 47 SER cc_start: 0.9290 (m) cc_final: 0.9033 (t) REVERT: e 51 ILE cc_start: 0.9324 (pt) cc_final: 0.9063 (pt) REVERT: e 98 LYS cc_start: 0.8817 (mttt) cc_final: 0.8268 (tptt) REVERT: e 105 ILE cc_start: 0.9445 (mt) cc_final: 0.8924 (tt) REVERT: e 146 ARG cc_start: 0.7622 (mmm-85) cc_final: 0.7155 (mpt180) REVERT: e 205 ASP cc_start: 0.8645 (t0) cc_final: 0.8134 (t0) REVERT: e 209 ARG cc_start: 0.8010 (ptm-80) cc_final: 0.7568 (mtt-85) REVERT: e 226 LEU cc_start: 0.9286 (tp) cc_final: 0.8986 (tp) REVERT: e 242 ARG cc_start: 0.7554 (mmm-85) cc_final: 0.6995 (ppt170) REVERT: e 262 ARG cc_start: 0.7903 (mtp180) cc_final: 0.7684 (mtt-85) REVERT: f 13 VAL cc_start: 0.9402 (t) cc_final: 0.9063 (p) REVERT: f 15 GLN cc_start: 0.9182 (tt0) cc_final: 0.8961 (tt0) REVERT: f 91 MET cc_start: 0.8683 (mmm) cc_final: 0.8471 (mmt) REVERT: f 129 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8480 (mm-30) REVERT: f 191 PHE cc_start: 0.9275 (m-80) cc_final: 0.9026 (m-10) REVERT: f 214 ASN cc_start: 0.9025 (t0) cc_final: 0.8819 (t0) REVERT: f 264 ARG cc_start: 0.6357 (ptt180) cc_final: 0.4696 (mtt-85) REVERT: g 10 SER cc_start: 0.9123 (t) cc_final: 0.8835 (p) REVERT: g 77 SER cc_start: 0.9076 (t) cc_final: 0.8642 (m) REVERT: g 91 ASP cc_start: 0.8258 (t0) cc_final: 0.8025 (t0) REVERT: g 178 CYS cc_start: 0.8697 (m) cc_final: 0.8454 (m) REVERT: g 232 GLN cc_start: 0.8894 (tt0) cc_final: 0.6491 (pm20) REVERT: g 234 LYS cc_start: 0.7486 (mmtt) cc_final: 0.6806 (tttm) REVERT: h 24 THR cc_start: 0.9092 (p) cc_final: 0.8864 (t) REVERT: i 47 SER cc_start: 0.9006 (m) cc_final: 0.8593 (p) REVERT: i 55 VAL cc_start: 0.9155 (m) cc_final: 0.8944 (m) REVERT: i 58 THR cc_start: 0.9427 (p) cc_final: 0.9071 (p) REVERT: i 78 ARG cc_start: 0.8326 (mmt-90) cc_final: 0.7367 (mtm180) REVERT: i 90 SER cc_start: 0.8890 (p) cc_final: 0.8566 (m) REVERT: i 146 ARG cc_start: 0.7707 (tpp-160) cc_final: 0.7160 (ptp-170) REVERT: i 172 SER cc_start: 0.8538 (m) cc_final: 0.8158 (p) REVERT: i 182 TYR cc_start: 0.8902 (t80) cc_final: 0.8700 (t80) REVERT: i 264 TRP cc_start: 0.8248 (m100) cc_final: 0.7699 (m100) REVERT: j 26 GLN cc_start: 0.9080 (mt0) cc_final: 0.8816 (mt0) REVERT: j 132 MET cc_start: 0.8697 (mtp) cc_final: 0.8375 (mtm) REVERT: j 145 TYR cc_start: 0.9031 (t80) cc_final: 0.8753 (t80) REVERT: j 214 ASN cc_start: 0.9070 (t0) cc_final: 0.8719 (t0) REVERT: j 256 MET cc_start: 0.8969 (mtp) cc_final: 0.8610 (mtm) REVERT: k 42 ASN cc_start: 0.8153 (t0) cc_final: 0.7837 (t0) REVERT: k 43 MET cc_start: 0.9001 (mmm) cc_final: 0.8396 (mmm) REVERT: k 157 LEU cc_start: 0.9172 (mt) cc_final: 0.8870 (mt) REVERT: k 197 ILE cc_start: 0.9030 (mt) cc_final: 0.8821 (mt) REVERT: k 205 THR cc_start: 0.8721 (p) cc_final: 0.7954 (p) outliers start: 0 outliers final: 0 residues processed: 789 average time/residue: 0.3325 time to fit residues: 394.5313 Evaluate side-chains 513 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 513 time to evaluate : 2.355 ------------------------------------------------------------------------------- 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: 2.9990 chunk 138 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 211 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 128 optimal weight: 5.9990 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 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 Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21409 Z= 0.232 Angle : 0.641 8.311 29223 Z= 0.339 Chirality : 0.046 0.183 3300 Planarity : 0.004 0.044 3804 Dihedral : 5.726 44.772 3000 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.31 % Allowed : 10.24 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.16), residues: 2516 helix: -2.06 (0.33), residues: 184 sheet: 1.19 (0.19), residues: 655 loop : 0.41 (0.15), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP b 80 HIS 0.008 0.002 HIS i 99 PHE 0.025 0.002 PHE c 115 TYR 0.031 0.002 TYR c 68 ARG 0.008 0.001 ARG a 114 *********************** 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 647 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 596 time to evaluate : 2.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 78 ARG cc_start: 0.8494 (mmt-90) cc_final: 0.6346 (ttt180) REVERT: a 97 LYS cc_start: 0.8843 (pttt) cc_final: 0.8595 (pptt) REVERT: b 103 ARG cc_start: 0.9151 (ttt90) cc_final: 0.8883 (ttt-90) REVERT: b 145 TYR cc_start: 0.8985 (t80) cc_final: 0.8579 (t80) REVERT: b 193 TYR cc_start: 0.9159 (m-80) cc_final: 0.8901 (m-10) REVERT: b 214 ASN cc_start: 0.8825 (t0) cc_final: 0.8601 (m-40) REVERT: c 49 ILE cc_start: 0.8855 (mt) cc_final: 0.8631 (mt) REVERT: c 74 ASP cc_start: 0.8142 (p0) cc_final: 0.7912 (t0) REVERT: c 176 ARG cc_start: 0.9133 (mtt-85) cc_final: 0.8874 (mtt-85) REVERT: c 218 ASP cc_start: 0.8802 (p0) cc_final: 0.8598 (p0) REVERT: d 9 LYS cc_start: 0.8428 (tppt) cc_final: 0.8165 (tppt) REVERT: d 14 GLU cc_start: 0.7050 (tm-30) cc_final: 0.6702 (tm-30) REVERT: d 36 SER cc_start: 0.8092 (p) cc_final: 0.7622 (t) REVERT: d 44 GLN cc_start: 0.7641 (tt0) cc_final: 0.7376 (tt0) REVERT: e 31 VAL cc_start: 0.9391 (t) cc_final: 0.8995 (p) REVERT: e 47 SER cc_start: 0.9195 (m) cc_final: 0.8887 (t) REVERT: e 97 LYS cc_start: 0.8283 (pttm) cc_final: 0.7999 (tptt) REVERT: e 98 LYS cc_start: 0.8716 (mttt) cc_final: 0.8290 (tptt) REVERT: e 135 GLU cc_start: 0.5628 (OUTLIER) cc_final: 0.5410 (tt0) REVERT: e 146 ARG cc_start: 0.7702 (mmm-85) cc_final: 0.7261 (mpt180) REVERT: e 154 TYR cc_start: 0.8828 (t80) cc_final: 0.8502 (t80) REVERT: e 209 ARG cc_start: 0.7949 (ptm-80) cc_final: 0.7344 (mtt90) REVERT: e 240 VAL cc_start: 0.9233 (m) cc_final: 0.8999 (t) REVERT: e 242 ARG cc_start: 0.7465 (mmm-85) cc_final: 0.6951 (ptt180) REVERT: f 13 VAL cc_start: 0.9259 (t) cc_final: 0.8962 (p) REVERT: f 91 MET cc_start: 0.8219 (mmm) cc_final: 0.7929 (mmt) REVERT: f 223 LYS cc_start: 0.9286 (mttm) cc_final: 0.8993 (mtmm) REVERT: g 10 SER cc_start: 0.9078 (t) cc_final: 0.8787 (p) REVERT: g 61 LYS cc_start: 0.8856 (mmtt) cc_final: 0.8617 (mmtm) REVERT: g 77 SER cc_start: 0.8991 (t) cc_final: 0.8492 (m) REVERT: g 91 ASP cc_start: 0.8128 (t0) cc_final: 0.7833 (t0) REVERT: g 178 CYS cc_start: 0.8768 (m) cc_final: 0.8410 (m) REVERT: g 232 GLN cc_start: 0.8664 (tt0) cc_final: 0.6299 (pm20) REVERT: g 234 LYS cc_start: 0.7560 (mmtt) cc_final: 0.7076 (tmtt) REVERT: h 59 ASP cc_start: 0.8231 (m-30) cc_final: 0.7982 (m-30) REVERT: i 47 SER cc_start: 0.8728 (m) cc_final: 0.8216 (p) REVERT: i 78 ARG cc_start: 0.8199 (mmt-90) cc_final: 0.7458 (mtm180) REVERT: i 90 SER cc_start: 0.8689 (p) cc_final: 0.8410 (t) REVERT: i 105 ILE cc_start: 0.9266 (mt) cc_final: 0.9036 (mt) REVERT: i 146 ARG cc_start: 0.7839 (tpp-160) cc_final: 0.6991 (ptm160) REVERT: i 172 SER cc_start: 0.8710 (m) cc_final: 0.8187 (p) REVERT: i 205 ASP cc_start: 0.8152 (t0) cc_final: 0.7934 (t0) REVERT: i 264 TRP cc_start: 0.7909 (m100) cc_final: 0.7384 (m100) REVERT: j 33 VAL cc_start: 0.9576 (t) cc_final: 0.9085 (m) REVERT: j 89 MET cc_start: 0.8333 (mtp) cc_final: 0.7920 (mtp) REVERT: j 141 SER cc_start: 0.8409 (p) cc_final: 0.8142 (p) REVERT: j 183 SER cc_start: 0.8740 (p) cc_final: 0.8499 (p) REVERT: j 252 THR cc_start: 0.9596 (m) cc_final: 0.9144 (p) REVERT: j 256 MET cc_start: 0.8880 (mtp) cc_final: 0.8483 (mtm) REVERT: k 59 ASP cc_start: 0.7419 (t0) cc_final: 0.7016 (p0) REVERT: k 61 LYS cc_start: 0.9094 (mmtp) cc_final: 0.8874 (mptt) REVERT: k 75 ASN cc_start: 0.8406 (t0) cc_final: 0.7896 (p0) REVERT: k 157 LEU cc_start: 0.9272 (mt) cc_final: 0.9034 (mt) outliers start: 51 outliers final: 34 residues processed: 624 average time/residue: 0.3183 time to fit residues: 304.0723 Evaluate side-chains 543 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 508 time to evaluate : 2.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 33 SER Chi-restraints excluded: chain a residue 51 ILE Chi-restraints excluded: chain a residue 63 ASN Chi-restraints excluded: chain a residue 88 THR Chi-restraints excluded: chain b residue 79 TRP Chi-restraints excluded: chain b residue 115 SER Chi-restraints excluded: chain b residue 247 VAL Chi-restraints excluded: chain b residue 252 THR Chi-restraints excluded: chain b residue 265 ASN Chi-restraints excluded: chain c residue 76 LEU Chi-restraints excluded: chain c residue 162 SER Chi-restraints excluded: chain c residue 182 ASP Chi-restraints excluded: chain e residue 29 SER Chi-restraints excluded: chain e residue 40 THR Chi-restraints excluded: chain e residue 62 VAL Chi-restraints excluded: chain e residue 100 PHE Chi-restraints excluded: chain e residue 106 THR Chi-restraints excluded: chain e residue 135 GLU Chi-restraints excluded: chain e residue 140 THR Chi-restraints excluded: chain e residue 175 ASN Chi-restraints excluded: chain e residue 280 ASP Chi-restraints excluded: chain e residue 284 SER Chi-restraints excluded: chain e residue 293 ASP Chi-restraints excluded: chain f residue 10 SER Chi-restraints excluded: chain f residue 115 SER Chi-restraints excluded: chain g residue 7 THR Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 148 MET Chi-restraints excluded: chain i residue 51 ILE Chi-restraints excluded: chain i residue 175 ASN Chi-restraints excluded: chain i residue 280 ASP Chi-restraints excluded: chain j residue 153 ARG Chi-restraints excluded: chain k residue 7 THR Chi-restraints excluded: chain k residue 182 ASP Chi-restraints excluded: chain k residue 227 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 136 optimal weight: 10.0000 chunk 76 optimal weight: 0.0270 chunk 204 optimal weight: 9.9990 chunk 166 optimal weight: 10.0000 chunk 67 optimal weight: 3.9990 chunk 245 optimal weight: 9.9990 chunk 265 optimal weight: 20.0000 chunk 218 optimal weight: 0.0170 chunk 243 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 197 optimal weight: 9.9990 overall best weight: 1.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 34 GLN a 63 ASN d 4 GLN d 21 ASN ** e 49 GLN ** 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 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 56 ASN g 69 GLN g 73 ASN ** 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: 0.8250 moved from start: 0.3151 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= 0.193 Angle : 0.563 8.095 29223 Z= 0.289 Chirality : 0.044 0.173 3300 Planarity : 0.004 0.045 3804 Dihedral : 5.336 49.054 3000 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 4.08 % Allowed : 11.64 % Favored : 84.28 % 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: 0.37 (0.16), residues: 2516 helix: -1.84 (0.34), residues: 198 sheet: 0.99 (0.19), residues: 670 loop : 0.29 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP j 80 HIS 0.006 0.001 HIS b 195 PHE 0.032 0.002 PHE j 239 TYR 0.022 0.001 TYR a 180 ARG 0.005 0.000 ARG a 114 *********************** 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 620 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 530 time to evaluate : 2.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 78 ARG cc_start: 0.8542 (mmt-90) cc_final: 0.6445 (mtm180) REVERT: a 97 LYS cc_start: 0.8861 (pttt) cc_final: 0.8575 (pptt) REVERT: a 113 LEU cc_start: 0.9131 (tp) cc_final: 0.8702 (tp) REVERT: b 172 ARG cc_start: 0.6614 (mpt180) cc_final: 0.6331 (mmt-90) REVERT: b 193 TYR cc_start: 0.9165 (m-80) cc_final: 0.8861 (m-10) REVERT: c 55 MET cc_start: 0.9039 (tpp) cc_final: 0.8688 (tpp) REVERT: c 115 PHE cc_start: 0.8641 (m-80) cc_final: 0.8381 (m-80) REVERT: c 176 ARG cc_start: 0.9053 (mtt-85) cc_final: 0.8766 (mtt-85) REVERT: d 9 LYS cc_start: 0.8444 (tppt) cc_final: 0.8207 (tppt) REVERT: d 14 GLU cc_start: 0.7133 (tm-30) cc_final: 0.6802 (tm-30) REVERT: d 36 SER cc_start: 0.8034 (p) cc_final: 0.7581 (t) REVERT: d 44 GLN cc_start: 0.7758 (tt0) cc_final: 0.7497 (tt0) REVERT: e 31 VAL cc_start: 0.9415 (t) cc_final: 0.9077 (p) REVERT: e 97 LYS cc_start: 0.8288 (pttm) cc_final: 0.7988 (tptt) REVERT: e 98 LYS cc_start: 0.8752 (mttt) cc_final: 0.8332 (tptt) REVERT: e 135 GLU cc_start: 0.5763 (OUTLIER) cc_final: 0.5468 (tt0) REVERT: e 146 ARG cc_start: 0.7687 (mmm-85) cc_final: 0.7260 (mpt180) REVERT: e 209 ARG cc_start: 0.7922 (ptm-80) cc_final: 0.7364 (mtt90) REVERT: e 240 VAL cc_start: 0.9149 (m) cc_final: 0.8803 (t) REVERT: e 242 ARG cc_start: 0.7382 (mmm-85) cc_final: 0.6796 (ptt180) REVERT: f 13 VAL cc_start: 0.9270 (t) cc_final: 0.8997 (p) REVERT: f 91 MET cc_start: 0.8267 (mmm) cc_final: 0.7853 (mmt) REVERT: g 10 SER cc_start: 0.9097 (t) cc_final: 0.8807 (p) REVERT: g 43 MET cc_start: 0.8900 (mmm) cc_final: 0.8612 (tpp) REVERT: g 51 THR cc_start: 0.9535 (OUTLIER) cc_final: 0.9196 (m) REVERT: g 77 SER cc_start: 0.8974 (t) cc_final: 0.8502 (m) REVERT: g 91 ASP cc_start: 0.8190 (t0) cc_final: 0.7888 (t0) REVERT: g 175 TYR cc_start: 0.9049 (m-80) cc_final: 0.8841 (m-80) REVERT: g 178 CYS cc_start: 0.8721 (m) cc_final: 0.8354 (m) REVERT: g 232 GLN cc_start: 0.8649 (tt0) cc_final: 0.6324 (pm20) REVERT: g 234 LYS cc_start: 0.7517 (mmtt) cc_final: 0.6986 (tttm) REVERT: h 59 ASP cc_start: 0.8176 (m-30) cc_final: 0.7952 (m-30) REVERT: i 78 ARG cc_start: 0.8282 (mmt-90) cc_final: 0.7507 (mtm180) REVERT: i 90 SER cc_start: 0.8807 (p) cc_final: 0.8440 (t) REVERT: i 146 ARG cc_start: 0.7977 (tpp-160) cc_final: 0.7070 (ptp-170) REVERT: i 172 SER cc_start: 0.8688 (m) cc_final: 0.8144 (p) REVERT: i 205 ASP cc_start: 0.8257 (t0) cc_final: 0.7955 (t0) REVERT: i 261 ILE cc_start: 0.9545 (tt) cc_final: 0.9317 (tt) REVERT: i 264 TRP cc_start: 0.7976 (m100) cc_final: 0.7362 (m100) REVERT: j 33 VAL cc_start: 0.9547 (t) cc_final: 0.9135 (m) REVERT: j 89 MET cc_start: 0.8484 (mtp) cc_final: 0.8054 (mtp) REVERT: j 141 SER cc_start: 0.8379 (p) cc_final: 0.8170 (p) REVERT: j 252 THR cc_start: 0.9603 (m) cc_final: 0.9160 (p) REVERT: j 256 MET cc_start: 0.8822 (mtp) cc_final: 0.8496 (mtm) REVERT: k 55 MET cc_start: 0.8533 (tpp) cc_final: 0.8311 (tpp) REVERT: k 59 ASP cc_start: 0.7331 (t0) cc_final: 0.6891 (p0) REVERT: k 75 ASN cc_start: 0.8294 (t0) cc_final: 0.7736 (m-40) REVERT: k 145 LYS cc_start: 0.8755 (mttt) cc_final: 0.8534 (tptt) REVERT: k 206 SER cc_start: 0.8719 (t) cc_final: 0.8422 (p) outliers start: 90 outliers final: 60 residues processed: 576 average time/residue: 0.3168 time to fit residues: 277.0676 Evaluate side-chains 540 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 478 time to evaluate : 2.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 51 ILE Chi-restraints excluded: chain a residue 63 ASN Chi-restraints excluded: chain a residue 88 THR Chi-restraints excluded: chain a residue 196 ILE Chi-restraints excluded: chain a residue 280 ASP Chi-restraints excluded: chain a residue 282 ILE Chi-restraints excluded: chain b residue 79 TRP Chi-restraints excluded: chain b residue 115 SER Chi-restraints excluded: chain b residue 247 VAL Chi-restraints excluded: chain b residue 252 THR Chi-restraints excluded: chain b residue 265 ASN Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 58 VAL Chi-restraints excluded: chain c residue 118 LEU Chi-restraints excluded: chain c residue 162 SER Chi-restraints excluded: chain c residue 182 ASP Chi-restraints excluded: chain c residue 205 THR Chi-restraints excluded: chain c residue 216 CYS Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain d residue 57 VAL Chi-restraints excluded: chain e residue 29 SER Chi-restraints excluded: chain e residue 40 THR Chi-restraints excluded: chain e residue 51 ILE Chi-restraints excluded: chain e residue 62 VAL Chi-restraints excluded: chain e residue 100 PHE Chi-restraints excluded: chain e residue 135 GLU Chi-restraints excluded: chain e residue 140 THR Chi-restraints excluded: chain e residue 169 THR Chi-restraints excluded: chain e residue 175 ASN Chi-restraints excluded: chain e residue 229 ILE Chi-restraints excluded: chain e residue 280 ASP Chi-restraints excluded: chain e residue 293 ASP Chi-restraints excluded: chain f residue 74 THR Chi-restraints excluded: chain f residue 115 SER Chi-restraints excluded: chain f residue 203 ASN Chi-restraints excluded: chain g residue 7 THR Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 56 ASN Chi-restraints excluded: chain g residue 67 MET Chi-restraints excluded: chain g residue 107 THR Chi-restraints excluded: chain g residue 142 THR Chi-restraints excluded: chain g residue 148 MET Chi-restraints excluded: chain g residue 173 THR Chi-restraints excluded: chain g residue 190 THR Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain h residue 42 THR Chi-restraints excluded: chain i residue 51 ILE Chi-restraints excluded: chain i residue 175 ASN Chi-restraints excluded: chain i residue 252 VAL Chi-restraints excluded: chain i residue 280 ASP Chi-restraints excluded: chain j residue 23 ILE Chi-restraints excluded: chain j residue 50 VAL Chi-restraints excluded: chain j residue 84 ASP Chi-restraints excluded: chain j residue 153 ARG Chi-restraints excluded: chain j residue 226 ASN Chi-restraints excluded: chain k residue 7 THR Chi-restraints excluded: chain k residue 132 SER Chi-restraints excluded: chain k residue 163 CYS Chi-restraints excluded: chain k residue 182 ASP Chi-restraints excluded: chain k residue 219 PHE Chi-restraints excluded: chain k residue 227 THR Chi-restraints excluded: chain l residue 42 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 242 optimal weight: 0.0370 chunk 184 optimal weight: 8.9990 chunk 127 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 117 optimal weight: 10.0000 chunk 164 optimal weight: 8.9990 chunk 246 optimal weight: 9.9990 chunk 260 optimal weight: 10.0000 chunk 128 optimal weight: 10.0000 chunk 233 optimal weight: 0.5980 chunk 70 optimal weight: 10.0000 overall best weight: 5.7264 ------------------------------------------------------------------------------- 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** c 11 ASN ** e 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 112 GLN ** 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 g 73 ASN i 32 ASN ** i 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 230 ASN j 261 ASN 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 21409 Z= 0.394 Angle : 0.650 8.919 29223 Z= 0.334 Chirality : 0.047 0.167 3300 Planarity : 0.005 0.044 3804 Dihedral : 5.661 55.920 3000 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 4.89 % Allowed : 11.83 % Favored : 83.28 % 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: -0.15 (0.16), residues: 2516 helix: -1.79 (0.33), residues: 215 sheet: 0.56 (0.20), residues: 652 loop : -0.07 (0.15), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP j 80 HIS 0.007 0.002 HIS h 13 PHE 0.026 0.002 PHE j 239 TYR 0.017 0.002 TYR a 180 ARG 0.009 0.001 ARG f 153 *********************** 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 606 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 498 time to evaluate : 2.357 Fit side-chains REVERT: a 78 ARG cc_start: 0.8749 (mmt-90) cc_final: 0.6387 (mtm180) REVERT: a 97 LYS cc_start: 0.8898 (pttt) cc_final: 0.8578 (pptt) REVERT: a 107 TYR cc_start: 0.9052 (p90) cc_final: 0.8813 (p90) REVERT: a 189 MET cc_start: 0.8033 (ptp) cc_final: 0.7754 (ptt) REVERT: a 196 ILE cc_start: 0.8935 (OUTLIER) cc_final: 0.8726 (pt) REVERT: a 209 ARG cc_start: 0.5705 (mmt-90) cc_final: 0.5253 (ttp-170) REVERT: b 172 ARG cc_start: 0.6650 (mpt180) cc_final: 0.6280 (mmt-90) REVERT: b 221 MET cc_start: 0.8025 (mmt) cc_final: 0.7766 (mmt) REVERT: c 176 ARG cc_start: 0.9077 (mtt-85) cc_final: 0.8837 (mtt-85) REVERT: d 14 GLU cc_start: 0.7244 (tm-30) cc_final: 0.7032 (tm-30) REVERT: d 32 TYR cc_start: 0.9179 (m-80) cc_final: 0.8804 (m-80) REVERT: d 36 SER cc_start: 0.8052 (p) cc_final: 0.7608 (t) REVERT: d 44 GLN cc_start: 0.7790 (tt0) cc_final: 0.7341 (tt0) REVERT: e 97 LYS cc_start: 0.8333 (pttm) cc_final: 0.8069 (tptt) REVERT: e 98 LYS cc_start: 0.8816 (mttt) cc_final: 0.8361 (tptt) REVERT: e 135 GLU cc_start: 0.6074 (OUTLIER) cc_final: 0.5476 (tt0) REVERT: e 146 ARG cc_start: 0.7864 (mmm-85) cc_final: 0.7299 (mpt180) REVERT: e 154 TYR cc_start: 0.9098 (t80) cc_final: 0.8764 (t80) REVERT: e 209 ARG cc_start: 0.8293 (ptm-80) cc_final: 0.7555 (mtt-85) REVERT: e 242 ARG cc_start: 0.7637 (mmm-85) cc_final: 0.6945 (ptt180) REVERT: f 13 VAL cc_start: 0.9300 (t) cc_final: 0.9007 (p) REVERT: f 192 VAL cc_start: 0.9368 (OUTLIER) cc_final: 0.9053 (t) REVERT: g 10 SER cc_start: 0.9143 (t) cc_final: 0.8827 (p) REVERT: g 43 MET cc_start: 0.8948 (mmm) cc_final: 0.8734 (tpp) REVERT: g 77 SER cc_start: 0.8896 (t) cc_final: 0.8613 (m) REVERT: g 178 CYS cc_start: 0.8693 (m) cc_final: 0.8439 (m) REVERT: g 232 GLN cc_start: 0.8885 (tt0) cc_final: 0.6643 (pm20) REVERT: g 234 LYS cc_start: 0.7731 (mmtt) cc_final: 0.7087 (tttm) REVERT: h 14 GLU cc_start: 0.8257 (tm-30) cc_final: 0.8056 (tm-30) REVERT: h 39 ASN cc_start: 0.8826 (m-40) cc_final: 0.8596 (m-40) REVERT: i 78 ARG cc_start: 0.8376 (mmt-90) cc_final: 0.7538 (mtm180) REVERT: i 90 SER cc_start: 0.8896 (p) cc_final: 0.8525 (t) REVERT: i 146 ARG cc_start: 0.8512 (tpp-160) cc_final: 0.7188 (ptp-170) REVERT: i 169 THR cc_start: 0.9090 (p) cc_final: 0.8692 (t) REVERT: i 172 SER cc_start: 0.8768 (m) cc_final: 0.8257 (p) REVERT: i 188 ARG cc_start: 0.7280 (ptp-170) cc_final: 0.6911 (ptp-170) REVERT: i 264 TRP cc_start: 0.8296 (m100) cc_final: 0.7517 (m100) REVERT: j 33 VAL cc_start: 0.9539 (t) cc_final: 0.9137 (m) REVERT: j 44 ASP cc_start: 0.8652 (m-30) cc_final: 0.8393 (m-30) REVERT: j 89 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8340 (mtp) REVERT: j 100 TYR cc_start: 0.8642 (t80) cc_final: 0.8417 (t80) REVERT: j 183 SER cc_start: 0.9077 (p) cc_final: 0.8810 (p) REVERT: j 256 MET cc_start: 0.8779 (mtp) cc_final: 0.8561 (mtm) REVERT: k 55 MET cc_start: 0.8625 (tpp) cc_final: 0.8378 (tpp) REVERT: k 59 ASP cc_start: 0.7574 (t0) cc_final: 0.6962 (p0) REVERT: k 75 ASN cc_start: 0.8375 (t0) cc_final: 0.8041 (p0) REVERT: k 157 LEU cc_start: 0.9215 (mt) cc_final: 0.8902 (mt) outliers start: 108 outliers final: 85 residues processed: 557 average time/residue: 0.3277 time to fit residues: 277.7068 Evaluate side-chains 565 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 476 time to evaluate : 2.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 51 ILE Chi-restraints excluded: chain a residue 63 ASN Chi-restraints excluded: chain a residue 88 THR Chi-restraints excluded: chain a residue 177 SER Chi-restraints excluded: chain a residue 181 MET Chi-restraints excluded: chain a residue 196 ILE Chi-restraints excluded: chain a residue 280 ASP Chi-restraints excluded: chain a residue 282 ILE Chi-restraints excluded: chain b residue 72 LYS Chi-restraints excluded: chain b residue 74 THR Chi-restraints excluded: chain b residue 79 TRP Chi-restraints excluded: chain b residue 181 LEU Chi-restraints excluded: chain b residue 214 ASN Chi-restraints excluded: chain b residue 247 VAL Chi-restraints excluded: chain b residue 252 THR Chi-restraints excluded: chain b residue 265 ASN Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 58 VAL Chi-restraints excluded: chain c residue 118 LEU Chi-restraints excluded: chain c residue 148 MET Chi-restraints excluded: chain c residue 162 SER Chi-restraints excluded: chain c residue 182 ASP Chi-restraints excluded: chain c residue 205 THR Chi-restraints excluded: chain c residue 216 CYS Chi-restraints excluded: chain c residue 221 VAL Chi-restraints excluded: chain d residue 42 THR Chi-restraints excluded: chain d residue 57 VAL Chi-restraints excluded: chain e residue 29 SER Chi-restraints excluded: chain e residue 40 THR Chi-restraints excluded: chain e residue 62 VAL Chi-restraints excluded: chain e residue 100 PHE Chi-restraints excluded: chain e residue 106 THR Chi-restraints excluded: chain e residue 135 GLU Chi-restraints excluded: chain e residue 140 THR Chi-restraints excluded: chain e residue 169 THR Chi-restraints excluded: chain e residue 175 ASN Chi-restraints excluded: chain e residue 229 ILE Chi-restraints excluded: chain e residue 281 MET Chi-restraints excluded: chain e residue 284 SER Chi-restraints excluded: chain e residue 289 LEU Chi-restraints excluded: chain e residue 293 ASP Chi-restraints excluded: chain f residue 10 SER Chi-restraints excluded: chain f residue 38 TRP Chi-restraints excluded: chain f residue 40 THR Chi-restraints excluded: chain f residue 58 VAL Chi-restraints excluded: chain f residue 74 THR Chi-restraints excluded: chain f residue 115 SER Chi-restraints excluded: chain f residue 192 VAL Chi-restraints excluded: chain f residue 201 ARG Chi-restraints excluded: chain g residue 7 THR Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 55 MET Chi-restraints excluded: chain g residue 107 THR Chi-restraints excluded: chain g residue 126 THR Chi-restraints excluded: chain g residue 142 THR Chi-restraints excluded: chain g residue 148 MET Chi-restraints excluded: chain g residue 173 THR Chi-restraints excluded: chain g residue 190 THR Chi-restraints excluded: chain g residue 206 SER Chi-restraints excluded: chain g residue 227 THR Chi-restraints excluded: chain h residue 4 GLN Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain h residue 42 THR Chi-restraints excluded: chain i residue 51 ILE Chi-restraints excluded: chain i residue 71 CYS Chi-restraints excluded: chain i residue 175 ASN Chi-restraints excluded: chain i residue 252 VAL Chi-restraints excluded: chain i residue 280 ASP Chi-restraints excluded: chain i residue 293 ASP Chi-restraints excluded: chain j residue 23 ILE Chi-restraints excluded: chain j residue 50 VAL Chi-restraints excluded: chain j residue 84 ASP Chi-restraints excluded: chain j residue 89 MET Chi-restraints excluded: chain j residue 153 ARG Chi-restraints excluded: chain j residue 226 ASN Chi-restraints excluded: chain k residue 7 THR Chi-restraints excluded: chain k residue 18 ASP Chi-restraints excluded: chain k residue 27 ASN Chi-restraints excluded: chain k residue 30 VAL Chi-restraints excluded: chain k residue 50 ASP Chi-restraints excluded: chain k residue 132 SER Chi-restraints excluded: chain k residue 163 CYS Chi-restraints excluded: chain k residue 182 ASP Chi-restraints excluded: chain k residue 205 THR Chi-restraints excluded: chain k residue 219 PHE Chi-restraints excluded: chain k residue 227 THR Chi-restraints excluded: chain l residue 42 THR Chi-restraints excluded: chain l residue 57 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 217 optimal weight: 6.9990 chunk 148 optimal weight: 7.9990 chunk 3 optimal weight: 30.0000 chunk 194 optimal weight: 20.0000 chunk 107 optimal weight: 10.0000 chunk 222 optimal weight: 1.9990 chunk 180 optimal weight: 10.0000 chunk 0 optimal weight: 40.0000 chunk 133 optimal weight: 5.9990 chunk 234 optimal weight: 6.9990 chunk 65 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 63 ASN a 198 ASN b 30 ASN ** b 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 44 GLN e 34 GLN ** e 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** f 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 56 ASN g 69 GLN ** i 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 21409 Z= 0.404 Angle : 0.634 9.632 29223 Z= 0.325 Chirality : 0.047 0.180 3300 Planarity : 0.005 0.046 3804 Dihedral : 5.717 56.217 3000 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 5.48 % Allowed : 13.59 % Favored : 80.92 % 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: -0.37 (0.16), residues: 2516 helix: -1.59 (0.35), residues: 202 sheet: 0.28 (0.20), residues: 656 loop : -0.23 (0.15), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP j 80 HIS 0.009 0.001 HIS g 96 PHE 0.022 0.002 PHE j 239 TYR 0.020 0.002 TYR f 100 ARG 0.009 0.001 ARG b 76 *********************** 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 620 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 499 time to evaluate : 2.490 Fit side-chains REVERT: a 78 ARG cc_start: 0.8856 (mmt-90) cc_final: 0.6318 (mtm180) REVERT: a 97 LYS cc_start: 0.8967 (pttt) cc_final: 0.8657 (pptt) REVERT: a 154 TYR cc_start: 0.8882 (t80) cc_final: 0.8500 (t80) REVERT: a 209 ARG cc_start: 0.5894 (mmt-90) cc_final: 0.4449 (mtt-85) REVERT: a 229 ILE cc_start: 0.8682 (pt) cc_final: 0.7998 (tp) REVERT: c 55 MET cc_start: 0.9061 (tpp) cc_final: 0.8625 (ttm) REVERT: c 176 ARG cc_start: 0.9104 (mtt-85) cc_final: 0.8827 (mtt-85) REVERT: d 44 GLN cc_start: 0.7832 (tt0) cc_final: 0.7596 (tt0) REVERT: e 97 LYS cc_start: 0.8357 (pttm) cc_final: 0.8082 (tptt) REVERT: e 98 LYS cc_start: 0.8867 (mttt) cc_final: 0.8459 (mmtt) REVERT: e 146 ARG cc_start: 0.7960 (mmm-85) cc_final: 0.7358 (mpt180) REVERT: e 154 TYR cc_start: 0.9117 (t80) cc_final: 0.8758 (t80) REVERT: e 209 ARG cc_start: 0.8350 (ptm-80) cc_final: 0.7591 (mtt-85) REVERT: e 242 ARG cc_start: 0.7796 (mmm-85) cc_final: 0.6847 (ptt180) REVERT: f 13 VAL cc_start: 0.9304 (t) cc_final: 0.9026 (p) REVERT: f 192 VAL cc_start: 0.9374 (OUTLIER) cc_final: 0.9065 (t) REVERT: f 203 ASN cc_start: 0.8424 (OUTLIER) cc_final: 0.8172 (m-40) REVERT: f 221 MET cc_start: 0.8756 (mtp) cc_final: 0.8482 (mtp) REVERT: g 10 SER cc_start: 0.9154 (t) cc_final: 0.8824 (p) REVERT: g 77 SER cc_start: 0.8806 (t) cc_final: 0.8536 (m) REVERT: g 98 MET cc_start: 0.9418 (tpp) cc_final: 0.9075 (tpt) REVERT: g 178 CYS cc_start: 0.8594 (m) cc_final: 0.8104 (m) REVERT: g 232 GLN cc_start: 0.8964 (tt0) cc_final: 0.6880 (pm20) REVERT: g 234 LYS cc_start: 0.7705 (mmtt) cc_final: 0.7087 (tttm) REVERT: i 57 GLU cc_start: 0.7116 (pp20) cc_final: 0.6833 (tm-30) REVERT: i 78 ARG cc_start: 0.8422 (mmt-90) cc_final: 0.7518 (mtm180) REVERT: i 90 SER cc_start: 0.8960 (p) cc_final: 0.8517 (t) REVERT: i 146 ARG cc_start: 0.8383 (tpp-160) cc_final: 0.6993 (ptp-170) REVERT: i 169 THR cc_start: 0.9127 (p) cc_final: 0.8746 (t) REVERT: i 172 SER cc_start: 0.8920 (m) cc_final: 0.8469 (p) REVERT: i 264 TRP cc_start: 0.8331 (m100) cc_final: 0.7597 (m100) REVERT: j 33 VAL cc_start: 0.9561 (t) cc_final: 0.9239 (m) REVERT: j 44 ASP cc_start: 0.8639 (m-30) cc_final: 0.8378 (m-30) REVERT: j 183 SER cc_start: 0.9089 (p) cc_final: 0.8875 (p) REVERT: k 75 ASN cc_start: 0.8290 (t0) cc_final: 0.8057 (p0) REVERT: k 157 LEU cc_start: 0.9234 (mt) cc_final: 0.8932 (mt) REVERT: k 218 ASP cc_start: 0.8230 (p0) cc_final: 0.7960 (p0) outliers start: 121 outliers final: 94 residues processed: 559 average time/residue: 0.3200 time to fit residues: 274.0339 Evaluate side-chains 561 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 465 time to evaluate : 2.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 51 ILE Chi-restraints excluded: chain a residue 88 THR Chi-restraints excluded: chain a residue 181 MET Chi-restraints excluded: chain a residue 280 ASP Chi-restraints excluded: chain a residue 282 ILE Chi-restraints excluded: chain b residue 17 THR Chi-restraints excluded: chain b residue 22 THR Chi-restraints excluded: chain b residue 72 LYS Chi-restraints excluded: chain b residue 79 TRP Chi-restraints excluded: chain b residue 104 SER Chi-restraints excluded: chain b residue 115 SER Chi-restraints excluded: chain b residue 181 LEU Chi-restraints excluded: chain b residue 214 ASN Chi-restraints excluded: chain b residue 252 THR Chi-restraints excluded: chain b residue 265 ASN Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 58 VAL Chi-restraints excluded: chain c residue 118 LEU Chi-restraints excluded: chain c residue 162 SER Chi-restraints excluded: chain c residue 182 ASP Chi-restraints excluded: chain c residue 205 THR Chi-restraints excluded: chain c residue 216 CYS Chi-restraints excluded: chain c residue 221 VAL Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain d residue 42 THR Chi-restraints excluded: chain d residue 46 LEU Chi-restraints excluded: chain d residue 57 VAL Chi-restraints excluded: chain e residue 29 SER Chi-restraints excluded: chain e residue 40 THR Chi-restraints excluded: chain e residue 62 VAL Chi-restraints excluded: chain e residue 100 PHE Chi-restraints excluded: chain e residue 106 THR Chi-restraints excluded: chain e residue 135 GLU Chi-restraints excluded: chain e residue 140 THR Chi-restraints excluded: chain e residue 169 THR Chi-restraints excluded: chain e residue 175 ASN Chi-restraints excluded: chain e residue 229 ILE Chi-restraints excluded: chain e residue 251 SER Chi-restraints excluded: chain e residue 281 MET Chi-restraints excluded: chain e residue 284 SER Chi-restraints excluded: chain e residue 289 LEU Chi-restraints excluded: chain e residue 293 ASP Chi-restraints excluded: chain f residue 10 SER Chi-restraints excluded: chain f residue 38 TRP Chi-restraints excluded: chain f residue 40 THR Chi-restraints excluded: chain f residue 74 THR Chi-restraints excluded: chain f residue 111 GLN Chi-restraints excluded: chain f residue 115 SER Chi-restraints excluded: chain f residue 143 VAL Chi-restraints excluded: chain f residue 160 THR Chi-restraints excluded: chain f residue 183 SER Chi-restraints excluded: chain f residue 192 VAL Chi-restraints excluded: chain f residue 201 ARG Chi-restraints excluded: chain f residue 203 ASN Chi-restraints excluded: chain g residue 7 THR Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 58 VAL Chi-restraints excluded: chain g residue 107 THR Chi-restraints excluded: chain g residue 126 THR Chi-restraints excluded: chain g residue 142 THR Chi-restraints excluded: chain g residue 148 MET Chi-restraints excluded: chain g residue 173 THR Chi-restraints excluded: chain g residue 190 THR Chi-restraints excluded: chain g residue 227 THR Chi-restraints excluded: chain h residue 4 GLN Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain h residue 42 THR Chi-restraints excluded: chain h residue 57 VAL Chi-restraints excluded: chain i residue 51 ILE Chi-restraints excluded: chain i residue 71 CYS Chi-restraints excluded: chain i residue 175 ASN Chi-restraints excluded: chain i residue 190 SER Chi-restraints excluded: chain i residue 252 VAL Chi-restraints excluded: chain i residue 280 ASP Chi-restraints excluded: chain i residue 293 ASP Chi-restraints excluded: chain j residue 23 ILE Chi-restraints excluded: chain j residue 50 VAL Chi-restraints excluded: chain j residue 84 ASP Chi-restraints excluded: chain j residue 226 ASN Chi-restraints excluded: chain j residue 252 THR Chi-restraints excluded: chain k residue 7 THR Chi-restraints excluded: chain k residue 18 ASP Chi-restraints excluded: chain k residue 27 ASN Chi-restraints excluded: chain k residue 30 VAL Chi-restraints excluded: chain k residue 50 ASP Chi-restraints excluded: chain k residue 163 CYS Chi-restraints excluded: chain k residue 182 ASP Chi-restraints excluded: chain k residue 203 THR Chi-restraints excluded: chain k residue 205 THR Chi-restraints excluded: chain k residue 219 PHE Chi-restraints excluded: chain k residue 227 THR Chi-restraints excluded: chain l residue 24 THR Chi-restraints excluded: chain l residue 42 THR Chi-restraints excluded: chain l residue 57 VAL Chi-restraints excluded: chain l residue 61 MET 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: 10.0000 chunk 153 optimal weight: 8.9990 chunk 64 optimal weight: 9.9990 chunk 261 optimal weight: 8.9990 chunk 216 optimal weight: 7.9990 chunk 120 optimal weight: 10.0000 chunk 21 optimal weight: 0.0000 chunk 86 optimal weight: 3.9990 chunk 137 optimal weight: 8.9990 overall best weight: 4.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 63 ASN ** b 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 34 GLN ** e 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 63 ASN g 69 GLN i 32 ASN i 230 ASN ** k 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 194 GLN ** 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 21409 Z= 0.342 Angle : 0.608 10.876 29223 Z= 0.309 Chirality : 0.046 0.174 3300 Planarity : 0.004 0.043 3804 Dihedral : 5.548 54.792 3000 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 5.30 % Allowed : 15.18 % Favored : 79.52 % 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: -0.53 (0.16), residues: 2516 helix: -1.79 (0.33), residues: 220 sheet: 0.22 (0.20), residues: 656 loop : -0.33 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP f 80 HIS 0.005 0.001 HIS g 96 PHE 0.018 0.002 PHE j 239 TYR 0.017 0.002 TYR c 193 ARG 0.007 0.001 ARG b 76 *********************** 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 597 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 480 time to evaluate : 2.325 Fit side-chains REVERT: a 97 LYS cc_start: 0.8966 (pttt) cc_final: 0.8670 (pptt) REVERT: a 154 TYR cc_start: 0.8828 (t80) cc_final: 0.8541 (t80) REVERT: a 209 ARG cc_start: 0.6043 (mmt-90) cc_final: 0.4353 (mtt-85) REVERT: a 229 ILE cc_start: 0.8663 (pt) cc_final: 0.7969 (tp) REVERT: a 238 ARG cc_start: 0.9021 (OUTLIER) cc_final: 0.8788 (ttp-170) REVERT: c 176 ARG cc_start: 0.9077 (mtt-85) cc_final: 0.8826 (mtt-85) REVERT: e 97 LYS cc_start: 0.8341 (pttm) cc_final: 0.8045 (tptt) REVERT: e 98 LYS cc_start: 0.8877 (mttt) cc_final: 0.8454 (mmtt) REVERT: e 146 ARG cc_start: 0.7922 (mmm-85) cc_final: 0.7321 (mpt180) REVERT: e 154 TYR cc_start: 0.9120 (t80) cc_final: 0.8755 (t80) REVERT: f 13 VAL cc_start: 0.9283 (t) cc_final: 0.8933 (p) REVERT: f 91 MET cc_start: 0.8029 (tpp) cc_final: 0.7747 (tpp) REVERT: f 192 VAL cc_start: 0.9357 (OUTLIER) cc_final: 0.9032 (t) REVERT: f 203 ASN cc_start: 0.8339 (OUTLIER) cc_final: 0.7856 (m-40) REVERT: g 10 SER cc_start: 0.9149 (t) cc_final: 0.8801 (p) REVERT: g 77 SER cc_start: 0.8815 (t) cc_final: 0.8484 (m) REVERT: g 98 MET cc_start: 0.9477 (tpp) cc_final: 0.9123 (tpt) REVERT: g 178 CYS cc_start: 0.8516 (m) cc_final: 0.8010 (m) REVERT: g 232 GLN cc_start: 0.8952 (tt0) cc_final: 0.6922 (pm20) REVERT: g 234 LYS cc_start: 0.7685 (mmtt) cc_final: 0.7126 (tttm) REVERT: i 78 ARG cc_start: 0.8502 (mmt-90) cc_final: 0.7559 (mtm180) REVERT: i 90 SER cc_start: 0.8878 (p) cc_final: 0.8672 (t) REVERT: i 146 ARG cc_start: 0.8367 (tpp-160) cc_final: 0.6865 (ptp-170) REVERT: i 169 THR cc_start: 0.9090 (p) cc_final: 0.8769 (t) REVERT: i 172 SER cc_start: 0.8954 (m) cc_final: 0.8523 (p) REVERT: i 264 TRP cc_start: 0.8305 (m100) cc_final: 0.7634 (m100) REVERT: j 33 VAL cc_start: 0.9555 (t) cc_final: 0.9249 (m) REVERT: j 44 ASP cc_start: 0.8622 (m-30) cc_final: 0.8370 (m-30) REVERT: j 183 SER cc_start: 0.9099 (p) cc_final: 0.8803 (p) REVERT: j 264 ARG cc_start: 0.5834 (mtt180) cc_final: 0.4793 (mtt-85) REVERT: k 159 LEU cc_start: 0.8613 (mt) cc_final: 0.7440 (tt) REVERT: k 165 MET cc_start: 0.9010 (tmm) cc_final: 0.8708 (ttt) REVERT: k 206 SER cc_start: 0.8916 (t) cc_final: 0.8668 (p) outliers start: 117 outliers final: 94 residues processed: 547 average time/residue: 0.3137 time to fit residues: 264.4510 Evaluate side-chains 564 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 467 time to evaluate : 2.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 51 ILE Chi-restraints excluded: chain a residue 88 THR Chi-restraints excluded: chain a residue 145 VAL Chi-restraints excluded: chain a residue 177 SER Chi-restraints excluded: chain a residue 178 ILE Chi-restraints excluded: chain a residue 181 MET Chi-restraints excluded: chain a residue 238 ARG Chi-restraints excluded: chain a residue 280 ASP Chi-restraints excluded: chain a residue 282 ILE Chi-restraints excluded: chain b residue 17 THR Chi-restraints excluded: chain b residue 72 LYS Chi-restraints excluded: chain b residue 74 THR Chi-restraints excluded: chain b residue 79 TRP Chi-restraints excluded: chain b residue 112 CYS Chi-restraints excluded: chain b residue 115 SER Chi-restraints excluded: chain b residue 181 LEU Chi-restraints excluded: chain b residue 214 ASN Chi-restraints excluded: chain b residue 252 THR Chi-restraints excluded: chain b residue 265 ASN Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 58 VAL Chi-restraints excluded: chain c residue 118 LEU Chi-restraints excluded: chain c residue 162 SER Chi-restraints excluded: chain c residue 182 ASP Chi-restraints excluded: chain c residue 205 THR Chi-restraints excluded: chain c residue 216 CYS Chi-restraints excluded: chain c residue 221 VAL Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain d residue 42 THR Chi-restraints excluded: chain d residue 46 LEU Chi-restraints excluded: chain d residue 57 VAL Chi-restraints excluded: chain e residue 28 THR Chi-restraints excluded: chain e residue 29 SER Chi-restraints excluded: chain e residue 40 THR Chi-restraints excluded: chain e residue 62 VAL Chi-restraints excluded: chain e residue 68 SER Chi-restraints excluded: chain e residue 100 PHE Chi-restraints excluded: chain e residue 106 THR Chi-restraints excluded: chain e residue 135 GLU Chi-restraints excluded: chain e residue 140 THR Chi-restraints excluded: chain e residue 169 THR Chi-restraints excluded: chain e residue 175 ASN Chi-restraints excluded: chain e residue 229 ILE Chi-restraints excluded: chain e residue 281 MET Chi-restraints excluded: chain e residue 284 SER Chi-restraints excluded: chain e residue 289 LEU Chi-restraints excluded: chain e residue 293 ASP Chi-restraints excluded: chain f residue 10 SER Chi-restraints excluded: chain f residue 40 THR Chi-restraints excluded: chain f residue 58 VAL Chi-restraints excluded: chain f residue 69 VAL Chi-restraints excluded: chain f residue 74 THR Chi-restraints excluded: chain f residue 115 SER Chi-restraints excluded: chain f residue 160 THR Chi-restraints excluded: chain f residue 183 SER Chi-restraints excluded: chain f residue 192 VAL Chi-restraints excluded: chain f residue 201 ARG Chi-restraints excluded: chain f residue 203 ASN Chi-restraints excluded: chain g residue 7 THR Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 58 VAL Chi-restraints excluded: chain g residue 107 THR Chi-restraints excluded: chain g residue 126 THR Chi-restraints excluded: chain g residue 142 THR Chi-restraints excluded: chain g residue 148 MET Chi-restraints excluded: chain g residue 173 THR Chi-restraints excluded: chain g residue 190 THR Chi-restraints excluded: chain g residue 227 THR Chi-restraints excluded: chain h residue 4 GLN Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain h residue 42 THR Chi-restraints excluded: chain i residue 71 CYS Chi-restraints excluded: chain i residue 175 ASN Chi-restraints excluded: chain i residue 190 SER Chi-restraints excluded: chain i residue 252 VAL Chi-restraints excluded: chain i residue 280 ASP Chi-restraints excluded: chain i residue 293 ASP Chi-restraints excluded: chain j residue 23 ILE Chi-restraints excluded: chain j residue 50 VAL Chi-restraints excluded: chain j residue 82 LEU Chi-restraints excluded: chain j residue 84 ASP Chi-restraints excluded: chain j residue 213 VAL Chi-restraints excluded: chain j residue 226 ASN Chi-restraints excluded: chain j residue 252 THR Chi-restraints excluded: chain k residue 7 THR Chi-restraints excluded: chain k residue 18 ASP Chi-restraints excluded: chain k residue 27 ASN Chi-restraints excluded: chain k residue 30 VAL Chi-restraints excluded: chain k residue 50 ASP Chi-restraints excluded: chain k residue 122 SER Chi-restraints excluded: chain k residue 163 CYS Chi-restraints excluded: chain k residue 182 ASP Chi-restraints excluded: chain k residue 203 THR Chi-restraints excluded: chain k residue 205 THR Chi-restraints excluded: chain k residue 227 THR Chi-restraints excluded: chain l residue 42 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 251 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 148 optimal weight: 8.9990 chunk 190 optimal weight: 0.3980 chunk 147 optimal weight: 2.9990 chunk 219 optimal weight: 0.3980 chunk 145 optimal weight: 9.9990 chunk 260 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 158 optimal weight: 0.3980 chunk 120 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 34 GLN a 63 ASN ** b 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 49 GLN ** e 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** h 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** 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: 0.4435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 21409 Z= 0.150 Angle : 0.533 8.863 29223 Z= 0.268 Chirality : 0.043 0.180 3300 Planarity : 0.004 0.040 3804 Dihedral : 5.155 57.922 3000 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.85 % Allowed : 17.58 % Favored : 79.57 % 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: -0.24 (0.16), residues: 2516 helix: -1.53 (0.35), residues: 208 sheet: 0.42 (0.20), residues: 652 loop : -0.15 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP f 80 HIS 0.008 0.001 HIS g 96 PHE 0.016 0.001 PHE j 239 TYR 0.019 0.001 TYR e 255 ARG 0.005 0.000 ARG b 153 *********************** 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 568 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 505 time to evaluate : 2.426 Fit side-chains REVERT: a 78 ARG cc_start: 0.8798 (mmt-90) cc_final: 0.6231 (ttt180) REVERT: a 97 LYS cc_start: 0.8910 (pttt) cc_final: 0.8606 (pptt) REVERT: a 107 TYR cc_start: 0.9016 (p90) cc_final: 0.8728 (p90) REVERT: a 189 MET cc_start: 0.7971 (ptp) cc_final: 0.7768 (ptm) REVERT: a 209 ARG cc_start: 0.5961 (mmt-90) cc_final: 0.4395 (mtt90) REVERT: a 229 ILE cc_start: 0.8436 (pt) cc_final: 0.7777 (tp) REVERT: c 218 ASP cc_start: 0.8963 (p0) cc_final: 0.8561 (p0) REVERT: d 9 LYS cc_start: 0.8050 (tppt) cc_final: 0.7381 (tppt) REVERT: d 36 SER cc_start: 0.7842 (p) cc_final: 0.7395 (t) REVERT: e 31 VAL cc_start: 0.9382 (t) cc_final: 0.9167 (p) REVERT: e 97 LYS cc_start: 0.8234 (pttm) cc_final: 0.7966 (tptt) REVERT: e 98 LYS cc_start: 0.8826 (mttt) cc_final: 0.8398 (mmtt) REVERT: e 105 ILE cc_start: 0.9301 (mt) cc_final: 0.8933 (tt) REVERT: e 146 ARG cc_start: 0.7822 (mmm-85) cc_final: 0.7204 (mpt180) REVERT: e 154 TYR cc_start: 0.9052 (t80) cc_final: 0.8730 (t80) REVERT: f 13 VAL cc_start: 0.9246 (t) cc_final: 0.8996 (p) REVERT: f 91 MET cc_start: 0.7741 (tpp) cc_final: 0.7412 (tpp) REVERT: f 191 PHE cc_start: 0.9285 (m-80) cc_final: 0.9047 (m-10) REVERT: f 266 ILE cc_start: 0.8696 (tp) cc_final: 0.8450 (tp) REVERT: g 10 SER cc_start: 0.9170 (t) cc_final: 0.8812 (p) REVERT: g 77 SER cc_start: 0.8717 (t) cc_final: 0.8423 (m) REVERT: g 98 MET cc_start: 0.9350 (tpp) cc_final: 0.9003 (tpt) REVERT: g 178 CYS cc_start: 0.8449 (m) cc_final: 0.7886 (m) REVERT: g 232 GLN cc_start: 0.8812 (tt0) cc_final: 0.6794 (pm20) REVERT: g 234 LYS cc_start: 0.7621 (mmtt) cc_final: 0.7005 (tttm) REVERT: i 78 ARG cc_start: 0.8380 (mmt-90) cc_final: 0.7434 (mtm180) REVERT: i 146 ARG cc_start: 0.8307 (tpp-160) cc_final: 0.6919 (ptt180) REVERT: i 172 SER cc_start: 0.8868 (m) cc_final: 0.8353 (p) REVERT: i 205 ASP cc_start: 0.8283 (t0) cc_final: 0.7956 (t0) REVERT: i 264 TRP cc_start: 0.8122 (m100) cc_final: 0.7517 (m100) REVERT: j 33 VAL cc_start: 0.9473 (t) cc_final: 0.9236 (m) REVERT: j 183 SER cc_start: 0.8951 (p) cc_final: 0.8665 (p) REVERT: j 264 ARG cc_start: 0.5767 (mtt180) cc_final: 0.4833 (mtt-85) REVERT: k 123 MET cc_start: 0.7266 (ttp) cc_final: 0.6927 (ttp) REVERT: k 159 LEU cc_start: 0.8548 (mt) cc_final: 0.7494 (tt) REVERT: k 165 MET cc_start: 0.8979 (tmm) cc_final: 0.8566 (ttt) REVERT: k 206 SER cc_start: 0.8805 (t) cc_final: 0.8501 (p) REVERT: k 218 ASP cc_start: 0.8130 (p0) cc_final: 0.7710 (p0) outliers start: 63 outliers final: 50 residues processed: 542 average time/residue: 0.3347 time to fit residues: 276.2501 Evaluate side-chains 525 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 475 time to evaluate : 2.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 42 VAL Chi-restraints excluded: chain a residue 51 ILE Chi-restraints excluded: chain a residue 63 ASN Chi-restraints excluded: chain a residue 88 THR Chi-restraints excluded: chain a residue 145 VAL Chi-restraints excluded: chain a residue 280 ASP Chi-restraints excluded: chain a residue 282 ILE Chi-restraints excluded: chain b residue 72 LYS Chi-restraints excluded: chain b residue 79 TRP Chi-restraints excluded: chain b residue 214 ASN Chi-restraints excluded: chain b residue 247 VAL Chi-restraints excluded: chain b residue 265 ASN Chi-restraints excluded: chain c residue 120 CYS Chi-restraints excluded: chain c residue 162 SER Chi-restraints excluded: chain c residue 182 ASP Chi-restraints excluded: chain c residue 205 THR Chi-restraints excluded: chain c residue 221 VAL Chi-restraints excluded: chain c residue 227 THR Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain d residue 57 VAL Chi-restraints excluded: chain e residue 40 THR Chi-restraints excluded: chain e residue 62 VAL Chi-restraints excluded: chain e residue 100 PHE Chi-restraints excluded: chain e residue 135 GLU Chi-restraints excluded: chain e residue 140 THR Chi-restraints excluded: chain e residue 280 ASP Chi-restraints excluded: chain e residue 281 MET Chi-restraints excluded: chain e residue 289 LEU Chi-restraints excluded: chain e residue 293 ASP Chi-restraints excluded: chain f residue 10 SER Chi-restraints excluded: chain f residue 115 SER Chi-restraints excluded: chain f residue 201 ARG Chi-restraints excluded: chain f residue 217 VAL Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 53 ILE Chi-restraints excluded: chain g residue 58 VAL Chi-restraints excluded: chain g residue 67 MET Chi-restraints excluded: chain g residue 190 THR Chi-restraints excluded: chain h residue 42 THR Chi-restraints excluded: chain h residue 51 SER Chi-restraints excluded: chain i residue 252 VAL Chi-restraints excluded: chain i residue 280 ASP Chi-restraints excluded: chain j residue 23 ILE Chi-restraints excluded: chain j residue 84 ASP Chi-restraints excluded: chain j residue 217 VAL Chi-restraints excluded: chain j residue 226 ASN Chi-restraints excluded: chain k residue 50 ASP Chi-restraints excluded: chain k residue 163 CYS Chi-restraints excluded: chain k residue 182 ASP Chi-restraints excluded: chain l residue 24 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 160 optimal weight: 10.0000 chunk 103 optimal weight: 0.1980 chunk 155 optimal weight: 8.9990 chunk 78 optimal weight: 0.0970 chunk 51 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 165 optimal weight: 8.9990 chunk 177 optimal weight: 2.9990 chunk 128 optimal weight: 0.3980 chunk 24 optimal weight: 0.4980 chunk 204 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 48 ASN ** b 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 198 ASN ** f 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 196 GLN g 63 ASN g 69 GLN ** h 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** 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: 0.8301 moved from start: 0.4554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 21409 Z= 0.158 Angle : 0.536 8.469 29223 Z= 0.270 Chirality : 0.043 0.187 3300 Planarity : 0.004 0.039 3804 Dihedral : 5.079 59.756 3000 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.85 % Allowed : 18.35 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.16), residues: 2516 helix: -1.48 (0.35), residues: 209 sheet: 0.59 (0.20), residues: 646 loop : -0.10 (0.15), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP j 227 HIS 0.006 0.001 HIS a 60 PHE 0.017 0.001 PHE f 63 TYR 0.032 0.001 TYR g 175 ARG 0.008 0.000 ARG b 153 *********************** 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 555 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 492 time to evaluate : 2.155 Fit side-chains revert: symmetry clash REVERT: a 78 ARG cc_start: 0.8752 (mmt-90) cc_final: 0.6228 (ttt180) REVERT: a 97 LYS cc_start: 0.8862 (pttt) cc_final: 0.8576 (pptt) REVERT: a 107 TYR cc_start: 0.8953 (p90) cc_final: 0.8638 (p90) REVERT: a 189 MET cc_start: 0.7926 (ptp) cc_final: 0.7690 (ptt) REVERT: a 209 ARG cc_start: 0.5879 (mmt-90) cc_final: 0.4226 (mtt-85) REVERT: a 229 ILE cc_start: 0.8430 (pt) cc_final: 0.7740 (tp) REVERT: c 218 ASP cc_start: 0.8908 (p0) cc_final: 0.8512 (p0) REVERT: d 36 SER cc_start: 0.7830 (p) cc_final: 0.7399 (t) REVERT: e 97 LYS cc_start: 0.8241 (pttm) cc_final: 0.7985 (tptt) REVERT: e 98 LYS cc_start: 0.8736 (mttt) cc_final: 0.8314 (mmtt) REVERT: e 146 ARG cc_start: 0.7815 (mmm-85) cc_final: 0.7192 (mpt180) REVERT: e 154 TYR cc_start: 0.9061 (t80) cc_final: 0.8721 (t80) REVERT: f 13 VAL cc_start: 0.9237 (t) cc_final: 0.8988 (p) REVERT: f 91 MET cc_start: 0.7793 (tpp) cc_final: 0.7506 (tpp) REVERT: f 191 PHE cc_start: 0.9260 (m-80) cc_final: 0.9045 (m-10) REVERT: f 192 VAL cc_start: 0.9262 (p) cc_final: 0.8928 (t) REVERT: f 266 ILE cc_start: 0.8648 (tp) cc_final: 0.8410 (tp) REVERT: g 10 SER cc_start: 0.9156 (t) cc_final: 0.8788 (p) REVERT: g 77 SER cc_start: 0.8725 (t) cc_final: 0.8458 (m) REVERT: g 98 MET cc_start: 0.9330 (tpp) cc_final: 0.9053 (tpt) REVERT: g 178 CYS cc_start: 0.8418 (m) cc_final: 0.7850 (m) REVERT: g 232 GLN cc_start: 0.8745 (tt0) cc_final: 0.6759 (pm20) REVERT: g 234 LYS cc_start: 0.7577 (mmtt) cc_final: 0.7004 (tttm) REVERT: i 34 GLN cc_start: 0.8273 (mm-40) cc_final: 0.7790 (mm-40) REVERT: i 78 ARG cc_start: 0.8269 (mmt-90) cc_final: 0.7481 (mtm180) REVERT: i 146 ARG cc_start: 0.8276 (tpp-160) cc_final: 0.6910 (ptt180) REVERT: i 172 SER cc_start: 0.8856 (m) cc_final: 0.8328 (p) REVERT: i 205 ASP cc_start: 0.8197 (t0) cc_final: 0.7894 (t0) REVERT: i 264 TRP cc_start: 0.8090 (m100) cc_final: 0.7558 (m100) REVERT: j 183 SER cc_start: 0.8931 (p) cc_final: 0.8625 (p) REVERT: j 264 ARG cc_start: 0.5801 (mtt180) cc_final: 0.4832 (mtt-85) REVERT: k 159 LEU cc_start: 0.8529 (mt) cc_final: 0.7394 (tt) REVERT: k 165 MET cc_start: 0.8952 (tmm) cc_final: 0.8541 (ttt) REVERT: k 206 SER cc_start: 0.8799 (t) cc_final: 0.8499 (p) REVERT: k 218 ASP cc_start: 0.8142 (p0) cc_final: 0.7638 (p0) outliers start: 63 outliers final: 47 residues processed: 523 average time/residue: 0.3233 time to fit residues: 257.9369 Evaluate side-chains 506 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 459 time to evaluate : 2.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 88 THR Chi-restraints excluded: chain a residue 145 VAL Chi-restraints excluded: chain a residue 280 ASP Chi-restraints excluded: chain a residue 282 ILE Chi-restraints excluded: chain b residue 72 LYS Chi-restraints excluded: chain b residue 79 TRP Chi-restraints excluded: chain b residue 181 LEU Chi-restraints excluded: chain b residue 214 ASN Chi-restraints excluded: chain b residue 247 VAL Chi-restraints excluded: chain b residue 265 ASN Chi-restraints excluded: chain b residue 266 ILE Chi-restraints excluded: chain c residue 120 CYS Chi-restraints excluded: chain c residue 148 MET Chi-restraints excluded: chain c residue 162 SER Chi-restraints excluded: chain c residue 182 ASP Chi-restraints excluded: chain c residue 205 THR Chi-restraints excluded: chain c residue 221 VAL Chi-restraints excluded: chain c residue 227 THR Chi-restraints excluded: chain d residue 42 THR Chi-restraints excluded: chain d residue 57 VAL Chi-restraints excluded: chain e residue 39 LEU Chi-restraints excluded: chain e residue 40 THR Chi-restraints excluded: chain e residue 62 VAL Chi-restraints excluded: chain e residue 135 GLU Chi-restraints excluded: chain e residue 140 THR Chi-restraints excluded: chain e residue 251 SER Chi-restraints excluded: chain e residue 280 ASP Chi-restraints excluded: chain e residue 281 MET Chi-restraints excluded: chain e residue 289 LEU Chi-restraints excluded: chain e residue 293 ASP Chi-restraints excluded: chain f residue 115 SER Chi-restraints excluded: chain f residue 201 ARG Chi-restraints excluded: chain f residue 217 VAL Chi-restraints excluded: chain g residue 190 THR Chi-restraints excluded: chain h residue 42 THR Chi-restraints excluded: chain i residue 252 VAL Chi-restraints excluded: chain i residue 280 ASP Chi-restraints excluded: chain j residue 23 ILE Chi-restraints excluded: chain j residue 84 ASP Chi-restraints excluded: chain j residue 217 VAL Chi-restraints excluded: chain j residue 226 ASN Chi-restraints excluded: chain j residue 252 THR Chi-restraints excluded: chain k residue 18 ASP Chi-restraints excluded: chain k residue 50 ASP Chi-restraints excluded: chain k residue 163 CYS Chi-restraints excluded: chain k residue 182 ASP Chi-restraints excluded: chain k residue 203 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 236 optimal weight: 20.0000 chunk 249 optimal weight: 10.0000 chunk 227 optimal weight: 5.9990 chunk 242 optimal weight: 3.9990 chunk 145 optimal weight: 20.0000 chunk 105 optimal weight: 20.0000 chunk 190 optimal weight: 0.0270 chunk 74 optimal weight: 10.0000 chunk 219 optimal weight: 9.9990 chunk 229 optimal weight: 0.0270 chunk 241 optimal weight: 0.5980 overall best weight: 2.1300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 63 ASN ** b 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 8 GLN ** e 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.4641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21409 Z= 0.203 Angle : 0.546 8.834 29223 Z= 0.274 Chirality : 0.044 0.290 3300 Planarity : 0.004 0.040 3804 Dihedral : 5.039 57.034 3000 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.95 % Allowed : 18.62 % Favored : 78.43 % 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: -0.11 (0.16), residues: 2516 helix: -1.40 (0.35), residues: 209 sheet: 0.55 (0.20), residues: 648 loop : -0.08 (0.15), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP f 80 HIS 0.005 0.001 HIS g 96 PHE 0.018 0.001 PHE f 63 TYR 0.022 0.001 TYR f 100 ARG 0.008 0.000 ARG b 153 *********************** 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 542 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 477 time to evaluate : 2.195 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 78 ARG cc_start: 0.8776 (mmt-90) cc_final: 0.6260 (ttt180) REVERT: a 97 LYS cc_start: 0.8888 (pttt) cc_final: 0.8593 (pptt) REVERT: a 107 TYR cc_start: 0.9009 (p90) cc_final: 0.8664 (p90) REVERT: a 189 MET cc_start: 0.7992 (ptp) cc_final: 0.7781 (ptt) REVERT: a 209 ARG cc_start: 0.5883 (mmt-90) cc_final: 0.4207 (mtt-85) REVERT: a 229 ILE cc_start: 0.8399 (pt) cc_final: 0.7707 (tp) REVERT: c 218 ASP cc_start: 0.8945 (p0) cc_final: 0.8509 (p0) REVERT: d 36 SER cc_start: 0.7871 (p) cc_final: 0.7454 (t) REVERT: e 24 SER cc_start: 0.8482 (m) cc_final: 0.7993 (p) REVERT: e 97 LYS cc_start: 0.8250 (pttm) cc_final: 0.7997 (tptt) REVERT: e 98 LYS cc_start: 0.8772 (mttt) cc_final: 0.8334 (mmtt) REVERT: e 146 ARG cc_start: 0.7826 (mmm-85) cc_final: 0.7229 (mpt180) REVERT: e 154 TYR cc_start: 0.9068 (t80) cc_final: 0.8704 (t80) REVERT: e 240 VAL cc_start: 0.9077 (m) cc_final: 0.8853 (t) REVERT: f 13 VAL cc_start: 0.9202 (t) cc_final: 0.8932 (p) REVERT: f 91 MET cc_start: 0.7894 (tpp) cc_final: 0.7605 (tpp) REVERT: f 266 ILE cc_start: 0.8626 (tp) cc_final: 0.8391 (tp) REVERT: g 10 SER cc_start: 0.9167 (t) cc_final: 0.8815 (p) REVERT: g 77 SER cc_start: 0.8731 (t) cc_final: 0.8484 (m) REVERT: g 123 MET cc_start: 0.8585 (ppp) cc_final: 0.8106 (tmm) REVERT: g 178 CYS cc_start: 0.8444 (m) cc_final: 0.7844 (m) REVERT: g 232 GLN cc_start: 0.8793 (tt0) cc_final: 0.6802 (pm20) REVERT: g 234 LYS cc_start: 0.7490 (mmtt) cc_final: 0.6944 (tttm) REVERT: i 34 GLN cc_start: 0.8276 (mm-40) cc_final: 0.7718 (mm-40) REVERT: i 78 ARG cc_start: 0.8274 (mmt-90) cc_final: 0.7528 (mtm180) REVERT: i 146 ARG cc_start: 0.8371 (tpp-160) cc_final: 0.6929 (ptt180) REVERT: i 172 SER cc_start: 0.8824 (m) cc_final: 0.8330 (p) REVERT: i 205 ASP cc_start: 0.8223 (t0) cc_final: 0.7908 (t0) REVERT: i 264 TRP cc_start: 0.8167 (m100) cc_final: 0.7582 (m100) REVERT: j 183 SER cc_start: 0.8938 (p) cc_final: 0.8630 (p) REVERT: j 264 ARG cc_start: 0.5522 (mtt180) cc_final: 0.4815 (mtt-85) REVERT: k 65 MET cc_start: 0.7492 (mtm) cc_final: 0.7238 (mtm) REVERT: k 123 MET cc_start: 0.7235 (ttp) cc_final: 0.6901 (ttp) REVERT: k 159 LEU cc_start: 0.8500 (mt) cc_final: 0.7385 (tt) REVERT: k 165 MET cc_start: 0.8931 (tmm) cc_final: 0.8704 (ttt) REVERT: k 206 SER cc_start: 0.8818 (t) cc_final: 0.8504 (p) REVERT: k 218 ASP cc_start: 0.8125 (p0) cc_final: 0.7657 (p0) outliers start: 65 outliers final: 56 residues processed: 513 average time/residue: 0.3178 time to fit residues: 249.7042 Evaluate side-chains 522 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 466 time to evaluate : 2.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 39 LEU Chi-restraints excluded: chain a residue 88 THR Chi-restraints excluded: chain a residue 145 VAL Chi-restraints excluded: chain a residue 280 ASP Chi-restraints excluded: chain a residue 282 ILE Chi-restraints excluded: chain b residue 72 LYS Chi-restraints excluded: chain b residue 79 TRP Chi-restraints excluded: chain b residue 181 LEU Chi-restraints excluded: chain b residue 247 VAL Chi-restraints excluded: chain b residue 265 ASN Chi-restraints excluded: chain b residue 266 ILE Chi-restraints excluded: chain c residue 120 CYS Chi-restraints excluded: chain c residue 148 MET Chi-restraints excluded: chain c residue 162 SER Chi-restraints excluded: chain c residue 182 ASP Chi-restraints excluded: chain c residue 205 THR Chi-restraints excluded: chain c residue 221 VAL Chi-restraints excluded: chain c residue 227 THR Chi-restraints excluded: chain d residue 57 VAL Chi-restraints excluded: chain e residue 28 THR Chi-restraints excluded: chain e residue 39 LEU Chi-restraints excluded: chain e residue 40 THR Chi-restraints excluded: chain e residue 62 VAL Chi-restraints excluded: chain e residue 135 GLU Chi-restraints excluded: chain e residue 140 THR Chi-restraints excluded: chain e residue 175 ASN Chi-restraints excluded: chain e residue 251 SER Chi-restraints excluded: chain e residue 280 ASP Chi-restraints excluded: chain e residue 281 MET Chi-restraints excluded: chain e residue 289 LEU Chi-restraints excluded: chain e residue 293 ASP Chi-restraints excluded: chain f residue 58 VAL Chi-restraints excluded: chain f residue 111 GLN Chi-restraints excluded: chain f residue 115 SER Chi-restraints excluded: chain f residue 143 VAL Chi-restraints excluded: chain f residue 201 ARG Chi-restraints excluded: chain f residue 217 VAL Chi-restraints excluded: chain g residue 107 THR Chi-restraints excluded: chain g residue 113 ILE Chi-restraints excluded: chain g residue 142 THR Chi-restraints excluded: chain g residue 190 THR Chi-restraints excluded: chain g residue 206 SER Chi-restraints excluded: chain h residue 42 THR Chi-restraints excluded: chain i residue 252 VAL Chi-restraints excluded: chain i residue 280 ASP Chi-restraints excluded: chain j residue 23 ILE Chi-restraints excluded: chain j residue 84 ASP Chi-restraints excluded: chain j residue 217 VAL Chi-restraints excluded: chain j residue 226 ASN Chi-restraints excluded: chain j residue 252 THR Chi-restraints excluded: chain k residue 18 ASP Chi-restraints excluded: chain k residue 50 ASP Chi-restraints excluded: chain k residue 163 CYS Chi-restraints excluded: chain k residue 182 ASP Chi-restraints excluded: chain k residue 203 THR Chi-restraints excluded: chain l residue 42 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 159 optimal weight: 8.9990 chunk 256 optimal weight: 9.9990 chunk 156 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 chunk 178 optimal weight: 10.0000 chunk 268 optimal weight: 9.9990 chunk 247 optimal weight: 10.0000 chunk 214 optimal weight: 9.9990 chunk 22 optimal weight: 20.0000 chunk 165 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 63 ASN ** b 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 8 GLN ** e 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 32 ASN ** 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: 0.8361 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 21409 Z= 0.301 Angle : 0.585 10.248 29223 Z= 0.296 Chirality : 0.045 0.218 3300 Planarity : 0.004 0.040 3804 Dihedral : 5.178 50.524 3000 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.95 % Allowed : 18.85 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.16), residues: 2516 helix: -1.50 (0.35), residues: 209 sheet: 0.39 (0.20), residues: 645 loop : -0.18 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP f 80 HIS 0.006 0.001 HIS e 99 PHE 0.019 0.002 PHE k 212 TYR 0.029 0.001 TYR g 175 ARG 0.008 0.001 ARG c 176 ********************** 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 522 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 457 time to evaluate : 2.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 97 LYS cc_start: 0.8967 (pttt) cc_final: 0.8704 (pptt) REVERT: a 107 TYR cc_start: 0.9017 (p90) cc_final: 0.8661 (p90) REVERT: a 154 TYR cc_start: 0.8862 (t80) cc_final: 0.8626 (t80) REVERT: a 189 MET cc_start: 0.8172 (ptp) cc_final: 0.7919 (ptt) REVERT: a 209 ARG cc_start: 0.5972 (mmt-90) cc_final: 0.4283 (mtt-85) REVERT: c 55 MET cc_start: 0.9098 (tpp) cc_final: 0.8707 (ttm) REVERT: d 36 SER cc_start: 0.7899 (p) cc_final: 0.7488 (t) REVERT: e 24 SER cc_start: 0.8634 (m) cc_final: 0.8111 (p) REVERT: e 97 LYS cc_start: 0.8233 (pttm) cc_final: 0.7992 (tptt) REVERT: e 98 LYS cc_start: 0.8864 (mttt) cc_final: 0.8449 (mmtt) REVERT: e 146 ARG cc_start: 0.7865 (mmm-85) cc_final: 0.7267 (mpt180) REVERT: e 154 TYR cc_start: 0.9088 (t80) cc_final: 0.8720 (t80) REVERT: e 240 VAL cc_start: 0.9118 (m) cc_final: 0.8811 (t) REVERT: f 91 MET cc_start: 0.7989 (tpp) cc_final: 0.7684 (tpp) REVERT: f 266 ILE cc_start: 0.8651 (tp) cc_final: 0.8441 (tp) REVERT: g 10 SER cc_start: 0.9154 (t) cc_final: 0.8820 (p) REVERT: g 77 SER cc_start: 0.8748 (t) cc_final: 0.8499 (m) REVERT: g 123 MET cc_start: 0.8594 (ppp) cc_final: 0.8270 (ptm) REVERT: g 178 CYS cc_start: 0.8496 (m) cc_final: 0.8026 (m) REVERT: g 232 GLN cc_start: 0.8856 (tt0) cc_final: 0.6853 (pm20) REVERT: g 234 LYS cc_start: 0.7391 (mmtt) cc_final: 0.6928 (tttm) REVERT: i 34 GLN cc_start: 0.8252 (mm-40) cc_final: 0.7644 (mm-40) REVERT: i 78 ARG cc_start: 0.8361 (mmt-90) cc_final: 0.7485 (mtm180) REVERT: i 146 ARG cc_start: 0.8445 (tpp-160) cc_final: 0.6896 (ptt180) REVERT: i 172 SER cc_start: 0.8803 (m) cc_final: 0.8349 (p) REVERT: i 205 ASP cc_start: 0.8221 (t0) cc_final: 0.8010 (t0) REVERT: i 264 TRP cc_start: 0.8248 (m100) cc_final: 0.7632 (m100) REVERT: j 221 MET cc_start: 0.8567 (mpp) cc_final: 0.8208 (mtt) REVERT: j 264 ARG cc_start: 0.5722 (mtt180) cc_final: 0.4694 (mtt-85) REVERT: k 65 MET cc_start: 0.7555 (mtm) cc_final: 0.7245 (mtm) REVERT: k 159 LEU cc_start: 0.8470 (mt) cc_final: 0.7391 (tt) REVERT: k 165 MET cc_start: 0.8915 (tmm) cc_final: 0.8585 (ttt) REVERT: k 206 SER cc_start: 0.8868 (t) cc_final: 0.8606 (p) REVERT: k 218 ASP cc_start: 0.8200 (p0) cc_final: 0.7806 (p0) outliers start: 65 outliers final: 60 residues processed: 494 average time/residue: 0.3119 time to fit residues: 237.6306 Evaluate side-chains 505 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 445 time to evaluate : 2.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 39 LEU Chi-restraints excluded: chain a residue 88 THR Chi-restraints excluded: chain a residue 145 VAL Chi-restraints excluded: chain a residue 181 MET Chi-restraints excluded: chain a residue 280 ASP Chi-restraints excluded: chain a residue 282 ILE Chi-restraints excluded: chain b residue 72 LYS Chi-restraints excluded: chain b residue 79 TRP Chi-restraints excluded: chain b residue 115 SER Chi-restraints excluded: chain b residue 247 VAL Chi-restraints excluded: chain b residue 265 ASN Chi-restraints excluded: chain c residue 58 VAL Chi-restraints excluded: chain c residue 120 CYS Chi-restraints excluded: chain c residue 148 MET Chi-restraints excluded: chain c residue 162 SER Chi-restraints excluded: chain c residue 182 ASP Chi-restraints excluded: chain c residue 205 THR Chi-restraints excluded: chain c residue 221 VAL Chi-restraints excluded: chain c residue 227 THR Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain d residue 42 THR Chi-restraints excluded: chain d residue 57 VAL Chi-restraints excluded: chain e residue 28 THR Chi-restraints excluded: chain e residue 39 LEU Chi-restraints excluded: chain e residue 40 THR Chi-restraints excluded: chain e residue 62 VAL Chi-restraints excluded: chain e residue 135 GLU Chi-restraints excluded: chain e residue 140 THR Chi-restraints excluded: chain e residue 175 ASN Chi-restraints excluded: chain e residue 229 ILE Chi-restraints excluded: chain e residue 251 SER Chi-restraints excluded: chain e residue 281 MET Chi-restraints excluded: chain e residue 289 LEU Chi-restraints excluded: chain e residue 293 ASP Chi-restraints excluded: chain f residue 58 VAL Chi-restraints excluded: chain f residue 111 GLN Chi-restraints excluded: chain f residue 115 SER Chi-restraints excluded: chain f residue 143 VAL Chi-restraints excluded: chain f residue 183 SER Chi-restraints excluded: chain f residue 201 ARG Chi-restraints excluded: chain f residue 217 VAL Chi-restraints excluded: chain g residue 107 THR Chi-restraints excluded: chain g residue 113 ILE Chi-restraints excluded: chain g residue 142 THR Chi-restraints excluded: chain g residue 190 THR Chi-restraints excluded: chain g residue 206 SER Chi-restraints excluded: chain h residue 42 THR Chi-restraints excluded: chain i residue 252 VAL Chi-restraints excluded: chain i residue 280 ASP Chi-restraints excluded: chain j residue 23 ILE Chi-restraints excluded: chain j residue 84 ASP Chi-restraints excluded: chain j residue 217 VAL Chi-restraints excluded: chain j residue 226 ASN Chi-restraints excluded: chain j residue 252 THR Chi-restraints excluded: chain k residue 18 ASP Chi-restraints excluded: chain k residue 50 ASP Chi-restraints excluded: chain k residue 163 CYS Chi-restraints excluded: chain k residue 182 ASP Chi-restraints excluded: chain k residue 203 THR Chi-restraints excluded: chain l residue 42 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 170 optimal weight: 10.0000 chunk 228 optimal weight: 0.6980 chunk 65 optimal weight: 7.9990 chunk 197 optimal weight: 9.9990 chunk 31 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 214 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 chunk 220 optimal weight: 3.9990 chunk 27 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 63 ASN ** b 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 8 GLN ** e 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 171 GLN ** f 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 32 ASN ** i 198 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.113320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.102040 restraints weight = 39108.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.104353 restraints weight = 19066.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.105893 restraints weight = 11520.451| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.4810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 21409 Z= 0.282 Angle : 0.585 10.105 29223 Z= 0.295 Chirality : 0.045 0.217 3300 Planarity : 0.004 0.039 3804 Dihedral : 5.190 54.018 3000 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.08 % Allowed : 19.12 % Favored : 77.80 % 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: -1.39 (0.35), residues: 205 sheet: 0.35 (0.20), residues: 640 loop : -0.26 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP f 80 HIS 0.006 0.001 HIS e 99 PHE 0.018 0.002 PHE i 75 TYR 0.025 0.001 TYR g 175 ARG 0.008 0.001 ARG b 153 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5161.18 seconds wall clock time: 93 minutes 25.88 seconds (5605.88 seconds total)