Starting phenix.real_space_refine on Tue Apr 9 04:41:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmu_33305/04_2024/7xmu_33305_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmu_33305/04_2024/7xmu_33305.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmu_33305/04_2024/7xmu_33305_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmu_33305/04_2024/7xmu_33305_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmu_33305/04_2024/7xmu_33305_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmu_33305/04_2024/7xmu_33305.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmu_33305/04_2024/7xmu_33305.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmu_33305/04_2024/7xmu_33305_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmu_33305/04_2024/7xmu_33305_updated.pdb" } resolution = 2.3 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= 0.012 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: 6 Type Number sf(0) Gaussians P 36 5.49 5 Mg 12 5.21 5 S 78 5.16 5 C 8898 2.51 5 N 2574 2.21 5 O 3696 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 14": "OE1" <-> "OE2" Residue "A ARG 79": "NH1" <-> "NH2" Residue "A GLU 133": "OE1" <-> "OE2" Residue "A GLU 154": "OE1" <-> "OE2" Residue "A ARG 195": "NH1" <-> "NH2" Residue "A GLU 238": "OE1" <-> "OE2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "A ASP 279": "OD1" <-> "OD2" Residue "A GLU 280": "OE1" <-> "OE2" Residue "A ARG 302": "NH1" <-> "NH2" Residue "A GLU 306": "OE1" <-> "OE2" Residue "D GLU 14": "OE1" <-> "OE2" Residue "D ARG 79": "NH1" <-> "NH2" Residue "D GLU 133": "OE1" <-> "OE2" Residue "D GLU 154": "OE1" <-> "OE2" Residue "D ARG 195": "NH1" <-> "NH2" Residue "D GLU 238": "OE1" <-> "OE2" Residue "D GLU 268": "OE1" <-> "OE2" Residue "D ASP 279": "OD1" <-> "OD2" Residue "D GLU 280": "OE1" <-> "OE2" Residue "D ARG 302": "NH1" <-> "NH2" Residue "D GLU 306": "OE1" <-> "OE2" Residue "B GLU 14": "OE1" <-> "OE2" Residue "B ARG 79": "NH1" <-> "NH2" Residue "B GLU 133": "OE1" <-> "OE2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B ARG 195": "NH1" <-> "NH2" Residue "B GLU 238": "OE1" <-> "OE2" Residue "B GLU 268": "OE1" <-> "OE2" Residue "B ASP 279": "OD1" <-> "OD2" Residue "B GLU 280": "OE1" <-> "OE2" Residue "B ARG 302": "NH1" <-> "NH2" Residue "B GLU 306": "OE1" <-> "OE2" Residue "E GLU 14": "OE1" <-> "OE2" Residue "E ARG 79": "NH1" <-> "NH2" Residue "E GLU 133": "OE1" <-> "OE2" Residue "E GLU 154": "OE1" <-> "OE2" Residue "E ARG 195": "NH1" <-> "NH2" Residue "E GLU 238": "OE1" <-> "OE2" Residue "E GLU 268": "OE1" <-> "OE2" Residue "E ASP 279": "OD1" <-> "OD2" Residue "E GLU 280": "OE1" <-> "OE2" Residue "E ARG 302": "NH1" <-> "NH2" Residue "E GLU 306": "OE1" <-> "OE2" Residue "F GLU 14": "OE1" <-> "OE2" Residue "F ARG 79": "NH1" <-> "NH2" Residue "F GLU 133": "OE1" <-> "OE2" Residue "F GLU 154": "OE1" <-> "OE2" Residue "F ARG 195": "NH1" <-> "NH2" Residue "F GLU 238": "OE1" <-> "OE2" Residue "F GLU 268": "OE1" <-> "OE2" Residue "F ASP 279": "OD1" <-> "OD2" Residue "F GLU 280": "OE1" <-> "OE2" Residue "F ARG 302": "NH1" <-> "NH2" Residue "F GLU 306": "OE1" <-> "OE2" Residue "C GLU 14": "OE1" <-> "OE2" Residue "C ARG 79": "NH1" <-> "NH2" Residue "C GLU 133": "OE1" <-> "OE2" Residue "C GLU 154": "OE1" <-> "OE2" Residue "C ARG 195": "NH1" <-> "NH2" Residue "C GLU 238": "OE1" <-> "OE2" Residue "C GLU 268": "OE1" <-> "OE2" Residue "C ASP 279": "OD1" <-> "OD2" Residue "C GLU 280": "OE1" <-> "OE2" Residue "C ARG 302": "NH1" <-> "NH2" Residue "C GLU 306": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 15294 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2337 Classifications: {'peptide': 307} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 295} Chain breaks: 1 Chain: "D" Number of atoms: 2337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2337 Classifications: {'peptide': 307} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 295} Chain breaks: 1 Chain: "B" Number of atoms: 2337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2337 Classifications: {'peptide': 307} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 295} Chain breaks: 1 Chain: "E" Number of atoms: 2337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2337 Classifications: {'peptide': 307} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 295} Chain breaks: 1 Chain: "F" Number of atoms: 2337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2337 Classifications: {'peptide': 307} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 295} Chain breaks: 1 Chain: "C" Number of atoms: 2337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2337 Classifications: {'peptide': 307} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 295} Chain breaks: 1 Chain: "A" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 102 Unusual residues: {' MG': 2, 'ADP': 3, 'HSX': 1, 'PO4': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "D" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {' MG': 2, 'ADP': 2, 'HSX': 1, 'PO4': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {' MG': 2, 'ADP': 2, 'HSX': 1, 'PO4': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "E" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {' MG': 2, 'ADP': 2, 'HSX': 1, 'PO4': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "F" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {' MG': 2, 'ADP': 1, 'HSX': 1, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {' MG': 2, 'ADP': 2, 'HSX': 1, 'PO4': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "A" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 144 Classifications: {'water': 144} Link IDs: {None: 143} Chain: "D" Number of atoms: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 141 Classifications: {'water': 141} Link IDs: {None: 140} Chain: "B" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 135 Classifications: {'water': 135} Link IDs: {None: 134} Chain: "E" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 135 Classifications: {'water': 135} Link IDs: {None: 134} Chain: "F" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 132 Classifications: {'water': 132} Link IDs: {None: 131} Chain: "C" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 135 Classifications: {'water': 135} Link IDs: {None: 134} Time building chain proxies: 8.62, per 1000 atoms: 0.56 Number of scatterers: 15294 At special positions: 0 Unit cell: (119.78, 126.14, 83.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 78 16.00 P 36 15.00 Mg 12 11.99 O 3696 8.00 N 2574 7.00 C 8898 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: 6.76 Conformation dependent library (CDL) restraints added in 2.7 seconds 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3444 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 18 sheets defined 35.2% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.26 Creating SS restraints... Processing helix chain 'A' and resid 13 through 22 Processing helix chain 'A' and resid 63 through 79 Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 109 through 120 Processing helix chain 'A' and resid 133 through 138 Processing helix chain 'A' and resid 149 through 158 removed outlier: 3.659A pdb=" N GLN A 158 " --> pdb=" O GLU A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 183 removed outlier: 4.932A pdb=" N VAL A 175 " --> pdb=" O GLY A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 238 Processing helix chain 'A' and resid 257 through 262 Processing helix chain 'A' and resid 279 through 282 No H-bonds generated for 'chain 'A' and resid 279 through 282' Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 310 through 312 No H-bonds generated for 'chain 'A' and resid 310 through 312' Processing helix chain 'D' and resid 13 through 22 Processing helix chain 'D' and resid 63 through 79 Processing helix chain 'D' and resid 101 through 103 No H-bonds generated for 'chain 'D' and resid 101 through 103' Processing helix chain 'D' and resid 109 through 120 Processing helix chain 'D' and resid 133 through 138 Processing helix chain 'D' and resid 149 through 158 removed outlier: 3.658A pdb=" N GLN D 158 " --> pdb=" O GLU D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 183 removed outlier: 4.932A pdb=" N VAL D 175 " --> pdb=" O GLY D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 238 Processing helix chain 'D' and resid 257 through 262 Processing helix chain 'D' and resid 279 through 282 No H-bonds generated for 'chain 'D' and resid 279 through 282' Processing helix chain 'D' and resid 293 through 304 Processing helix chain 'D' and resid 310 through 312 No H-bonds generated for 'chain 'D' and resid 310 through 312' Processing helix chain 'B' and resid 13 through 22 Processing helix chain 'B' and resid 63 through 79 Processing helix chain 'B' and resid 101 through 103 No H-bonds generated for 'chain 'B' and resid 101 through 103' Processing helix chain 'B' and resid 109 through 120 Processing helix chain 'B' and resid 133 through 138 Processing helix chain 'B' and resid 149 through 158 removed outlier: 3.659A pdb=" N GLN B 158 " --> pdb=" O GLU B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 183 removed outlier: 4.932A pdb=" N VAL B 175 " --> pdb=" O GLY B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 238 Processing helix chain 'B' and resid 257 through 262 Processing helix chain 'B' and resid 279 through 282 No H-bonds generated for 'chain 'B' and resid 279 through 282' Processing helix chain 'B' and resid 293 through 304 Processing helix chain 'B' and resid 310 through 312 No H-bonds generated for 'chain 'B' and resid 310 through 312' Processing helix chain 'E' and resid 13 through 22 Processing helix chain 'E' and resid 63 through 79 Processing helix chain 'E' and resid 101 through 103 No H-bonds generated for 'chain 'E' and resid 101 through 103' Processing helix chain 'E' and resid 109 through 120 Processing helix chain 'E' and resid 133 through 138 Processing helix chain 'E' and resid 149 through 158 removed outlier: 3.659A pdb=" N GLN E 158 " --> pdb=" O GLU E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 183 removed outlier: 4.932A pdb=" N VAL E 175 " --> pdb=" O GLY E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 238 Processing helix chain 'E' and resid 257 through 262 Processing helix chain 'E' and resid 279 through 282 No H-bonds generated for 'chain 'E' and resid 279 through 282' Processing helix chain 'E' and resid 293 through 304 Processing helix chain 'E' and resid 310 through 312 No H-bonds generated for 'chain 'E' and resid 310 through 312' Processing helix chain 'F' and resid 13 through 22 Processing helix chain 'F' and resid 63 through 79 Processing helix chain 'F' and resid 101 through 103 No H-bonds generated for 'chain 'F' and resid 101 through 103' Processing helix chain 'F' and resid 109 through 120 Processing helix chain 'F' and resid 133 through 138 Processing helix chain 'F' and resid 149 through 158 removed outlier: 3.659A pdb=" N GLN F 158 " --> pdb=" O GLU F 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 171 through 183 removed outlier: 4.932A pdb=" N VAL F 175 " --> pdb=" O GLY F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 238 Processing helix chain 'F' and resid 257 through 262 Processing helix chain 'F' and resid 279 through 282 No H-bonds generated for 'chain 'F' and resid 279 through 282' Processing helix chain 'F' and resid 293 through 304 Processing helix chain 'F' and resid 310 through 312 No H-bonds generated for 'chain 'F' and resid 310 through 312' Processing helix chain 'C' and resid 13 through 22 Processing helix chain 'C' and resid 63 through 79 Processing helix chain 'C' and resid 101 through 103 No H-bonds generated for 'chain 'C' and resid 101 through 103' Processing helix chain 'C' and resid 109 through 120 Processing helix chain 'C' and resid 133 through 138 Processing helix chain 'C' and resid 149 through 158 removed outlier: 3.659A pdb=" N GLN C 158 " --> pdb=" O GLU C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 183 removed outlier: 4.932A pdb=" N VAL C 175 " --> pdb=" O GLY C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 238 Processing helix chain 'C' and resid 257 through 262 Processing helix chain 'C' and resid 279 through 282 No H-bonds generated for 'chain 'C' and resid 279 through 282' Processing helix chain 'C' and resid 293 through 304 Processing helix chain 'C' and resid 310 through 312 No H-bonds generated for 'chain 'C' and resid 310 through 312' Processing sheet with id= A, first strand: chain 'A' and resid 4 through 8 removed outlier: 6.343A pdb=" N ASP A 52 " --> pdb=" O LYS A 5 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N PHE A 7 " --> pdb=" O ASP A 52 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N PHE A 54 " --> pdb=" O PHE A 7 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ARG A 84 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ILE A 55 " --> pdb=" O ARG A 84 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR A 86 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ARG A 124 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ILE A 89 " --> pdb=" O ARG A 124 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N LEU A 126 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N THR A 127 " --> pdb=" O PRO A 142 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ASP A 144 " --> pdb=" O THR A 127 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 30 through 34 Processing sheet with id= C, first strand: chain 'A' and resid 287 through 289 removed outlier: 6.275A pdb=" N VAL A 269 " --> pdb=" O ARG A 288 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU A 268 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N CYS A 216 " --> pdb=" O PHE A 245 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N TYR A 247 " --> pdb=" O CYS A 216 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU A 218 " --> pdb=" O TYR A 247 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE A 165 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N VAL A 219 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL A 167 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASP A 188 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N SER A 168 " --> pdb=" O ASP A 188 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ALA A 190 " --> pdb=" O SER A 168 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 204 " --> pdb=" O ARG A 195 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 4 through 8 removed outlier: 6.343A pdb=" N ASP D 52 " --> pdb=" O LYS D 5 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N PHE D 7 " --> pdb=" O ASP D 52 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N PHE D 54 " --> pdb=" O PHE D 7 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ARG D 84 " --> pdb=" O ILE D 53 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ILE D 55 " --> pdb=" O ARG D 84 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR D 86 " --> pdb=" O ILE D 55 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ARG D 124 " --> pdb=" O ALA D 87 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ILE D 89 " --> pdb=" O ARG D 124 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LEU D 126 " --> pdb=" O ILE D 89 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N THR D 127 " --> pdb=" O PRO D 142 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ASP D 144 " --> pdb=" O THR D 127 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'D' and resid 30 through 34 Processing sheet with id= F, first strand: chain 'D' and resid 287 through 289 removed outlier: 6.275A pdb=" N VAL D 269 " --> pdb=" O ARG D 288 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU D 268 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N CYS D 216 " --> pdb=" O PHE D 245 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N TYR D 247 " --> pdb=" O CYS D 216 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU D 218 " --> pdb=" O TYR D 247 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE D 165 " --> pdb=" O VAL D 217 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N VAL D 219 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL D 167 " --> pdb=" O VAL D 219 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ASP D 188 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N SER D 168 " --> pdb=" O ASP D 188 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ALA D 190 " --> pdb=" O SER D 168 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL D 204 " --> pdb=" O ARG D 195 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 4 through 8 removed outlier: 6.343A pdb=" N ASP B 52 " --> pdb=" O LYS B 5 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N PHE B 7 " --> pdb=" O ASP B 52 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N PHE B 54 " --> pdb=" O PHE B 7 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ARG B 84 " --> pdb=" O ILE B 53 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ILE B 55 " --> pdb=" O ARG B 84 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR B 86 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ARG B 124 " --> pdb=" O ALA B 87 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ILE B 89 " --> pdb=" O ARG B 124 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N LEU B 126 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N THR B 127 " --> pdb=" O PRO B 142 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ASP B 144 " --> pdb=" O THR B 127 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 30 through 34 Processing sheet with id= I, first strand: chain 'B' and resid 287 through 289 removed outlier: 6.275A pdb=" N VAL B 269 " --> pdb=" O ARG B 288 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU B 268 " --> pdb=" O VAL B 244 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N CYS B 216 " --> pdb=" O PHE B 245 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N TYR B 247 " --> pdb=" O CYS B 216 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LEU B 218 " --> pdb=" O TYR B 247 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE B 165 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N VAL B 219 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL B 167 " --> pdb=" O VAL B 219 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASP B 188 " --> pdb=" O VAL B 166 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N SER B 168 " --> pdb=" O ASP B 188 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ALA B 190 " --> pdb=" O SER B 168 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL B 204 " --> pdb=" O ARG B 195 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 4 through 8 removed outlier: 6.343A pdb=" N ASP E 52 " --> pdb=" O LYS E 5 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N PHE E 7 " --> pdb=" O ASP E 52 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N PHE E 54 " --> pdb=" O PHE E 7 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ARG E 84 " --> pdb=" O ILE E 53 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N ILE E 55 " --> pdb=" O ARG E 84 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR E 86 " --> pdb=" O ILE E 55 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ARG E 124 " --> pdb=" O ALA E 87 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ILE E 89 " --> pdb=" O ARG E 124 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LEU E 126 " --> pdb=" O ILE E 89 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N THR E 127 " --> pdb=" O PRO E 142 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ASP E 144 " --> pdb=" O THR E 127 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'E' and resid 30 through 34 Processing sheet with id= L, first strand: chain 'E' and resid 287 through 289 removed outlier: 6.275A pdb=" N VAL E 269 " --> pdb=" O ARG E 288 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU E 268 " --> pdb=" O VAL E 244 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N CYS E 216 " --> pdb=" O PHE E 245 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N TYR E 247 " --> pdb=" O CYS E 216 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LEU E 218 " --> pdb=" O TYR E 247 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE E 165 " --> pdb=" O VAL E 217 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N VAL E 219 " --> pdb=" O ILE E 165 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL E 167 " --> pdb=" O VAL E 219 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ASP E 188 " --> pdb=" O VAL E 166 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N SER E 168 " --> pdb=" O ASP E 188 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ALA E 190 " --> pdb=" O SER E 168 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL E 204 " --> pdb=" O ARG E 195 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 4 through 8 removed outlier: 6.343A pdb=" N ASP F 52 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N PHE F 7 " --> pdb=" O ASP F 52 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N PHE F 54 " --> pdb=" O PHE F 7 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ARG F 84 " --> pdb=" O ILE F 53 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ILE F 55 " --> pdb=" O ARG F 84 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR F 86 " --> pdb=" O ILE F 55 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ARG F 124 " --> pdb=" O ALA F 87 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ILE F 89 " --> pdb=" O ARG F 124 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N LEU F 126 " --> pdb=" O ILE F 89 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N THR F 127 " --> pdb=" O PRO F 142 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ASP F 144 " --> pdb=" O THR F 127 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'F' and resid 30 through 34 Processing sheet with id= O, first strand: chain 'F' and resid 287 through 289 removed outlier: 6.275A pdb=" N VAL F 269 " --> pdb=" O ARG F 288 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU F 268 " --> pdb=" O VAL F 244 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N CYS F 216 " --> pdb=" O PHE F 245 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N TYR F 247 " --> pdb=" O CYS F 216 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU F 218 " --> pdb=" O TYR F 247 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE F 165 " --> pdb=" O VAL F 217 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N VAL F 219 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL F 167 " --> pdb=" O VAL F 219 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASP F 188 " --> pdb=" O VAL F 166 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N SER F 168 " --> pdb=" O ASP F 188 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ALA F 190 " --> pdb=" O SER F 168 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL F 204 " --> pdb=" O ARG F 195 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 4 through 8 removed outlier: 6.344A pdb=" N ASP C 52 " --> pdb=" O LYS C 5 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N PHE C 7 " --> pdb=" O ASP C 52 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N PHE C 54 " --> pdb=" O PHE C 7 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ARG C 84 " --> pdb=" O ILE C 53 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ILE C 55 " --> pdb=" O ARG C 84 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR C 86 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ARG C 124 " --> pdb=" O ALA C 87 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ILE C 89 " --> pdb=" O ARG C 124 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N LEU C 126 " --> pdb=" O ILE C 89 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N THR C 127 " --> pdb=" O PRO C 142 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ASP C 144 " --> pdb=" O THR C 127 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'C' and resid 30 through 34 Processing sheet with id= R, first strand: chain 'C' and resid 287 through 289 removed outlier: 6.274A pdb=" N VAL C 269 " --> pdb=" O ARG C 288 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU C 268 " --> pdb=" O VAL C 244 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N CYS C 216 " --> pdb=" O PHE C 245 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N TYR C 247 " --> pdb=" O CYS C 216 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LEU C 218 " --> pdb=" O TYR C 247 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE C 165 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N VAL C 219 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL C 167 " --> pdb=" O VAL C 219 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASP C 188 " --> pdb=" O VAL C 166 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N SER C 168 " --> pdb=" O ASP C 188 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ALA C 190 " --> pdb=" O SER C 168 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL C 204 " --> pdb=" O ARG C 195 " (cutoff:3.500A) 444 hydrogen bonds defined for protein. 1116 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: 5.08 Time building geometry restraints manager: 7.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4941 1.34 - 1.46: 1792 1.46 - 1.57: 7727 1.57 - 1.69: 54 1.69 - 1.81: 132 Bond restraints: 14646 Sorted by residual: bond pdb=" C1 HSX F 401 " pdb=" O4 HSX F 401 " ideal model delta sigma weight residual 1.293 1.606 -0.313 2.00e-02 2.50e+03 2.45e+02 bond pdb=" C1 HSX E 401 " pdb=" O4 HSX E 401 " ideal model delta sigma weight residual 1.293 1.606 -0.313 2.00e-02 2.50e+03 2.44e+02 bond pdb=" C1 HSX A 401 " pdb=" O4 HSX A 401 " ideal model delta sigma weight residual 1.293 1.605 -0.312 2.00e-02 2.50e+03 2.44e+02 bond pdb=" C1 HSX D 401 " pdb=" O4 HSX D 401 " ideal model delta sigma weight residual 1.293 1.605 -0.312 2.00e-02 2.50e+03 2.44e+02 bond pdb=" C1 HSX B 401 " pdb=" O4 HSX B 401 " ideal model delta sigma weight residual 1.293 1.605 -0.312 2.00e-02 2.50e+03 2.43e+02 ... (remaining 14641 not shown) Histogram of bond angle deviations from ideal: 100.34 - 107.48: 577 107.48 - 114.63: 8876 114.63 - 121.77: 7180 121.77 - 128.91: 3245 128.91 - 136.05: 54 Bond angle restraints: 19932 Sorted by residual: angle pdb=" N1 ADP A 406 " pdb=" C6 ADP A 406 " pdb=" N6 ADP A 406 " ideal model delta sigma weight residual 109.60 121.65 -12.05 3.00e+00 1.11e-01 1.61e+01 angle pdb=" N1 ADP E 406 " pdb=" C6 ADP E 406 " pdb=" N6 ADP E 406 " ideal model delta sigma weight residual 109.60 121.65 -12.05 3.00e+00 1.11e-01 1.61e+01 angle pdb=" N1 ADP B 406 " pdb=" C6 ADP B 406 " pdb=" N6 ADP B 406 " ideal model delta sigma weight residual 109.60 121.64 -12.04 3.00e+00 1.11e-01 1.61e+01 angle pdb=" N1 ADP D 406 " pdb=" C6 ADP D 406 " pdb=" N6 ADP D 406 " ideal model delta sigma weight residual 109.60 121.63 -12.03 3.00e+00 1.11e-01 1.61e+01 angle pdb=" N1 ADP C 406 " pdb=" C6 ADP C 406 " pdb=" N6 ADP C 406 " ideal model delta sigma weight residual 109.60 121.62 -12.02 3.00e+00 1.11e-01 1.61e+01 ... (remaining 19927 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 7902 17.38 - 34.77: 684 34.77 - 52.15: 232 52.15 - 69.54: 89 69.54 - 86.92: 45 Dihedral angle restraints: 8952 sinusoidal: 3654 harmonic: 5298 Sorted by residual: dihedral pdb=" CG ARG F 22 " pdb=" CD ARG F 22 " pdb=" NE ARG F 22 " pdb=" CZ ARG F 22 " ideal model delta sinusoidal sigma weight residual -180.00 -135.04 -44.96 2 1.50e+01 4.44e-03 1.07e+01 dihedral pdb=" CG ARG D 22 " pdb=" CD ARG D 22 " pdb=" NE ARG D 22 " pdb=" CZ ARG D 22 " ideal model delta sinusoidal sigma weight residual -180.00 -135.06 -44.94 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CG ARG C 22 " pdb=" CD ARG C 22 " pdb=" NE ARG C 22 " pdb=" CZ ARG C 22 " ideal model delta sinusoidal sigma weight residual -180.00 -135.09 -44.91 2 1.50e+01 4.44e-03 1.06e+01 ... (remaining 8949 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1039 0.026 - 0.053: 655 0.053 - 0.079: 335 0.079 - 0.105: 201 0.105 - 0.132: 80 Chirality restraints: 2310 Sorted by residual: chirality pdb=" CA ILE C 275 " pdb=" N ILE C 275 " pdb=" C ILE C 275 " pdb=" CB ILE C 275 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.33e-01 chirality pdb=" CA ILE E 275 " pdb=" N ILE E 275 " pdb=" C ILE E 275 " pdb=" CB ILE E 275 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.28e-01 chirality pdb=" CA ILE D 275 " pdb=" N ILE D 275 " pdb=" C ILE D 275 " pdb=" CB ILE D 275 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.25e-01 ... (remaining 2307 not shown) Planarity restraints: 2568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 HSX C 401 " 0.212 2.00e-02 2.50e+03 6.71e-01 1.01e+04 pdb=" C2 HSX C 401 " 0.887 2.00e-02 2.50e+03 pdb=" C3 HSX C 401 " 0.069 2.00e-02 2.50e+03 pdb=" C4 HSX C 401 " -0.346 2.00e-02 2.50e+03 pdb=" C5 HSX C 401 " 0.504 2.00e-02 2.50e+03 pdb=" O1 HSX C 401 " -0.977 2.00e-02 2.50e+03 pdb=" O2 HSX C 401 " 0.868 2.00e-02 2.50e+03 pdb=" O3 HSX C 401 " -1.054 2.00e-02 2.50e+03 pdb=" O4 HSX C 401 " -0.163 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 HSX A 401 " 0.213 2.00e-02 2.50e+03 6.71e-01 1.01e+04 pdb=" C2 HSX A 401 " 0.886 2.00e-02 2.50e+03 pdb=" C3 HSX A 401 " 0.069 2.00e-02 2.50e+03 pdb=" C4 HSX A 401 " -0.345 2.00e-02 2.50e+03 pdb=" C5 HSX A 401 " 0.504 2.00e-02 2.50e+03 pdb=" O1 HSX A 401 " -0.976 2.00e-02 2.50e+03 pdb=" O2 HSX A 401 " 0.867 2.00e-02 2.50e+03 pdb=" O3 HSX A 401 " -1.055 2.00e-02 2.50e+03 pdb=" O4 HSX A 401 " -0.163 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 HSX F 401 " -0.212 2.00e-02 2.50e+03 6.71e-01 1.01e+04 pdb=" C2 HSX F 401 " -0.886 2.00e-02 2.50e+03 pdb=" C3 HSX F 401 " -0.069 2.00e-02 2.50e+03 pdb=" C4 HSX F 401 " 0.346 2.00e-02 2.50e+03 pdb=" C5 HSX F 401 " -0.504 2.00e-02 2.50e+03 pdb=" O1 HSX F 401 " 0.976 2.00e-02 2.50e+03 pdb=" O2 HSX F 401 " -0.867 2.00e-02 2.50e+03 pdb=" O3 HSX F 401 " 1.054 2.00e-02 2.50e+03 pdb=" O4 HSX F 401 " 0.164 2.00e-02 2.50e+03 ... (remaining 2565 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 262 2.50 - 3.10: 10947 3.10 - 3.70: 24147 3.70 - 4.30: 38487 4.30 - 4.90: 60144 Nonbonded interactions: 133987 Sorted by model distance: nonbonded pdb="MG MG E 404 " pdb=" O HOH E 501 " model vdw 1.897 2.170 nonbonded pdb="MG MG C 404 " pdb=" O HOH C 501 " model vdw 1.900 2.170 nonbonded pdb="MG MG B 404 " pdb=" O HOH B 508 " model vdw 1.902 2.170 nonbonded pdb="MG MG A 404 " pdb=" O HOH A 501 " model vdw 1.904 2.170 nonbonded pdb="MG MG B 404 " pdb=" O HOH B 501 " model vdw 1.905 2.170 ... (remaining 133982 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 315 or resid 401 through 405)) selection = (chain 'B' and (resid 3 through 315 or resid 401 through 405)) selection = (chain 'C' and (resid 3 through 315 or resid 401 through 405)) selection = (chain 'D' and (resid 3 through 315 or resid 401 through 405)) selection = (chain 'E' and (resid 3 through 315 or resid 401 through 405)) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.180 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 44.640 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.100 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:11.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 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 : 0.016 0.313 14646 Z= 1.045 Angle : 0.899 12.053 19932 Z= 0.408 Chirality : 0.048 0.132 2310 Planarity : 0.042 0.671 2568 Dihedral : 17.556 86.924 5508 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.57 % Allowed : 9.02 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.19), residues: 1818 helix: 0.78 (0.19), residues: 726 sheet: 0.76 (0.24), residues: 414 loop : -1.51 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 131 PHE 0.015 0.001 PHE C 139 TYR 0.005 0.001 TYR E 91 ARG 0.001 0.000 ARG B 100 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 236 time to evaluate : 1.793 Fit side-chains REVERT: A 307 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8364 (mt-10) REVERT: E 73 MET cc_start: 0.8238 (mtt) cc_final: 0.8005 (mtp) REVERT: C 307 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8415 (mt-10) outliers start: 24 outliers final: 3 residues processed: 236 average time/residue: 1.8190 time to fit residues: 461.3948 Evaluate side-chains 173 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 170 time to evaluate : 1.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 280 GLU Chi-restraints excluded: chain E residue 280 GLU Chi-restraints excluded: chain F residue 280 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 5.9990 chunk 136 optimal weight: 8.9990 chunk 75 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 85 optimal weight: 0.4980 chunk 105 optimal weight: 4.9990 chunk 163 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 GLN B 57 GLN B 158 GLN E 57 GLN E 158 GLN F 163 ASN C 158 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.0837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14646 Z= 0.220 Angle : 1.825 47.059 19932 Z= 0.641 Chirality : 0.046 0.129 2310 Planarity : 0.004 0.041 2568 Dihedral : 15.615 87.714 2235 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.70 % Allowed : 10.07 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.16 (0.19), residues: 1818 helix: 0.62 (0.19), residues: 726 sheet: 0.64 (0.22), residues: 468 loop : -1.52 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 131 PHE 0.011 0.001 PHE A 139 TYR 0.006 0.001 TYR D 91 ARG 0.002 0.000 ARG C 178 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 181 time to evaluate : 1.888 Fit side-chains REVERT: A 5 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8560 (mttp) REVERT: A 57 GLN cc_start: 0.9110 (OUTLIER) cc_final: 0.8436 (tt0) REVERT: A 140 ASP cc_start: 0.8019 (OUTLIER) cc_final: 0.7721 (m-30) REVERT: D 156 MET cc_start: 0.8604 (mtt) cc_final: 0.8319 (mtp) REVERT: D 306 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7620 (mm-30) REVERT: B 194 LYS cc_start: 0.8868 (ttpp) cc_final: 0.8612 (ttpp) REVERT: E 280 GLU cc_start: 0.7845 (tp30) cc_final: 0.7629 (tp30) REVERT: F 156 MET cc_start: 0.8609 (mtt) cc_final: 0.8340 (mtp) REVERT: F 306 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7617 (mm-30) REVERT: C 57 GLN cc_start: 0.9117 (OUTLIER) cc_final: 0.8470 (tt0) REVERT: C 140 ASP cc_start: 0.7878 (OUTLIER) cc_final: 0.7551 (m-30) REVERT: C 188 ASP cc_start: 0.7942 (m-30) cc_final: 0.7694 (m-30) REVERT: C 282 LYS cc_start: 0.8715 (mtmt) cc_final: 0.8506 (mtpt) REVERT: C 306 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7776 (mt-10) outliers start: 26 outliers final: 3 residues processed: 195 average time/residue: 1.6546 time to fit residues: 349.9715 Evaluate side-chains 183 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 172 time to evaluate : 1.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain E residue 140 ASP Chi-restraints excluded: chain F residue 306 GLU Chi-restraints excluded: chain C residue 57 GLN Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 306 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 136 optimal weight: 7.9990 chunk 111 optimal weight: 3.9990 chunk 45 optimal weight: 0.0970 chunk 163 optimal weight: 0.5980 chunk 176 optimal weight: 8.9990 chunk 145 optimal weight: 0.5980 chunk 162 optimal weight: 6.9990 chunk 55 optimal weight: 0.0070 chunk 131 optimal weight: 3.9990 overall best weight: 1.0598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 GLN F 163 ASN C 158 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14646 Z= 0.199 Angle : 1.808 47.643 19932 Z= 0.631 Chirality : 0.045 0.124 2310 Planarity : 0.004 0.039 2568 Dihedral : 14.843 89.848 2226 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.57 % Allowed : 10.65 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 (0.19), residues: 1818 helix: 0.62 (0.19), residues: 726 sheet: 0.78 (0.23), residues: 456 loop : -1.50 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 250 PHE 0.011 0.001 PHE C 139 TYR 0.005 0.001 TYR C 91 ARG 0.002 0.000 ARG E 79 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 196 time to evaluate : 1.728 Fit side-chains REVERT: A 5 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8571 (mttp) REVERT: A 57 GLN cc_start: 0.9097 (OUTLIER) cc_final: 0.8430 (tt0) REVERT: A 140 ASP cc_start: 0.7892 (OUTLIER) cc_final: 0.7565 (m-30) REVERT: D 5 LYS cc_start: 0.8887 (mttp) cc_final: 0.8543 (mmtp) REVERT: D 140 ASP cc_start: 0.7866 (OUTLIER) cc_final: 0.7455 (m-30) REVERT: D 156 MET cc_start: 0.8577 (mtt) cc_final: 0.8342 (mtp) REVERT: D 306 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7694 (mm-30) REVERT: B 5 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8521 (mttm) REVERT: B 29 ASP cc_start: 0.8003 (t0) cc_final: 0.7769 (t0) REVERT: B 194 LYS cc_start: 0.8875 (ttpp) cc_final: 0.8253 (tttm) REVERT: E 5 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8526 (mttm) REVERT: E 14 GLU cc_start: 0.7202 (pm20) cc_final: 0.6998 (pm20) REVERT: E 29 ASP cc_start: 0.7994 (t0) cc_final: 0.7752 (t0) REVERT: E 133 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7712 (mt-10) REVERT: F 140 ASP cc_start: 0.7863 (OUTLIER) cc_final: 0.7484 (m-30) REVERT: F 156 MET cc_start: 0.8576 (mtt) cc_final: 0.8363 (mtp) REVERT: F 306 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7650 (mm-30) REVERT: C 57 GLN cc_start: 0.9102 (OUTLIER) cc_final: 0.8456 (tt0) REVERT: C 140 ASP cc_start: 0.7876 (OUTLIER) cc_final: 0.7541 (m-30) REVERT: C 182 LYS cc_start: 0.8358 (mtmt) cc_final: 0.8143 (mtmm) REVERT: C 188 ASP cc_start: 0.7967 (m-30) cc_final: 0.7736 (m-30) outliers start: 24 outliers final: 5 residues processed: 209 average time/residue: 1.6229 time to fit residues: 368.4418 Evaluate side-chains 193 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 177 time to evaluate : 1.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 158 GLN Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain E residue 5 LYS Chi-restraints excluded: chain E residue 140 ASP Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain F residue 306 GLU Chi-restraints excluded: chain C residue 57 GLN Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 158 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 6.9990 chunk 123 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 78 optimal weight: 5.9990 chunk 109 optimal weight: 0.0670 chunk 164 optimal weight: 0.9980 chunk 173 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 155 optimal weight: 0.4980 chunk 46 optimal weight: 0.4980 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 GLN B 158 GLN E 158 GLN F 163 ASN C 158 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14646 Z= 0.183 Angle : 1.804 47.680 19932 Z= 0.627 Chirality : 0.045 0.122 2310 Planarity : 0.003 0.038 2568 Dihedral : 14.476 89.955 2226 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.37 % Allowed : 11.50 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.01 (0.19), residues: 1818 helix: 0.71 (0.20), residues: 726 sheet: 0.84 (0.23), residues: 468 loop : -1.46 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 250 PHE 0.011 0.001 PHE F 139 TYR 0.005 0.001 TYR A 91 ARG 0.001 0.000 ARG E 100 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 185 time to evaluate : 1.702 Fit side-chains REVERT: A 57 GLN cc_start: 0.9081 (OUTLIER) cc_final: 0.8421 (tt0) REVERT: A 140 ASP cc_start: 0.7882 (OUTLIER) cc_final: 0.7560 (m-30) REVERT: D 5 LYS cc_start: 0.8857 (mttp) cc_final: 0.8523 (mmtp) REVERT: D 156 MET cc_start: 0.8538 (mtt) cc_final: 0.8307 (mtp) REVERT: D 306 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7665 (mm-30) REVERT: B 5 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8589 (mttp) REVERT: B 29 ASP cc_start: 0.8002 (t0) cc_final: 0.7793 (t0) REVERT: B 133 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7685 (mt-10) REVERT: B 194 LYS cc_start: 0.8900 (ttpp) cc_final: 0.8276 (tttm) REVERT: E 5 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8550 (mttp) REVERT: E 14 GLU cc_start: 0.7172 (pm20) cc_final: 0.6963 (pm20) REVERT: E 29 ASP cc_start: 0.7993 (t0) cc_final: 0.7778 (t0) REVERT: E 239 ARG cc_start: 0.7949 (mmm-85) cc_final: 0.7711 (mmt180) REVERT: F 140 ASP cc_start: 0.7866 (OUTLIER) cc_final: 0.7554 (m-30) REVERT: F 156 MET cc_start: 0.8565 (mtt) cc_final: 0.8343 (mtp) REVERT: F 306 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7659 (mm-30) REVERT: C 57 GLN cc_start: 0.9091 (OUTLIER) cc_final: 0.8439 (tt0) REVERT: C 140 ASP cc_start: 0.7863 (OUTLIER) cc_final: 0.7517 (m-30) REVERT: C 191 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8611 (mm) outliers start: 21 outliers final: 5 residues processed: 193 average time/residue: 1.6120 time to fit residues: 337.9862 Evaluate side-chains 192 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 177 time to evaluate : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain D residue 188 ASP Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain E residue 5 LYS Chi-restraints excluded: chain E residue 140 ASP Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain F residue 188 ASP Chi-restraints excluded: chain F residue 306 GLU Chi-restraints excluded: chain C residue 57 GLN Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 191 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 10.0000 chunk 98 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 chunk 120 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 88 optimal weight: 0.1980 chunk 156 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 158 GLN C 256 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14646 Z= 0.273 Angle : 1.821 47.452 19932 Z= 0.639 Chirality : 0.047 0.128 2310 Planarity : 0.004 0.040 2568 Dihedral : 14.241 88.484 2226 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.50 % Allowed : 11.50 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.13 (0.19), residues: 1818 helix: 0.66 (0.19), residues: 726 sheet: 0.71 (0.23), residues: 450 loop : -1.51 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 131 PHE 0.015 0.002 PHE D 139 TYR 0.008 0.001 TYR A 91 ARG 0.003 0.000 ARG E 78 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 188 time to evaluate : 1.688 Fit side-chains REVERT: A 5 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8669 (mttp) REVERT: A 57 GLN cc_start: 0.9164 (OUTLIER) cc_final: 0.8416 (tt0) REVERT: A 140 ASP cc_start: 0.8018 (OUTLIER) cc_final: 0.7712 (m-30) REVERT: A 306 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7791 (mt-10) REVERT: D 5 LYS cc_start: 0.8872 (mttp) cc_final: 0.8608 (mmtp) REVERT: D 140 ASP cc_start: 0.7893 (OUTLIER) cc_final: 0.7503 (m-30) REVERT: D 156 MET cc_start: 0.8572 (mtt) cc_final: 0.8312 (mtp) REVERT: D 306 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7694 (mm-30) REVERT: B 29 ASP cc_start: 0.7992 (t0) cc_final: 0.7786 (t70) REVERT: B 133 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7810 (mt-10) REVERT: B 194 LYS cc_start: 0.8894 (ttpp) cc_final: 0.8263 (tttm) REVERT: E 14 GLU cc_start: 0.7217 (pm20) cc_final: 0.6965 (pm20) REVERT: E 29 ASP cc_start: 0.8021 (t0) cc_final: 0.7807 (t70) REVERT: F 140 ASP cc_start: 0.7921 (OUTLIER) cc_final: 0.7554 (m-30) REVERT: F 156 MET cc_start: 0.8583 (mtt) cc_final: 0.8343 (mtp) REVERT: F 306 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7730 (mm-30) REVERT: C 5 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8657 (mttp) REVERT: C 57 GLN cc_start: 0.9170 (OUTLIER) cc_final: 0.8448 (tt0) REVERT: C 140 ASP cc_start: 0.8000 (OUTLIER) cc_final: 0.7679 (m-30) outliers start: 23 outliers final: 5 residues processed: 202 average time/residue: 1.6830 time to fit residues: 368.8029 Evaluate side-chains 199 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 183 time to evaluate : 1.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 188 ASP Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain E residue 140 ASP Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain F residue 188 ASP Chi-restraints excluded: chain F residue 306 GLU Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 57 GLN Chi-restraints excluded: chain C residue 140 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 0.9990 chunk 156 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 174 optimal weight: 2.9990 chunk 144 optimal weight: 10.0000 chunk 80 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 GLN B 256 ASN E 158 GLN F 163 ASN C 158 GLN C 256 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14646 Z= 0.230 Angle : 1.812 47.726 19932 Z= 0.633 Chirality : 0.046 0.127 2310 Planarity : 0.004 0.040 2568 Dihedral : 14.063 89.172 2226 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.70 % Allowed : 11.63 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 (0.19), residues: 1818 helix: 0.67 (0.19), residues: 726 sheet: 0.67 (0.23), residues: 456 loop : -1.46 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 131 PHE 0.013 0.001 PHE B 139 TYR 0.006 0.001 TYR A 91 ARG 0.002 0.000 ARG B 100 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 186 time to evaluate : 1.826 Fit side-chains REVERT: A 5 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8662 (mttp) REVERT: A 57 GLN cc_start: 0.9119 (OUTLIER) cc_final: 0.8411 (tt0) REVERT: A 140 ASP cc_start: 0.7898 (OUTLIER) cc_final: 0.7572 (m-30) REVERT: D 5 LYS cc_start: 0.8868 (mttp) cc_final: 0.8602 (mmtp) REVERT: D 140 ASP cc_start: 0.7883 (OUTLIER) cc_final: 0.7471 (m-30) REVERT: D 156 MET cc_start: 0.8535 (mtt) cc_final: 0.8310 (mtp) REVERT: D 306 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7701 (mm-30) REVERT: B 29 ASP cc_start: 0.7972 (t0) cc_final: 0.7761 (t70) REVERT: B 133 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7589 (mt-10) REVERT: B 194 LYS cc_start: 0.8903 (ttpp) cc_final: 0.8262 (tttm) REVERT: E 14 GLU cc_start: 0.7194 (pm20) cc_final: 0.6977 (pm20) REVERT: E 29 ASP cc_start: 0.8017 (t0) cc_final: 0.7806 (t70) REVERT: E 133 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7771 (mt-10) REVERT: E 194 LYS cc_start: 0.8795 (ttpt) cc_final: 0.8189 (tttm) REVERT: F 140 ASP cc_start: 0.7869 (OUTLIER) cc_final: 0.7563 (m-30) REVERT: F 156 MET cc_start: 0.8546 (mtt) cc_final: 0.8319 (mtp) REVERT: F 306 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7714 (mm-30) REVERT: C 5 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8652 (mttp) REVERT: C 57 GLN cc_start: 0.9130 (OUTLIER) cc_final: 0.8447 (tt0) REVERT: C 140 ASP cc_start: 0.7878 (OUTLIER) cc_final: 0.7546 (m-30) outliers start: 26 outliers final: 5 residues processed: 197 average time/residue: 1.6715 time to fit residues: 357.5726 Evaluate side-chains 194 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 179 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 188 ASP Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain E residue 140 ASP Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain F residue 188 ASP Chi-restraints excluded: chain F residue 306 GLU Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 57 GLN Chi-restraints excluded: chain C residue 140 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 4.9990 chunk 19 optimal weight: 8.9990 chunk 99 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 chunk 146 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 173 optimal weight: 10.0000 chunk 108 optimal weight: 4.9990 chunk 105 optimal weight: 0.4980 chunk 80 optimal weight: 10.0000 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 GLN B 158 GLN B 256 ASN F 163 ASN C 158 GLN C 256 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14646 Z= 0.206 Angle : 1.807 47.829 19932 Z= 0.630 Chirality : 0.045 0.129 2310 Planarity : 0.003 0.040 2568 Dihedral : 13.853 89.510 2226 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.63 % Allowed : 11.90 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.02 (0.19), residues: 1818 helix: 0.73 (0.20), residues: 726 sheet: 0.72 (0.23), residues: 456 loop : -1.40 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 250 PHE 0.012 0.001 PHE F 139 TYR 0.005 0.001 TYR A 91 ARG 0.001 0.000 ARG E 100 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 192 time to evaluate : 1.793 Fit side-chains REVERT: A 5 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8678 (mttp) REVERT: A 57 GLN cc_start: 0.9095 (OUTLIER) cc_final: 0.8406 (tt0) REVERT: A 140 ASP cc_start: 0.7878 (OUTLIER) cc_final: 0.7552 (m-30) REVERT: D 5 LYS cc_start: 0.8863 (mttp) cc_final: 0.8600 (mmtp) REVERT: D 140 ASP cc_start: 0.7874 (OUTLIER) cc_final: 0.7443 (m-30) REVERT: D 156 MET cc_start: 0.8521 (mtt) cc_final: 0.8296 (mtp) REVERT: D 306 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7709 (mm-30) REVERT: B 5 LYS cc_start: 0.8706 (mttp) cc_final: 0.8460 (mttp) REVERT: B 133 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7648 (mt-10) REVERT: B 194 LYS cc_start: 0.8872 (ttpp) cc_final: 0.8248 (tttm) REVERT: E 29 ASP cc_start: 0.8018 (t0) cc_final: 0.7815 (t70) REVERT: E 133 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7694 (mt-10) REVERT: E 194 LYS cc_start: 0.8809 (ttpt) cc_final: 0.8189 (tttm) REVERT: F 140 ASP cc_start: 0.7882 (OUTLIER) cc_final: 0.7572 (m-30) REVERT: F 156 MET cc_start: 0.8531 (mtt) cc_final: 0.8305 (mtp) REVERT: F 306 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7678 (mm-30) REVERT: C 5 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8665 (mttp) REVERT: C 57 GLN cc_start: 0.9106 (OUTLIER) cc_final: 0.8438 (tt0) REVERT: C 140 ASP cc_start: 0.7858 (OUTLIER) cc_final: 0.7528 (m-30) outliers start: 25 outliers final: 6 residues processed: 203 average time/residue: 1.6696 time to fit residues: 367.3877 Evaluate side-chains 201 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 185 time to evaluate : 1.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 188 ASP Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain E residue 140 ASP Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain F residue 188 ASP Chi-restraints excluded: chain F residue 306 GLU Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 57 GLN Chi-restraints excluded: chain C residue 140 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 103 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 110 optimal weight: 9.9990 chunk 118 optimal weight: 0.2980 chunk 85 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 136 optimal weight: 0.0670 overall best weight: 0.9920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 GLN B 158 GLN B 256 ASN E 158 GLN F 163 ASN C 158 GLN C 256 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14646 Z= 0.192 Angle : 1.804 47.895 19932 Z= 0.627 Chirality : 0.045 0.126 2310 Planarity : 0.003 0.040 2568 Dihedral : 13.690 89.831 2226 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.44 % Allowed : 12.22 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.04 (0.19), residues: 1818 helix: 0.77 (0.20), residues: 726 sheet: 0.76 (0.23), residues: 456 loop : -1.37 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 250 PHE 0.012 0.001 PHE D 139 TYR 0.005 0.001 TYR A 91 ARG 0.001 0.000 ARG F 239 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 185 time to evaluate : 1.712 Fit side-chains REVERT: A 5 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8681 (mttp) REVERT: A 57 GLN cc_start: 0.9086 (OUTLIER) cc_final: 0.8408 (tt0) REVERT: A 140 ASP cc_start: 0.7894 (OUTLIER) cc_final: 0.7566 (m-30) REVERT: A 188 ASP cc_start: 0.7984 (m-30) cc_final: 0.7748 (m-30) REVERT: D 5 LYS cc_start: 0.8856 (mttp) cc_final: 0.8595 (mmtp) REVERT: D 140 ASP cc_start: 0.7864 (OUTLIER) cc_final: 0.7434 (m-30) REVERT: D 156 MET cc_start: 0.8514 (mtt) cc_final: 0.8279 (mtp) REVERT: D 306 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7699 (mm-30) REVERT: B 5 LYS cc_start: 0.8681 (mttp) cc_final: 0.8423 (mttp) REVERT: B 133 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7647 (mt-10) REVERT: B 194 LYS cc_start: 0.8942 (ttpp) cc_final: 0.8305 (tttm) REVERT: E 133 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7710 (mt-10) REVERT: E 194 LYS cc_start: 0.8791 (ttpt) cc_final: 0.8167 (tttm) REVERT: F 156 MET cc_start: 0.8523 (mtt) cc_final: 0.8287 (mtp) REVERT: F 306 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7673 (mm-30) REVERT: C 5 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8644 (mttp) REVERT: C 57 GLN cc_start: 0.9099 (OUTLIER) cc_final: 0.8429 (tt0) REVERT: C 140 ASP cc_start: 0.7882 (OUTLIER) cc_final: 0.7547 (m-30) REVERT: C 188 ASP cc_start: 0.7984 (m-30) cc_final: 0.7736 (m-30) outliers start: 22 outliers final: 7 residues processed: 195 average time/residue: 1.6395 time to fit residues: 346.4568 Evaluate side-chains 200 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 184 time to evaluate : 1.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 188 ASP Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain E residue 140 ASP Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain F residue 188 ASP Chi-restraints excluded: chain F residue 306 GLU Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 57 GLN Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 237 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 0.6980 chunk 166 optimal weight: 5.9990 chunk 151 optimal weight: 7.9990 chunk 161 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 126 optimal weight: 0.6980 chunk 49 optimal weight: 9.9990 chunk 146 optimal weight: 3.9990 chunk 152 optimal weight: 4.9990 chunk 106 optimal weight: 0.0470 overall best weight: 1.4882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 GLN B 158 GLN B 256 ASN E 256 ASN F 163 ASN C 158 GLN C 256 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14646 Z= 0.228 Angle : 1.811 47.818 19932 Z= 0.632 Chirality : 0.046 0.127 2310 Planarity : 0.004 0.040 2568 Dihedral : 13.612 89.482 2226 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.44 % Allowed : 12.16 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.02 (0.19), residues: 1818 helix: 0.75 (0.20), residues: 726 sheet: 0.65 (0.23), residues: 456 loop : -1.38 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 131 PHE 0.013 0.001 PHE B 139 TYR 0.007 0.001 TYR A 91 ARG 0.002 0.000 ARG E 79 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 180 time to evaluate : 1.824 Fit side-chains REVERT: A 5 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8668 (mttp) REVERT: A 57 GLN cc_start: 0.9117 (OUTLIER) cc_final: 0.8402 (tt0) REVERT: A 140 ASP cc_start: 0.7882 (OUTLIER) cc_final: 0.7556 (m-30) REVERT: A 188 ASP cc_start: 0.7978 (m-30) cc_final: 0.7744 (m-30) REVERT: D 5 LYS cc_start: 0.8855 (mttp) cc_final: 0.8590 (mmtp) REVERT: D 140 ASP cc_start: 0.7889 (OUTLIER) cc_final: 0.7471 (m-30) REVERT: D 156 MET cc_start: 0.8533 (mtt) cc_final: 0.8307 (mtp) REVERT: D 306 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7689 (mm-30) REVERT: B 5 LYS cc_start: 0.8699 (mttp) cc_final: 0.8441 (mttp) REVERT: B 133 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7639 (mt-10) REVERT: B 194 LYS cc_start: 0.8818 (ttpp) cc_final: 0.8216 (tttm) REVERT: E 133 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7651 (mt-10) REVERT: E 194 LYS cc_start: 0.8772 (ttpt) cc_final: 0.8161 (tttm) REVERT: F 140 ASP cc_start: 0.7879 (OUTLIER) cc_final: 0.7560 (m-30) REVERT: F 156 MET cc_start: 0.8545 (mtt) cc_final: 0.8318 (mtp) REVERT: F 306 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7714 (mm-30) REVERT: C 5 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8671 (mttp) REVERT: C 57 GLN cc_start: 0.9131 (OUTLIER) cc_final: 0.8431 (tt0) REVERT: C 140 ASP cc_start: 0.7868 (OUTLIER) cc_final: 0.7542 (m-30) REVERT: C 188 ASP cc_start: 0.7979 (m-30) cc_final: 0.7738 (m-30) outliers start: 22 outliers final: 6 residues processed: 191 average time/residue: 1.7467 time to fit residues: 361.0616 Evaluate side-chains 198 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 182 time to evaluate : 1.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 188 ASP Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain E residue 140 ASP Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain F residue 188 ASP Chi-restraints excluded: chain F residue 306 GLU Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 57 GLN Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 237 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 9.9990 chunk 104 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 118 optimal weight: 8.9990 chunk 179 optimal weight: 5.9990 chunk 165 optimal weight: 9.9990 chunk 142 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 87 optimal weight: 0.0030 chunk 113 optimal weight: 9.9990 overall best weight: 2.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 GLN D 256 ASN B 158 GLN B 256 ASN E 256 ASN F 163 ASN F 256 ASN C 158 GLN C 256 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 14646 Z= 0.359 Angle : 1.836 47.536 19932 Z= 0.652 Chirality : 0.048 0.130 2310 Planarity : 0.005 0.040 2568 Dihedral : 13.645 89.245 2226 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.44 % Allowed : 12.29 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.30 (0.19), residues: 1818 helix: 0.59 (0.19), residues: 720 sheet: 0.48 (0.23), residues: 450 loop : -1.55 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 131 PHE 0.017 0.002 PHE E 139 TYR 0.010 0.002 TYR A 91 ARG 0.003 0.001 ARG B 78 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 180 time to evaluate : 1.842 Fit side-chains REVERT: A 5 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8693 (mttp) REVERT: A 140 ASP cc_start: 0.8036 (OUTLIER) cc_final: 0.7730 (m-30) REVERT: A 188 ASP cc_start: 0.7969 (m-30) cc_final: 0.7754 (m-30) REVERT: D 5 LYS cc_start: 0.8868 (mttp) cc_final: 0.8591 (mmtp) REVERT: D 156 MET cc_start: 0.8588 (mtt) cc_final: 0.8349 (mtp) REVERT: D 306 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7756 (mm-30) REVERT: B 133 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7664 (mt-10) REVERT: B 194 LYS cc_start: 0.8863 (ttpp) cc_final: 0.8195 (tttm) REVERT: E 194 LYS cc_start: 0.8768 (ttpt) cc_final: 0.8140 (tttm) REVERT: F 156 MET cc_start: 0.8592 (mtt) cc_final: 0.8350 (mtp) REVERT: F 306 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7746 (mm-30) REVERT: C 5 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8670 (mttp) REVERT: C 140 ASP cc_start: 0.8021 (OUTLIER) cc_final: 0.7709 (m-30) REVERT: C 188 ASP cc_start: 0.7972 (m-30) cc_final: 0.7749 (m-30) outliers start: 22 outliers final: 5 residues processed: 196 average time/residue: 1.6582 time to fit residues: 352.6481 Evaluate side-chains 191 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 180 time to evaluate : 1.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain D residue 188 ASP Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain E residue 140 ASP Chi-restraints excluded: chain F residue 188 ASP Chi-restraints excluded: chain F residue 306 GLU Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 140 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 5.9990 chunk 43 optimal weight: 0.5980 chunk 131 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 146 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 GLN D 256 ASN B 256 ASN E 256 ASN F 163 ASN F 256 ASN C 158 GLN C 256 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.130331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.095166 restraints weight = 15153.324| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.58 r_work: 0.2942 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14646 Z= 0.189 Angle : 1.805 47.920 19932 Z= 0.628 Chirality : 0.045 0.127 2310 Planarity : 0.003 0.040 2568 Dihedral : 13.492 89.737 2226 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.11 % Allowed : 12.81 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.04 (0.19), residues: 1818 helix: 0.69 (0.19), residues: 726 sheet: 0.72 (0.23), residues: 450 loop : -1.37 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 250 PHE 0.011 0.001 PHE F 139 TYR 0.004 0.001 TYR C 91 ARG 0.001 0.000 ARG C 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6059.37 seconds wall clock time: 108 minutes 57.49 seconds (6537.49 seconds total)