Starting phenix.real_space_refine on Fri Feb 16 09:15:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m66_30114/02_2024/6m66_30114.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m66_30114/02_2024/6m66_30114.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m66_30114/02_2024/6m66_30114.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m66_30114/02_2024/6m66_30114.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m66_30114/02_2024/6m66_30114.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m66_30114/02_2024/6m66_30114.pdb" } resolution = 4.1 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= 0.015 sd= 0.098 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 9975 2.51 5 N 2303 2.21 5 O 2590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 144": "OE1" <-> "OE2" Residue "A TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 144": "OE1" <-> "OE2" Residue "B TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 144": "OE1" <-> "OE2" Residue "C TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 144": "OE1" <-> "OE2" Residue "D TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 144": "OE1" <-> "OE2" Residue "E TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 144": "OE1" <-> "OE2" Residue "F TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 144": "OE1" <-> "OE2" Residue "G TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14938 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2134 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 11, 'TRANS': 253} Chain breaks: 1 Chain: "B" Number of atoms: 2134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2134 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 11, 'TRANS': 253} Chain breaks: 1 Chain: "C" Number of atoms: 2134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2134 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 11, 'TRANS': 253} Chain breaks: 1 Chain: "D" Number of atoms: 2134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2134 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 11, 'TRANS': 253} Chain breaks: 1 Chain: "E" Number of atoms: 2134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2134 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 11, 'TRANS': 253} Chain breaks: 1 Chain: "F" Number of atoms: 2134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2134 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 11, 'TRANS': 253} Chain breaks: 1 Chain: "G" Number of atoms: 2134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2134 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 11, 'TRANS': 253} Chain breaks: 1 Time building chain proxies: 7.66, per 1000 atoms: 0.51 Number of scatterers: 14938 At special positions: 0 Unit cell: (113.94, 113.94, 113.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 70 16.00 O 2590 8.00 N 2303 7.00 C 9975 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 265 " distance=2.03 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 246 " distance=2.02 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 265 " distance=2.03 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 246 " distance=2.02 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 265 " distance=2.03 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 246 " distance=2.02 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 265 " distance=2.03 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 246 " distance=2.02 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 265 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 246 " distance=2.02 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 265 " distance=2.03 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 246 " distance=2.02 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 265 " distance=2.03 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS G 246 " distance=2.02 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: 5.48 Conformation dependent library (CDL) restraints added in 2.6 seconds 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3612 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 7 sheets defined 72.5% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 35 through 59 removed outlier: 5.032A pdb=" N ILE A 41 " --> pdb=" O MET A 37 " (cutoff:3.500A) Proline residue: A 46 - end of helix removed outlier: 3.698A pdb=" N GLN A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER A 59 " --> pdb=" O ALA A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 87 Processing helix chain 'A' and resid 103 through 107 removed outlier: 3.595A pdb=" N HIS A 106 " --> pdb=" O LEU A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 131 removed outlier: 4.106A pdb=" N LEU A 115 " --> pdb=" O TYR A 111 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU A 120 " --> pdb=" O PHE A 116 " (cutoff:3.500A) Proline residue: A 123 - end of helix Processing helix chain 'A' and resid 131 through 157 Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 209 through 238 removed outlier: 3.770A pdb=" N TYR A 213 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N CYS A 216 " --> pdb=" O LYS A 212 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG A 217 " --> pdb=" O TYR A 213 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR A 220 " --> pdb=" O CYS A 216 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY A 232 " --> pdb=" O CYS A 228 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR A 234 " --> pdb=" O TYR A 230 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE A 235 " --> pdb=" O LEU A 231 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER A 236 " --> pdb=" O GLY A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 256 removed outlier: 4.139A pdb=" N ASN A 255 " --> pdb=" O GLY A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 275 removed outlier: 3.769A pdb=" N LEU A 275 " --> pdb=" O GLY A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 286 removed outlier: 3.564A pdb=" N LEU A 281 " --> pdb=" O SER A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 295 removed outlier: 4.121A pdb=" N VAL A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR A 294 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU A 295 " --> pdb=" O VAL A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 310 removed outlier: 4.442A pdb=" N GLU A 310 " --> pdb=" O LYS A 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 307 through 310' Processing helix chain 'A' and resid 311 through 321 removed outlier: 3.750A pdb=" N ASP A 316 " --> pdb=" O LEU A 312 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL A 317 " --> pdb=" O PRO A 313 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N HIS A 319 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 336 Processing helix chain 'B' and resid 36 through 59 removed outlier: 5.032A pdb=" N ILE B 41 " --> pdb=" O MET B 37 " (cutoff:3.500A) Proline residue: B 46 - end of helix removed outlier: 3.698A pdb=" N GLN B 56 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER B 59 " --> pdb=" O ALA B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 87 Processing helix chain 'B' and resid 103 through 107 removed outlier: 3.596A pdb=" N HIS B 106 " --> pdb=" O LEU B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 131 removed outlier: 4.107A pdb=" N LEU B 115 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU B 120 " --> pdb=" O PHE B 116 " (cutoff:3.500A) Proline residue: B 123 - end of helix Processing helix chain 'B' and resid 131 through 157 Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 198 through 203 Processing helix chain 'B' and resid 209 through 238 removed outlier: 3.770A pdb=" N TYR B 213 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N CYS B 216 " --> pdb=" O LYS B 212 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG B 217 " --> pdb=" O TYR B 213 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR B 220 " --> pdb=" O CYS B 216 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE B 223 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY B 232 " --> pdb=" O CYS B 228 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR B 234 " --> pdb=" O TYR B 230 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE B 235 " --> pdb=" O LEU B 231 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER B 236 " --> pdb=" O GLY B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 256 removed outlier: 4.139A pdb=" N ASN B 255 " --> pdb=" O GLY B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 275 removed outlier: 3.769A pdb=" N LEU B 275 " --> pdb=" O GLY B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 286 removed outlier: 3.564A pdb=" N LEU B 281 " --> pdb=" O SER B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 295 removed outlier: 4.121A pdb=" N VAL B 292 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR B 294 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU B 295 " --> pdb=" O VAL B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 310 removed outlier: 4.442A pdb=" N GLU B 310 " --> pdb=" O LYS B 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 307 through 310' Processing helix chain 'B' and resid 311 through 321 removed outlier: 3.750A pdb=" N ASP B 316 " --> pdb=" O LEU B 312 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL B 317 " --> pdb=" O PRO B 313 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N HIS B 319 " --> pdb=" O PHE B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 336 Processing helix chain 'C' and resid 36 through 59 removed outlier: 5.032A pdb=" N ILE C 41 " --> pdb=" O MET C 37 " (cutoff:3.500A) Proline residue: C 46 - end of helix removed outlier: 3.698A pdb=" N GLN C 56 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER C 59 " --> pdb=" O ALA C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 87 Processing helix chain 'C' and resid 103 through 107 removed outlier: 3.595A pdb=" N HIS C 106 " --> pdb=" O LEU C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 131 removed outlier: 4.107A pdb=" N LEU C 115 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU C 120 " --> pdb=" O PHE C 116 " (cutoff:3.500A) Proline residue: C 123 - end of helix Processing helix chain 'C' and resid 131 through 157 Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 198 through 203 Processing helix chain 'C' and resid 209 through 238 removed outlier: 3.770A pdb=" N TYR C 213 " --> pdb=" O LEU C 209 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N CYS C 216 " --> pdb=" O LYS C 212 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG C 217 " --> pdb=" O TYR C 213 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR C 220 " --> pdb=" O CYS C 216 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE C 223 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY C 232 " --> pdb=" O CYS C 228 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR C 234 " --> pdb=" O TYR C 230 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE C 235 " --> pdb=" O LEU C 231 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N SER C 236 " --> pdb=" O GLY C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 256 removed outlier: 4.139A pdb=" N ASN C 255 " --> pdb=" O GLY C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 275 removed outlier: 3.769A pdb=" N LEU C 275 " --> pdb=" O GLY C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 286 removed outlier: 3.564A pdb=" N LEU C 281 " --> pdb=" O SER C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 295 removed outlier: 4.121A pdb=" N VAL C 292 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR C 294 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU C 295 " --> pdb=" O VAL C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 310 removed outlier: 4.442A pdb=" N GLU C 310 " --> pdb=" O LYS C 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 307 through 310' Processing helix chain 'C' and resid 311 through 321 removed outlier: 3.749A pdb=" N ASP C 316 " --> pdb=" O LEU C 312 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL C 317 " --> pdb=" O PRO C 313 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N HIS C 319 " --> pdb=" O PHE C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 336 Processing helix chain 'D' and resid 36 through 59 removed outlier: 5.032A pdb=" N ILE D 41 " --> pdb=" O MET D 37 " (cutoff:3.500A) Proline residue: D 46 - end of helix removed outlier: 3.698A pdb=" N GLN D 56 " --> pdb=" O LEU D 52 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER D 59 " --> pdb=" O ALA D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 87 Processing helix chain 'D' and resid 103 through 107 removed outlier: 3.596A pdb=" N HIS D 106 " --> pdb=" O LEU D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 131 removed outlier: 4.107A pdb=" N LEU D 115 " --> pdb=" O TYR D 111 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU D 120 " --> pdb=" O PHE D 116 " (cutoff:3.500A) Proline residue: D 123 - end of helix Processing helix chain 'D' and resid 131 through 157 Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' Processing helix chain 'D' and resid 198 through 203 Processing helix chain 'D' and resid 209 through 238 removed outlier: 3.770A pdb=" N TYR D 213 " --> pdb=" O LEU D 209 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N CYS D 216 " --> pdb=" O LYS D 212 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG D 217 " --> pdb=" O TYR D 213 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR D 220 " --> pdb=" O CYS D 216 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE D 223 " --> pdb=" O LEU D 219 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY D 232 " --> pdb=" O CYS D 228 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR D 234 " --> pdb=" O TYR D 230 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE D 235 " --> pdb=" O LEU D 231 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER D 236 " --> pdb=" O GLY D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 256 removed outlier: 4.139A pdb=" N ASN D 255 " --> pdb=" O GLY D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 275 removed outlier: 3.769A pdb=" N LEU D 275 " --> pdb=" O GLY D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 286 removed outlier: 3.564A pdb=" N LEU D 281 " --> pdb=" O SER D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 295 removed outlier: 4.121A pdb=" N VAL D 292 " --> pdb=" O ALA D 288 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR D 294 " --> pdb=" O VAL D 290 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU D 295 " --> pdb=" O VAL D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 310 removed outlier: 4.443A pdb=" N GLU D 310 " --> pdb=" O LYS D 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 307 through 310' Processing helix chain 'D' and resid 311 through 321 removed outlier: 3.749A pdb=" N ASP D 316 " --> pdb=" O LEU D 312 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL D 317 " --> pdb=" O PRO D 313 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N HIS D 319 " --> pdb=" O PHE D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 336 Processing helix chain 'E' and resid 36 through 59 removed outlier: 5.031A pdb=" N ILE E 41 " --> pdb=" O MET E 37 " (cutoff:3.500A) Proline residue: E 46 - end of helix removed outlier: 3.697A pdb=" N GLN E 56 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER E 59 " --> pdb=" O ALA E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 87 Processing helix chain 'E' and resid 103 through 107 removed outlier: 3.596A pdb=" N HIS E 106 " --> pdb=" O LEU E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 131 removed outlier: 4.107A pdb=" N LEU E 115 " --> pdb=" O TYR E 111 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU E 120 " --> pdb=" O PHE E 116 " (cutoff:3.500A) Proline residue: E 123 - end of helix Processing helix chain 'E' and resid 131 through 157 Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 198 through 203 Processing helix chain 'E' and resid 209 through 238 removed outlier: 3.770A pdb=" N TYR E 213 " --> pdb=" O LEU E 209 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N CYS E 216 " --> pdb=" O LYS E 212 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG E 217 " --> pdb=" O TYR E 213 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR E 220 " --> pdb=" O CYS E 216 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE E 223 " --> pdb=" O LEU E 219 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY E 232 " --> pdb=" O CYS E 228 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR E 234 " --> pdb=" O TYR E 230 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE E 235 " --> pdb=" O LEU E 231 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER E 236 " --> pdb=" O GLY E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 256 removed outlier: 4.139A pdb=" N ASN E 255 " --> pdb=" O GLY E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 275 removed outlier: 3.769A pdb=" N LEU E 275 " --> pdb=" O GLY E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 286 removed outlier: 3.564A pdb=" N LEU E 281 " --> pdb=" O SER E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 295 removed outlier: 4.121A pdb=" N VAL E 292 " --> pdb=" O ALA E 288 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR E 294 " --> pdb=" O VAL E 290 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU E 295 " --> pdb=" O VAL E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 310 removed outlier: 4.442A pdb=" N GLU E 310 " --> pdb=" O LYS E 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 307 through 310' Processing helix chain 'E' and resid 311 through 321 removed outlier: 3.750A pdb=" N ASP E 316 " --> pdb=" O LEU E 312 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL E 317 " --> pdb=" O PRO E 313 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N HIS E 319 " --> pdb=" O PHE E 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 336 Processing helix chain 'F' and resid 36 through 59 removed outlier: 5.032A pdb=" N ILE F 41 " --> pdb=" O MET F 37 " (cutoff:3.500A) Proline residue: F 46 - end of helix removed outlier: 3.697A pdb=" N GLN F 56 " --> pdb=" O LEU F 52 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER F 59 " --> pdb=" O ALA F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 87 Processing helix chain 'F' and resid 103 through 107 removed outlier: 3.596A pdb=" N HIS F 106 " --> pdb=" O LEU F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 131 removed outlier: 4.107A pdb=" N LEU F 115 " --> pdb=" O TYR F 111 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU F 120 " --> pdb=" O PHE F 116 " (cutoff:3.500A) Proline residue: F 123 - end of helix Processing helix chain 'F' and resid 131 through 157 Processing helix chain 'F' and resid 195 through 197 No H-bonds generated for 'chain 'F' and resid 195 through 197' Processing helix chain 'F' and resid 198 through 203 Processing helix chain 'F' and resid 209 through 238 removed outlier: 3.771A pdb=" N TYR F 213 " --> pdb=" O LEU F 209 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N CYS F 216 " --> pdb=" O LYS F 212 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG F 217 " --> pdb=" O TYR F 213 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR F 220 " --> pdb=" O CYS F 216 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE F 223 " --> pdb=" O LEU F 219 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY F 232 " --> pdb=" O CYS F 228 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR F 234 " --> pdb=" O TYR F 230 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE F 235 " --> pdb=" O LEU F 231 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER F 236 " --> pdb=" O GLY F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 256 removed outlier: 4.139A pdb=" N ASN F 255 " --> pdb=" O GLY F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 275 removed outlier: 3.769A pdb=" N LEU F 275 " --> pdb=" O GLY F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 276 through 286 removed outlier: 3.564A pdb=" N LEU F 281 " --> pdb=" O SER F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 295 removed outlier: 4.121A pdb=" N VAL F 292 " --> pdb=" O ALA F 288 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR F 294 " --> pdb=" O VAL F 290 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU F 295 " --> pdb=" O VAL F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 310 removed outlier: 4.442A pdb=" N GLU F 310 " --> pdb=" O LYS F 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 307 through 310' Processing helix chain 'F' and resid 311 through 321 removed outlier: 3.750A pdb=" N ASP F 316 " --> pdb=" O LEU F 312 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL F 317 " --> pdb=" O PRO F 313 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N HIS F 319 " --> pdb=" O PHE F 315 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 through 336 Processing helix chain 'G' and resid 36 through 59 removed outlier: 5.032A pdb=" N ILE G 41 " --> pdb=" O MET G 37 " (cutoff:3.500A) Proline residue: G 46 - end of helix removed outlier: 3.697A pdb=" N GLN G 56 " --> pdb=" O LEU G 52 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER G 59 " --> pdb=" O ALA G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 87 Processing helix chain 'G' and resid 103 through 107 removed outlier: 3.596A pdb=" N HIS G 106 " --> pdb=" O LEU G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 131 removed outlier: 4.106A pdb=" N LEU G 115 " --> pdb=" O TYR G 111 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU G 120 " --> pdb=" O PHE G 116 " (cutoff:3.500A) Proline residue: G 123 - end of helix Processing helix chain 'G' and resid 131 through 157 Processing helix chain 'G' and resid 195 through 197 No H-bonds generated for 'chain 'G' and resid 195 through 197' Processing helix chain 'G' and resid 198 through 203 Processing helix chain 'G' and resid 209 through 238 removed outlier: 3.770A pdb=" N TYR G 213 " --> pdb=" O LEU G 209 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N CYS G 216 " --> pdb=" O LYS G 212 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG G 217 " --> pdb=" O TYR G 213 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR G 220 " --> pdb=" O CYS G 216 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE G 223 " --> pdb=" O LEU G 219 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY G 232 " --> pdb=" O CYS G 228 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR G 234 " --> pdb=" O TYR G 230 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE G 235 " --> pdb=" O LEU G 231 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER G 236 " --> pdb=" O GLY G 232 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 256 removed outlier: 4.138A pdb=" N ASN G 255 " --> pdb=" O GLY G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 275 removed outlier: 3.769A pdb=" N LEU G 275 " --> pdb=" O GLY G 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 276 through 286 removed outlier: 3.564A pdb=" N LEU G 281 " --> pdb=" O SER G 277 " (cutoff:3.500A) Processing helix chain 'G' and resid 287 through 295 removed outlier: 4.120A pdb=" N VAL G 292 " --> pdb=" O ALA G 288 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR G 294 " --> pdb=" O VAL G 290 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU G 295 " --> pdb=" O VAL G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 307 through 310 removed outlier: 4.442A pdb=" N GLU G 310 " --> pdb=" O LYS G 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 307 through 310' Processing helix chain 'G' and resid 311 through 321 removed outlier: 3.750A pdb=" N ASP G 316 " --> pdb=" O LEU G 312 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL G 317 " --> pdb=" O PRO G 313 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N HIS G 319 " --> pdb=" O PHE G 315 " (cutoff:3.500A) Processing helix chain 'G' and resid 329 through 336 Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 65 removed outlier: 3.911A pdb=" N LYS A 266 " --> pdb=" O SER A 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 65 removed outlier: 3.911A pdb=" N LYS B 266 " --> pdb=" O SER B 65 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 65 removed outlier: 3.910A pdb=" N LYS C 266 " --> pdb=" O SER C 65 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 64 through 65 removed outlier: 3.911A pdb=" N LYS D 266 " --> pdb=" O SER D 65 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 64 through 65 removed outlier: 3.910A pdb=" N LYS E 266 " --> pdb=" O SER E 65 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 64 through 65 removed outlier: 3.911A pdb=" N LYS F 266 " --> pdb=" O SER F 65 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 64 through 65 removed outlier: 3.911A pdb=" N LYS G 266 " --> pdb=" O SER G 65 " (cutoff:3.500A) 736 hydrogen bonds defined for protein. 2187 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: 3.68 Time building geometry restraints manager: 5.97 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: 4322 1.34 - 1.46: 3089 1.46 - 1.57: 7814 1.57 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 15309 Sorted by residual: bond pdb=" C VAL C 297 " pdb=" N PRO C 298 " ideal model delta sigma weight residual 1.335 1.360 -0.025 1.28e-02 6.10e+03 3.95e+00 bond pdb=" C VAL A 297 " pdb=" N PRO A 298 " ideal model delta sigma weight residual 1.335 1.360 -0.025 1.28e-02 6.10e+03 3.83e+00 bond pdb=" C VAL G 297 " pdb=" N PRO G 298 " ideal model delta sigma weight residual 1.335 1.360 -0.025 1.28e-02 6.10e+03 3.82e+00 bond pdb=" C VAL E 297 " pdb=" N PRO E 298 " ideal model delta sigma weight residual 1.335 1.360 -0.025 1.28e-02 6.10e+03 3.80e+00 bond pdb=" C VAL D 297 " pdb=" N PRO D 298 " ideal model delta sigma weight residual 1.335 1.359 -0.025 1.28e-02 6.10e+03 3.75e+00 ... (remaining 15304 not shown) Histogram of bond angle deviations from ideal: 100.79 - 107.43: 535 107.43 - 114.07: 8600 114.07 - 120.71: 6931 120.71 - 127.35: 4584 127.35 - 133.99: 175 Bond angle restraints: 20825 Sorted by residual: angle pdb=" N LEU B 122 " pdb=" CA LEU B 122 " pdb=" C LEU B 122 " ideal model delta sigma weight residual 109.81 117.99 -8.18 2.21e+00 2.05e-01 1.37e+01 angle pdb=" N LEU G 122 " pdb=" CA LEU G 122 " pdb=" C LEU G 122 " ideal model delta sigma weight residual 109.81 117.98 -8.17 2.21e+00 2.05e-01 1.37e+01 angle pdb=" N LEU D 122 " pdb=" CA LEU D 122 " pdb=" C LEU D 122 " ideal model delta sigma weight residual 109.81 117.97 -8.16 2.21e+00 2.05e-01 1.36e+01 angle pdb=" N LEU F 122 " pdb=" CA LEU F 122 " pdb=" C LEU F 122 " ideal model delta sigma weight residual 109.81 117.96 -8.15 2.21e+00 2.05e-01 1.36e+01 angle pdb=" N LEU A 122 " pdb=" CA LEU A 122 " pdb=" C LEU A 122 " ideal model delta sigma weight residual 109.81 117.95 -8.14 2.21e+00 2.05e-01 1.36e+01 ... (remaining 20820 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.27: 7305 14.27 - 28.53: 1291 28.53 - 42.80: 420 42.80 - 57.07: 84 57.07 - 71.33: 14 Dihedral angle restraints: 9114 sinusoidal: 3563 harmonic: 5551 Sorted by residual: dihedral pdb=" CA PRO C 260 " pdb=" C PRO C 260 " pdb=" N ASP C 261 " pdb=" CA ASP C 261 " ideal model delta harmonic sigma weight residual -180.00 -155.96 -24.04 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA PRO A 260 " pdb=" C PRO A 260 " pdb=" N ASP A 261 " pdb=" CA ASP A 261 " ideal model delta harmonic sigma weight residual 180.00 -155.97 -24.03 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA PRO D 260 " pdb=" C PRO D 260 " pdb=" N ASP D 261 " pdb=" CA ASP D 261 " ideal model delta harmonic sigma weight residual -180.00 -155.98 -24.02 0 5.00e+00 4.00e-02 2.31e+01 ... (remaining 9111 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1431 0.045 - 0.091: 758 0.091 - 0.136: 183 0.136 - 0.181: 85 0.181 - 0.226: 14 Chirality restraints: 2471 Sorted by residual: chirality pdb=" CA PHE C 109 " pdb=" N PHE C 109 " pdb=" C PHE C 109 " pdb=" CB PHE C 109 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA PHE A 109 " pdb=" N PHE A 109 " pdb=" C PHE A 109 " pdb=" CB PHE A 109 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA PHE F 109 " pdb=" N PHE F 109 " pdb=" C PHE F 109 " pdb=" CB PHE F 109 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 2468 not shown) Planarity restraints: 2520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 123 " -0.054 5.00e-02 4.00e+02 8.03e-02 1.03e+01 pdb=" N PRO A 124 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO A 124 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 124 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO G 123 " 0.054 5.00e-02 4.00e+02 8.02e-02 1.03e+01 pdb=" N PRO G 124 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO G 124 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO G 124 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 123 " -0.054 5.00e-02 4.00e+02 8.01e-02 1.03e+01 pdb=" N PRO C 124 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO C 124 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 124 " -0.045 5.00e-02 4.00e+02 ... (remaining 2517 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2999 2.76 - 3.30: 14723 3.30 - 3.83: 25889 3.83 - 4.37: 28545 4.37 - 4.90: 46095 Nonbonded interactions: 118251 Sorted by model distance: nonbonded pdb=" OH TYR C 111 " pdb=" O LEU D 275 " model vdw 2.231 2.440 nonbonded pdb=" OH TYR D 111 " pdb=" O LEU E 275 " model vdw 2.257 2.440 nonbonded pdb=" O ARG G 217 " pdb=" OG1 THR G 220 " model vdw 2.279 2.440 nonbonded pdb=" O ARG C 217 " pdb=" OG1 THR C 220 " model vdw 2.280 2.440 nonbonded pdb=" O ARG F 217 " pdb=" OG1 THR F 220 " model vdw 2.280 2.440 ... (remaining 118246 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 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: 4.250 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 37.650 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.080 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: 0.000 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 15309 Z= 0.348 Angle : 1.076 8.681 20825 Z= 0.566 Chirality : 0.060 0.226 2471 Planarity : 0.010 0.080 2520 Dihedral : 16.352 71.333 5460 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 0.00 % Allowed : 14.94 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.00 (0.14), residues: 1827 helix: -3.08 (0.11), residues: 1008 sheet: -4.52 (0.40), residues: 70 loop : -3.38 (0.19), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 127 HIS 0.004 0.001 HIS A 106 PHE 0.028 0.002 PHE E 109 TYR 0.017 0.002 TYR F 309 ARG 0.002 0.001 ARG B 254 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 1.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 VAL cc_start: 0.9217 (t) cc_final: 0.8970 (p) REVERT: A 144 GLU cc_start: 0.9404 (tm-30) cc_final: 0.9186 (tm-30) REVERT: B 38 VAL cc_start: 0.9216 (t) cc_final: 0.8999 (p) REVERT: B 128 ARG cc_start: 0.9427 (tmm-80) cc_final: 0.9216 (ttp-110) REVERT: B 141 PHE cc_start: 0.7595 (m-10) cc_final: 0.7358 (m-80) REVERT: B 144 GLU cc_start: 0.9464 (tm-30) cc_final: 0.9194 (tm-30) REVERT: C 141 PHE cc_start: 0.7613 (m-10) cc_final: 0.7411 (m-80) REVERT: C 144 GLU cc_start: 0.9422 (tm-30) cc_final: 0.9219 (tm-30) REVERT: C 152 ARG cc_start: 0.5779 (ttt180) cc_final: 0.5517 (ptt90) REVERT: D 128 ARG cc_start: 0.9498 (tmm-80) cc_final: 0.9250 (ttp-110) REVERT: D 141 PHE cc_start: 0.7765 (m-10) cc_final: 0.7422 (m-80) REVERT: D 144 GLU cc_start: 0.9451 (tm-30) cc_final: 0.9154 (tm-30) REVERT: D 152 ARG cc_start: 0.5509 (ttt180) cc_final: 0.5176 (ptt90) REVERT: E 128 ARG cc_start: 0.9452 (tmm-80) cc_final: 0.9141 (ttp-110) REVERT: F 38 VAL cc_start: 0.9311 (t) cc_final: 0.9097 (p) REVERT: F 152 ARG cc_start: 0.5709 (ttt180) cc_final: 0.5467 (ptt90) REVERT: G 38 VAL cc_start: 0.9324 (t) cc_final: 0.9100 (p) REVERT: G 144 GLU cc_start: 0.9419 (tm-30) cc_final: 0.9180 (tm-30) REVERT: G 152 ARG cc_start: 0.5803 (ttt180) cc_final: 0.5523 (ptt90) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.3106 time to fit residues: 109.2258 Evaluate side-chains 130 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 6.9990 chunk 137 optimal weight: 8.9990 chunk 76 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 142 optimal weight: 7.9990 chunk 55 optimal weight: 10.0000 chunk 86 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 chunk 165 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 HIS A 207 ASN A 319 HIS B 134 HIS B 207 ASN B 319 HIS C 134 HIS C 207 ASN C 319 HIS D 134 HIS D 207 ASN D 319 HIS E 134 HIS E 207 ASN E 319 HIS F 134 HIS F 207 ASN F 319 HIS G 134 HIS G 207 ASN G 319 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 15309 Z= 0.334 Angle : 0.898 8.750 20825 Z= 0.441 Chirality : 0.052 0.235 2471 Planarity : 0.007 0.049 2520 Dihedral : 7.004 23.948 1981 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 20.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 0.00 % Allowed : 11.38 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.17), residues: 1827 helix: -1.56 (0.13), residues: 1162 sheet: -4.68 (0.37), residues: 84 loop : -3.05 (0.23), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 127 HIS 0.003 0.001 HIS B 134 PHE 0.017 0.001 PHE E 141 TYR 0.032 0.002 TYR E 234 ARG 0.006 0.001 ARG A 254 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 1.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLN cc_start: 0.8364 (mm110) cc_final: 0.8091 (mm110) REVERT: A 128 ARG cc_start: 0.9410 (ttp-110) cc_final: 0.9206 (ttp-110) REVERT: A 141 PHE cc_start: 0.7721 (m-10) cc_final: 0.7503 (m-80) REVERT: A 272 ILE cc_start: 0.9500 (pt) cc_final: 0.9087 (tt) REVERT: B 36 LYS cc_start: 0.8930 (pptt) cc_final: 0.8668 (tmtt) REVERT: B 56 GLN cc_start: 0.8368 (mm-40) cc_final: 0.7958 (mm110) REVERT: B 128 ARG cc_start: 0.9546 (tmm-80) cc_final: 0.9262 (ttp-110) REVERT: B 141 PHE cc_start: 0.7525 (m-10) cc_final: 0.7323 (m-80) REVERT: B 272 ILE cc_start: 0.9511 (pt) cc_final: 0.9138 (tt) REVERT: C 36 LYS cc_start: 0.8968 (tmmt) cc_final: 0.8752 (tptt) REVERT: C 56 GLN cc_start: 0.8255 (mm110) cc_final: 0.7900 (mm110) REVERT: C 152 ARG cc_start: 0.5803 (ttt180) cc_final: 0.5484 (ptt90) REVERT: C 234 TYR cc_start: 0.7625 (t80) cc_final: 0.7375 (t80) REVERT: C 272 ILE cc_start: 0.9532 (pt) cc_final: 0.9258 (tt) REVERT: D 36 LYS cc_start: 0.9032 (pptt) cc_final: 0.8802 (tmtt) REVERT: D 37 MET cc_start: 0.7975 (ttp) cc_final: 0.7756 (mtp) REVERT: D 128 ARG cc_start: 0.9563 (tmm-80) cc_final: 0.9329 (ttp-110) REVERT: D 141 PHE cc_start: 0.7687 (m-10) cc_final: 0.7440 (m-80) REVERT: D 152 ARG cc_start: 0.5354 (ttt180) cc_final: 0.5057 (ptt90) REVERT: E 36 LYS cc_start: 0.8900 (pptt) cc_final: 0.8691 (tmtt) REVERT: E 56 GLN cc_start: 0.8249 (mm110) cc_final: 0.7911 (mm110) REVERT: E 128 ARG cc_start: 0.9489 (tmm-80) cc_final: 0.9158 (ttp-110) REVERT: E 272 ILE cc_start: 0.9545 (pt) cc_final: 0.9204 (tt) REVERT: F 128 ARG cc_start: 0.9404 (ttp-110) cc_final: 0.9182 (ttp-110) REVERT: F 141 PHE cc_start: 0.7733 (m-10) cc_final: 0.7525 (m-80) REVERT: F 152 ARG cc_start: 0.5681 (ttt180) cc_final: 0.5446 (ptt90) REVERT: G 36 LYS cc_start: 0.9068 (pptt) cc_final: 0.8825 (tmtt) REVERT: G 37 MET cc_start: 0.8499 (mtm) cc_final: 0.8111 (ttp) REVERT: G 141 PHE cc_start: 0.7625 (m-10) cc_final: 0.7367 (m-80) REVERT: G 144 GLU cc_start: 0.9458 (tm-30) cc_final: 0.9228 (tm-30) REVERT: G 152 ARG cc_start: 0.5749 (ttt180) cc_final: 0.5456 (ptt90) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.3061 time to fit residues: 78.5220 Evaluate side-chains 107 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 1.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 0.6980 chunk 51 optimal weight: 20.0000 chunk 137 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 165 optimal weight: 9.9990 chunk 178 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 164 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15309 Z= 0.189 Angle : 0.796 9.041 20825 Z= 0.381 Chirality : 0.048 0.222 2471 Planarity : 0.006 0.053 2520 Dihedral : 6.318 22.057 1981 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.18 % Favored : 89.82 % Rotamer: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.18), residues: 1827 helix: -0.86 (0.15), residues: 1106 sheet: -4.11 (0.46), residues: 84 loop : -2.78 (0.22), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 85 HIS 0.003 0.001 HIS D 106 PHE 0.025 0.001 PHE C 141 TYR 0.030 0.001 TYR D 234 ARG 0.004 0.000 ARG B 254 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 1.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLN cc_start: 0.8276 (mm110) cc_final: 0.7953 (mm110) REVERT: A 128 ARG cc_start: 0.9418 (ttp-110) cc_final: 0.9205 (ttp-110) REVERT: A 141 PHE cc_start: 0.7672 (m-10) cc_final: 0.7402 (m-80) REVERT: A 272 ILE cc_start: 0.9537 (pt) cc_final: 0.9222 (tt) REVERT: B 37 MET cc_start: 0.7898 (ttp) cc_final: 0.7691 (mtp) REVERT: B 128 ARG cc_start: 0.9553 (tmm-80) cc_final: 0.9294 (ttp-110) REVERT: C 56 GLN cc_start: 0.8166 (mm110) cc_final: 0.7605 (mm110) REVERT: C 152 ARG cc_start: 0.5859 (ttt180) cc_final: 0.5561 (ptt90) REVERT: C 272 ILE cc_start: 0.9486 (pt) cc_final: 0.9257 (tt) REVERT: D 36 LYS cc_start: 0.8962 (pptt) cc_final: 0.8697 (tmtt) REVERT: D 56 GLN cc_start: 0.8484 (mt0) cc_final: 0.8042 (mm110) REVERT: D 128 ARG cc_start: 0.9546 (tmm-80) cc_final: 0.9309 (ttp-110) REVERT: D 141 PHE cc_start: 0.7626 (m-10) cc_final: 0.7382 (m-80) REVERT: D 152 ARG cc_start: 0.5399 (ttt180) cc_final: 0.5109 (ptt90) REVERT: D 272 ILE cc_start: 0.9502 (pt) cc_final: 0.9118 (tt) REVERT: E 36 LYS cc_start: 0.8979 (pptt) cc_final: 0.8693 (tmtt) REVERT: E 56 GLN cc_start: 0.8209 (mm110) cc_final: 0.7872 (mm110) REVERT: E 128 ARG cc_start: 0.9543 (tmm-80) cc_final: 0.9250 (ttp-110) REVERT: E 272 ILE cc_start: 0.9542 (pt) cc_final: 0.9269 (tt) REVERT: F 56 GLN cc_start: 0.8335 (mt0) cc_final: 0.7945 (mm110) REVERT: F 128 ARG cc_start: 0.9423 (ttp-110) cc_final: 0.9189 (ttp-110) REVERT: F 272 ILE cc_start: 0.9557 (pt) cc_final: 0.9152 (tt) REVERT: G 56 GLN cc_start: 0.8550 (mt0) cc_final: 0.7936 (mm-40) REVERT: G 141 PHE cc_start: 0.7593 (m-10) cc_final: 0.7346 (m-80) REVERT: G 144 GLU cc_start: 0.9415 (tm-30) cc_final: 0.9185 (tm-30) REVERT: G 152 ARG cc_start: 0.5628 (ttt180) cc_final: 0.5386 (ptt90) REVERT: G 272 ILE cc_start: 0.9600 (pt) cc_final: 0.9231 (tt) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.2962 time to fit residues: 74.2636 Evaluate side-chains 114 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 1.9990 chunk 124 optimal weight: 0.4980 chunk 85 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 79 optimal weight: 7.9990 chunk 111 optimal weight: 2.9990 chunk 166 optimal weight: 7.9990 chunk 175 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 157 optimal weight: 8.9990 chunk 47 optimal weight: 6.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15309 Z= 0.202 Angle : 0.796 9.598 20825 Z= 0.383 Chirality : 0.049 0.194 2471 Planarity : 0.006 0.053 2520 Dihedral : 6.105 21.069 1981 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.45 % Favored : 89.55 % Rotamer: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.18), residues: 1827 helix: -0.59 (0.14), residues: 1155 sheet: -3.98 (0.52), residues: 84 loop : -2.87 (0.23), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 127 HIS 0.001 0.000 HIS G 134 PHE 0.028 0.001 PHE F 141 TYR 0.036 0.001 TYR G 234 ARG 0.006 0.001 ARG E 217 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLN cc_start: 0.8255 (mm110) cc_final: 0.7918 (mm110) REVERT: A 128 ARG cc_start: 0.9424 (ttp-110) cc_final: 0.9197 (ttp-110) REVERT: B 56 GLN cc_start: 0.8100 (mm110) cc_final: 0.7444 (mm-40) REVERT: B 128 ARG cc_start: 0.9505 (tmm-80) cc_final: 0.9162 (ttp80) REVERT: B 272 ILE cc_start: 0.9438 (pt) cc_final: 0.9125 (pt) REVERT: C 56 GLN cc_start: 0.8174 (mm110) cc_final: 0.7790 (mm-40) REVERT: C 272 ILE cc_start: 0.9461 (pt) cc_final: 0.9229 (pt) REVERT: D 36 LYS cc_start: 0.8972 (pptt) cc_final: 0.8726 (tmtt) REVERT: D 56 GLN cc_start: 0.8467 (mt0) cc_final: 0.8063 (mm110) REVERT: D 128 ARG cc_start: 0.9502 (tmm-80) cc_final: 0.9291 (ttp-110) REVERT: D 141 PHE cc_start: 0.7605 (m-10) cc_final: 0.7274 (m-80) REVERT: D 144 GLU cc_start: 0.9406 (tm-30) cc_final: 0.9196 (tm-30) REVERT: D 152 ARG cc_start: 0.5321 (ttt180) cc_final: 0.5046 (ptt90) REVERT: D 217 ARG cc_start: 0.9057 (ptp-170) cc_final: 0.8683 (ttp-170) REVERT: D 272 ILE cc_start: 0.9531 (pt) cc_final: 0.9109 (tt) REVERT: E 36 LYS cc_start: 0.8955 (pptt) cc_final: 0.8716 (tmtt) REVERT: E 128 ARG cc_start: 0.9548 (tmm-80) cc_final: 0.9248 (ttp-110) REVERT: F 128 ARG cc_start: 0.9424 (ttp-110) cc_final: 0.9148 (ttp-110) REVERT: G 56 GLN cc_start: 0.8544 (mt0) cc_final: 0.8177 (mm110) REVERT: G 141 PHE cc_start: 0.7607 (m-10) cc_final: 0.7388 (m-80) REVERT: G 152 ARG cc_start: 0.5648 (ttt180) cc_final: 0.5397 (ptt90) REVERT: G 272 ILE cc_start: 0.9547 (pt) cc_final: 0.9127 (tt) REVERT: G 280 ASN cc_start: 0.9080 (t0) cc_final: 0.8742 (t0) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.2620 time to fit residues: 68.0831 Evaluate side-chains 121 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 6.9990 chunk 99 optimal weight: 0.7980 chunk 2 optimal weight: 7.9990 chunk 130 optimal weight: 0.0470 chunk 72 optimal weight: 3.9990 chunk 150 optimal weight: 0.7980 chunk 121 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 89 optimal weight: 10.0000 chunk 157 optimal weight: 6.9990 chunk 44 optimal weight: 0.6980 overall best weight: 1.2680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN C 280 ASN F 280 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15309 Z= 0.176 Angle : 0.738 9.555 20825 Z= 0.357 Chirality : 0.046 0.179 2471 Planarity : 0.006 0.054 2520 Dihedral : 5.665 19.823 1981 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.19), residues: 1827 helix: -0.41 (0.15), residues: 1141 sheet: -4.00 (0.52), residues: 84 loop : -2.89 (0.22), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 127 HIS 0.001 0.000 HIS F 106 PHE 0.027 0.001 PHE A 141 TYR 0.023 0.001 TYR G 234 ARG 0.007 0.001 ARG G 128 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 1.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ARG cc_start: 0.9423 (ttp-110) cc_final: 0.9213 (ttp-110) REVERT: B 56 GLN cc_start: 0.8142 (mm110) cc_final: 0.7453 (mm-40) REVERT: B 128 ARG cc_start: 0.9376 (tmm-80) cc_final: 0.9008 (ttp80) REVERT: B 272 ILE cc_start: 0.9346 (pt) cc_final: 0.8974 (pt) REVERT: C 56 GLN cc_start: 0.8124 (mm110) cc_final: 0.7724 (mm-40) REVERT: C 272 ILE cc_start: 0.9466 (pt) cc_final: 0.9246 (pt) REVERT: D 36 LYS cc_start: 0.8880 (pptt) cc_final: 0.8656 (tmtt) REVERT: D 141 PHE cc_start: 0.7652 (m-10) cc_final: 0.7302 (m-80) REVERT: D 144 GLU cc_start: 0.9400 (tm-30) cc_final: 0.9196 (tm-30) REVERT: D 152 ARG cc_start: 0.5334 (ttt180) cc_final: 0.5048 (ptt90) REVERT: E 36 LYS cc_start: 0.8835 (pptt) cc_final: 0.8591 (tmtt) REVERT: E 37 MET cc_start: 0.8040 (ttp) cc_final: 0.7789 (ttt) REVERT: E 56 GLN cc_start: 0.8106 (mm110) cc_final: 0.7635 (mm-40) REVERT: E 272 ILE cc_start: 0.9380 (pt) cc_final: 0.9103 (pt) REVERT: F 56 GLN cc_start: 0.7980 (mm110) cc_final: 0.7561 (mm-40) REVERT: F 128 ARG cc_start: 0.9419 (ttp-110) cc_final: 0.9116 (ttp-110) REVERT: F 272 ILE cc_start: 0.9520 (pt) cc_final: 0.9238 (pt) REVERT: G 152 ARG cc_start: 0.5542 (ttt180) cc_final: 0.5322 (ptt90) REVERT: G 280 ASN cc_start: 0.9029 (t0) cc_final: 0.8691 (t0) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.2551 time to fit residues: 67.5320 Evaluate side-chains 123 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 1.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 3.9990 chunk 158 optimal weight: 20.0000 chunk 34 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 43 optimal weight: 0.0770 chunk 176 optimal weight: 0.9990 chunk 146 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 chunk 58 optimal weight: 7.9990 chunk 92 optimal weight: 6.9990 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 280 ASN D 332 ASN G 332 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15309 Z= 0.166 Angle : 0.755 9.695 20825 Z= 0.361 Chirality : 0.046 0.188 2471 Planarity : 0.006 0.054 2520 Dihedral : 5.433 18.872 1981 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.19), residues: 1827 helix: -0.12 (0.15), residues: 1155 sheet: -4.00 (0.51), residues: 84 loop : -2.90 (0.23), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 127 HIS 0.003 0.001 HIS B 106 PHE 0.032 0.001 PHE G 141 TYR 0.017 0.001 TYR A 234 ARG 0.007 0.001 ARG D 128 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 1.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ARG cc_start: 0.9433 (ttp-110) cc_final: 0.9222 (ttp80) REVERT: B 56 GLN cc_start: 0.8202 (mm110) cc_final: 0.7551 (mm-40) REVERT: B 128 ARG cc_start: 0.9420 (tmm-80) cc_final: 0.9207 (ttp-110) REVERT: B 144 GLU cc_start: 0.9416 (tm-30) cc_final: 0.9197 (tm-30) REVERT: B 272 ILE cc_start: 0.9387 (pt) cc_final: 0.8990 (pt) REVERT: C 56 GLN cc_start: 0.8180 (mm110) cc_final: 0.7783 (mm-40) REVERT: C 272 ILE cc_start: 0.9475 (pt) cc_final: 0.9236 (pt) REVERT: D 36 LYS cc_start: 0.8693 (pptt) cc_final: 0.8482 (tmtt) REVERT: D 56 GLN cc_start: 0.8079 (mm110) cc_final: 0.7458 (mm-40) REVERT: D 141 PHE cc_start: 0.7748 (m-10) cc_final: 0.7389 (m-80) REVERT: D 152 ARG cc_start: 0.5344 (ttt180) cc_final: 0.5065 (ptt90) REVERT: D 272 ILE cc_start: 0.9452 (pt) cc_final: 0.9221 (tt) REVERT: E 36 LYS cc_start: 0.8732 (pptt) cc_final: 0.8496 (tmtt) REVERT: E 37 MET cc_start: 0.7980 (ttp) cc_final: 0.7739 (ttt) REVERT: E 56 GLN cc_start: 0.8159 (mm110) cc_final: 0.7669 (mm-40) REVERT: E 272 ILE cc_start: 0.9419 (pt) cc_final: 0.9088 (pt) REVERT: F 56 GLN cc_start: 0.7961 (mm110) cc_final: 0.7479 (mm-40) REVERT: F 128 ARG cc_start: 0.9402 (ttp-110) cc_final: 0.9136 (ttp-110) REVERT: F 213 TYR cc_start: 0.8563 (t80) cc_final: 0.8328 (t80) REVERT: F 217 ARG cc_start: 0.9093 (ttm170) cc_final: 0.8333 (mtp85) REVERT: F 272 ILE cc_start: 0.9520 (pt) cc_final: 0.9256 (pt) REVERT: G 56 GLN cc_start: 0.8167 (mm110) cc_final: 0.7610 (mm110) REVERT: G 152 ARG cc_start: 0.5597 (ttt180) cc_final: 0.5365 (ptt90) REVERT: G 272 ILE cc_start: 0.9511 (pt) cc_final: 0.9309 (tt) REVERT: G 280 ASN cc_start: 0.9006 (t0) cc_final: 0.8627 (t0) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.2445 time to fit residues: 65.2758 Evaluate side-chains 130 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 128 optimal weight: 0.5980 chunk 99 optimal weight: 8.9990 chunk 148 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 175 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN C 280 ASN F 280 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15309 Z= 0.164 Angle : 0.741 9.682 20825 Z= 0.352 Chirality : 0.046 0.184 2471 Planarity : 0.006 0.054 2520 Dihedral : 5.237 18.129 1981 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.19), residues: 1827 helix: 0.10 (0.15), residues: 1155 sheet: -4.06 (0.50), residues: 84 loop : -2.84 (0.23), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 127 HIS 0.001 0.000 HIS E 106 PHE 0.021 0.001 PHE E 334 TYR 0.015 0.001 TYR A 284 ARG 0.006 0.001 ARG C 217 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 1.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LYS cc_start: 0.8998 (tmmt) cc_final: 0.8765 (tppt) REVERT: A 37 MET cc_start: 0.8616 (mtm) cc_final: 0.8396 (ttm) REVERT: B 56 GLN cc_start: 0.8217 (mm110) cc_final: 0.7601 (mm-40) REVERT: B 128 ARG cc_start: 0.9440 (tmm-80) cc_final: 0.9219 (ttp-110) REVERT: B 272 ILE cc_start: 0.9358 (pt) cc_final: 0.8949 (pt) REVERT: C 56 GLN cc_start: 0.8178 (mm110) cc_final: 0.7684 (mm-40) REVERT: C 272 ILE cc_start: 0.9445 (pt) cc_final: 0.9171 (pt) REVERT: D 37 MET cc_start: 0.7909 (ttt) cc_final: 0.7620 (mtp) REVERT: D 56 GLN cc_start: 0.8022 (mm110) cc_final: 0.7651 (mm-40) REVERT: D 152 ARG cc_start: 0.5393 (ttt180) cc_final: 0.5109 (ptt90) REVERT: D 272 ILE cc_start: 0.9438 (pt) cc_final: 0.9185 (pt) REVERT: E 36 LYS cc_start: 0.8720 (pptt) cc_final: 0.8518 (tmtt) REVERT: E 37 MET cc_start: 0.7895 (ttp) cc_final: 0.7635 (ttt) REVERT: E 56 GLN cc_start: 0.8208 (mm110) cc_final: 0.7683 (mm-40) REVERT: E 272 ILE cc_start: 0.9381 (pt) cc_final: 0.9040 (pt) REVERT: F 56 GLN cc_start: 0.8105 (mm110) cc_final: 0.7580 (mm-40) REVERT: F 128 ARG cc_start: 0.9403 (ttp-110) cc_final: 0.9159 (ttp-110) REVERT: F 272 ILE cc_start: 0.9480 (pt) cc_final: 0.9195 (pt) REVERT: G 152 ARG cc_start: 0.5574 (ttt180) cc_final: 0.5364 (ptt90) REVERT: G 280 ASN cc_start: 0.8849 (t0) cc_final: 0.8417 (t0) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.2580 time to fit residues: 68.0345 Evaluate side-chains 123 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 1.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 108 optimal weight: 0.9980 chunk 70 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 86 optimal weight: 0.9980 chunk 16 optimal weight: 0.0670 chunk 137 optimal weight: 3.9990 overall best weight: 1.6122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN D 280 ASN F 280 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.4552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15309 Z= 0.183 Angle : 0.751 9.705 20825 Z= 0.357 Chirality : 0.047 0.179 2471 Planarity : 0.006 0.056 2520 Dihedral : 5.192 18.445 1981 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.20), residues: 1827 helix: 0.27 (0.16), residues: 1155 sheet: -4.11 (0.50), residues: 84 loop : -2.83 (0.23), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 127 HIS 0.002 0.000 HIS E 106 PHE 0.017 0.001 PHE E 334 TYR 0.017 0.001 TYR B 284 ARG 0.008 0.001 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.903 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 LYS cc_start: 0.9173 (tmmt) cc_final: 0.8852 (tppt) REVERT: A 37 MET cc_start: 0.8676 (mtm) cc_final: 0.8396 (ttm) REVERT: B 56 GLN cc_start: 0.8270 (mm110) cc_final: 0.7615 (mm-40) REVERT: B 128 ARG cc_start: 0.9474 (tmm-80) cc_final: 0.9249 (ttp-110) REVERT: B 272 ILE cc_start: 0.9383 (pt) cc_final: 0.8979 (pt) REVERT: C 56 GLN cc_start: 0.8258 (mm110) cc_final: 0.7737 (mm-40) REVERT: C 272 ILE cc_start: 0.9481 (pt) cc_final: 0.9189 (pt) REVERT: D 37 MET cc_start: 0.7778 (ttt) cc_final: 0.7380 (mtp) REVERT: D 56 GLN cc_start: 0.8045 (mm110) cc_final: 0.7661 (mm-40) REVERT: D 152 ARG cc_start: 0.5377 (ttt180) cc_final: 0.5168 (ptt90) REVERT: D 272 ILE cc_start: 0.9451 (pt) cc_final: 0.9184 (pt) REVERT: E 36 LYS cc_start: 0.8829 (pptt) cc_final: 0.8599 (tmtt) REVERT: E 37 MET cc_start: 0.7942 (ttp) cc_final: 0.7689 (ttt) REVERT: E 128 ARG cc_start: 0.9589 (tmm-80) cc_final: 0.9301 (ttp-110) REVERT: F 56 GLN cc_start: 0.8111 (mm110) cc_final: 0.7577 (mm-40) REVERT: F 128 ARG cc_start: 0.9401 (ttp-110) cc_final: 0.9180 (ttp-110) REVERT: F 272 ILE cc_start: 0.9489 (pt) cc_final: 0.9177 (pt) REVERT: G 152 ARG cc_start: 0.5676 (ttt180) cc_final: 0.5402 (ptt90) REVERT: G 217 ARG cc_start: 0.8728 (ttm110) cc_final: 0.8369 (mtp85) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.2364 time to fit residues: 64.9936 Evaluate side-chains 119 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 0.0030 chunk 168 optimal weight: 20.0000 chunk 153 optimal weight: 4.9990 chunk 163 optimal weight: 0.0670 chunk 98 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 128 optimal weight: 0.1980 chunk 50 optimal weight: 6.9990 chunk 147 optimal weight: 0.4980 chunk 154 optimal weight: 20.0000 chunk 162 optimal weight: 7.9990 overall best weight: 0.7530 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN C 280 ASN D 280 ASN E 280 ASN F 280 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.4819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15309 Z= 0.163 Angle : 0.763 9.737 20825 Z= 0.360 Chirality : 0.047 0.211 2471 Planarity : 0.006 0.054 2520 Dihedral : 5.080 17.892 1981 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.20), residues: 1827 helix: 0.40 (0.16), residues: 1127 sheet: -4.03 (0.51), residues: 84 loop : -2.60 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 127 HIS 0.003 0.001 HIS C 106 PHE 0.023 0.001 PHE A 109 TYR 0.026 0.001 TYR B 234 ARG 0.008 0.001 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 1.755 Fit side-chains revert: symmetry clash REVERT: A 36 LYS cc_start: 0.9085 (tmmt) cc_final: 0.8864 (tppt) REVERT: A 37 MET cc_start: 0.8619 (mtm) cc_final: 0.8190 (ttm) REVERT: B 56 GLN cc_start: 0.8281 (mm110) cc_final: 0.7654 (mm-40) REVERT: B 128 ARG cc_start: 0.9501 (tmm-80) cc_final: 0.9285 (ttp-110) REVERT: B 272 ILE cc_start: 0.9356 (pt) cc_final: 0.8956 (pt) REVERT: B 280 ASN cc_start: 0.8742 (t0) cc_final: 0.8510 (t0) REVERT: C 56 GLN cc_start: 0.8269 (mm110) cc_final: 0.7842 (mm-40) REVERT: C 272 ILE cc_start: 0.9459 (pt) cc_final: 0.9179 (pt) REVERT: D 56 GLN cc_start: 0.8095 (mm110) cc_final: 0.7744 (mm-40) REVERT: D 272 ILE cc_start: 0.9402 (pt) cc_final: 0.9102 (pt) REVERT: E 36 LYS cc_start: 0.8804 (pptt) cc_final: 0.8569 (tmtt) REVERT: E 37 MET cc_start: 0.7905 (ttp) cc_final: 0.7658 (ttt) REVERT: E 56 GLN cc_start: 0.8230 (mm-40) cc_final: 0.7709 (mm-40) REVERT: E 272 ILE cc_start: 0.9338 (pt) cc_final: 0.9077 (pt) REVERT: F 56 GLN cc_start: 0.8148 (mm110) cc_final: 0.7620 (mm-40) REVERT: F 128 ARG cc_start: 0.9395 (ttp-110) cc_final: 0.9106 (ttp-110) REVERT: F 272 ILE cc_start: 0.9460 (pt) cc_final: 0.9148 (pt) REVERT: G 152 ARG cc_start: 0.5546 (ttt180) cc_final: 0.5287 (ptt90) REVERT: G 217 ARG cc_start: 0.8723 (ttm110) cc_final: 0.8449 (mtp85) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.2347 time to fit residues: 63.7824 Evaluate side-chains 119 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 0.9990 chunk 172 optimal weight: 0.0970 chunk 105 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 181 optimal weight: 10.0000 chunk 166 optimal weight: 4.9990 chunk 144 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 111 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 280 ASN D 280 ASN E 280 ASN G 56 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.4894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15309 Z= 0.188 Angle : 0.761 9.920 20825 Z= 0.361 Chirality : 0.048 0.212 2471 Planarity : 0.006 0.054 2520 Dihedral : 5.082 18.550 1981 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.20), residues: 1827 helix: 0.43 (0.16), residues: 1134 sheet: -4.18 (0.51), residues: 84 loop : -2.53 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 127 HIS 0.001 0.000 HIS E 106 PHE 0.022 0.001 PHE A 109 TYR 0.014 0.001 TYR F 284 ARG 0.008 0.001 ARG A 128 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 2.067 Fit side-chains revert: symmetry clash REVERT: A 37 MET cc_start: 0.8590 (mtm) cc_final: 0.8223 (ttm) REVERT: B 56 GLN cc_start: 0.8256 (mm110) cc_final: 0.7638 (mm-40) REVERT: B 128 ARG cc_start: 0.9519 (tmm-80) cc_final: 0.9292 (ttp-110) REVERT: B 272 ILE cc_start: 0.9327 (pt) cc_final: 0.8912 (pt) REVERT: B 280 ASN cc_start: 0.8776 (t0) cc_final: 0.8542 (t0) REVERT: C 56 GLN cc_start: 0.8232 (mm110) cc_final: 0.7854 (mm-40) REVERT: C 272 ILE cc_start: 0.9477 (pt) cc_final: 0.9194 (pt) REVERT: D 56 GLN cc_start: 0.8142 (mm110) cc_final: 0.7746 (mm-40) REVERT: D 272 ILE cc_start: 0.9423 (pt) cc_final: 0.9112 (pt) REVERT: E 36 LYS cc_start: 0.8818 (pptt) cc_final: 0.8583 (tmtt) REVERT: E 37 MET cc_start: 0.7918 (ttp) cc_final: 0.7655 (ttt) REVERT: E 56 GLN cc_start: 0.8300 (mm110) cc_final: 0.7759 (mm-40) REVERT: E 128 ARG cc_start: 0.9444 (ttp-110) cc_final: 0.9163 (ttp-110) REVERT: E 272 ILE cc_start: 0.9390 (pt) cc_final: 0.9116 (pt) REVERT: F 56 GLN cc_start: 0.8205 (mm110) cc_final: 0.7717 (mm-40) REVERT: F 128 ARG cc_start: 0.9403 (ttp-110) cc_final: 0.9138 (ttp-110) REVERT: F 272 ILE cc_start: 0.9467 (pt) cc_final: 0.9142 (pt) REVERT: G 152 ARG cc_start: 0.5581 (ttt180) cc_final: 0.5296 (ptt90) REVERT: G 217 ARG cc_start: 0.8738 (ttm110) cc_final: 0.8406 (mtp85) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.2399 time to fit residues: 62.3896 Evaluate side-chains 114 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 114 optimal weight: 20.0000 chunk 153 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 chunk 133 optimal weight: 0.0980 chunk 21 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 144 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 148 optimal weight: 0.9990 chunk 18 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 280 ASN D 280 ASN E 280 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.096600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.075133 restraints weight = 64957.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.076784 restraints weight = 42474.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.077921 restraints weight = 32039.046| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.4830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15309 Z= 0.238 Angle : 0.793 9.450 20825 Z= 0.380 Chirality : 0.050 0.233 2471 Planarity : 0.006 0.055 2520 Dihedral : 5.342 21.451 1981 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.20), residues: 1827 helix: 0.35 (0.15), residues: 1169 sheet: -4.27 (0.51), residues: 84 loop : -2.73 (0.24), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP G 127 HIS 0.002 0.001 HIS E 106 PHE 0.028 0.002 PHE A 109 TYR 0.013 0.001 TYR G 234 ARG 0.008 0.001 ARG A 128 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2543.91 seconds wall clock time: 48 minutes 0.66 seconds (2880.66 seconds total)