Starting phenix.real_space_refine on Fri Feb 16 20:17:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7byn_30246/02_2024/7byn_30246_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7byn_30246/02_2024/7byn_30246.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7byn_30246/02_2024/7byn_30246_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7byn_30246/02_2024/7byn_30246_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7byn_30246/02_2024/7byn_30246_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7byn_30246/02_2024/7byn_30246.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7byn_30246/02_2024/7byn_30246.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7byn_30246/02_2024/7byn_30246_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7byn_30246/02_2024/7byn_30246_neut_updated.pdb" } resolution = 3.3 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= 0.003 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 K 3 8.98 5 P 12 5.49 5 S 92 5.16 5 C 10510 2.51 5 N 2747 2.21 5 O 2985 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 81": "NH1" <-> "NH2" Residue "A ARG 82": "NH1" <-> "NH2" Residue "A GLU 126": "OE1" <-> "OE2" Residue "A ARG 161": "NH1" <-> "NH2" Residue "A ARG 168": "NH1" <-> "NH2" Residue "A ARG 213": "NH1" <-> "NH2" Residue "A GLU 237": "OE1" <-> "OE2" Residue "A GLU 328": "OE1" <-> "OE2" Residue "A ARG 339": "NH1" <-> "NH2" Residue "A GLU 551": "OE1" <-> "OE2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "C ARG 82": "NH1" <-> "NH2" Residue "C GLU 126": "OE1" <-> "OE2" Residue "C ARG 161": "NH1" <-> "NH2" Residue "C ARG 168": "NH1" <-> "NH2" Residue "C ARG 213": "NH1" <-> "NH2" Residue "C GLU 237": "OE1" <-> "OE2" Residue "C GLU 328": "OE1" <-> "OE2" Residue "C ARG 339": "NH1" <-> "NH2" Residue "C GLU 551": "OE1" <-> "OE2" Residue "E ARG 81": "NH1" <-> "NH2" Residue "E ARG 82": "NH1" <-> "NH2" Residue "E GLU 126": "OE1" <-> "OE2" Residue "E ARG 161": "NH1" <-> "NH2" Residue "E ARG 168": "NH1" <-> "NH2" Residue "E ARG 213": "NH1" <-> "NH2" Residue "E GLU 237": "OE1" <-> "OE2" Residue "E GLU 328": "OE1" <-> "OE2" Residue "E ARG 339": "NH1" <-> "NH2" Residue "E GLU 551": "OE1" <-> "OE2" Residue "G ARG 81": "NH1" <-> "NH2" Residue "G ARG 82": "NH1" <-> "NH2" Residue "G GLU 126": "OE1" <-> "OE2" Residue "G ARG 161": "NH1" <-> "NH2" Residue "G ARG 168": "NH1" <-> "NH2" Residue "G ARG 213": "NH1" <-> "NH2" Residue "G GLU 237": "OE1" <-> "OE2" Residue "G GLU 328": "OE1" <-> "OE2" Residue "G ARG 339": "NH1" <-> "NH2" Residue "G GLU 551": "OE1" <-> "OE2" Residue "B GLU 6": "OE1" <-> "OE2" Residue "B GLU 139": "OE1" <-> "OE2" Residue "D GLU 6": "OE1" <-> "OE2" Residue "D GLU 139": "OE1" <-> "OE2" Residue "F GLU 6": "OE1" <-> "OE2" Residue "F GLU 139": "OE1" <-> "OE2" Residue "H GLU 6": "OE1" <-> "OE2" Residue "H GLU 139": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16349 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2872 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 7, 'TRANS': 346} Chain breaks: 2 Chain: "C" Number of atoms: 2872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2872 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 7, 'TRANS': 346} Chain breaks: 2 Chain: "E" Number of atoms: 2872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2872 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 7, 'TRANS': 346} Chain breaks: 2 Chain: "G" Number of atoms: 2872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2872 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 7, 'TRANS': 346} Chain breaks: 2 Chain: "B" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1151 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 2, 'TRANS': 143} Chain: "D" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1151 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 2, 'TRANS': 143} Chain: "F" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1151 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 2, 'TRANS': 143} Chain: "H" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1151 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 2, 'TRANS': 143} Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 59 Unusual residues: {' K': 3, 'PT5': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'PT5:plan-6': 1} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'FCC': 1, 'PT5': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'PT5:plan-6': 1} Unresolved non-hydrogen planarities: 2 Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 56 Unusual residues: {'PT5': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'PT5:plan-6': 1} Unresolved non-hydrogen planarities: 2 Chain: "G" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 56 Unusual residues: {'PT5': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'PT5:plan-6': 1} Unresolved non-hydrogen planarities: 2 Time building chain proxies: 9.20, per 1000 atoms: 0.56 Number of scatterers: 16349 At special positions: 0 Unit cell: (135.875, 135.875, 125.005, 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) K 3 19.00 S 92 16.00 P 12 15.00 O 2985 8.00 N 2747 7.00 C 10510 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.08 Conformation dependent library (CDL) restraints added in 2.7 seconds 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3736 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 88 helices and 4 sheets defined 74.4% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.86 Creating SS restraints... Processing helix chain 'A' and resid 75 through 92 Processing helix chain 'A' and resid 96 through 120 removed outlier: 3.708A pdb=" N PHE A 99 " --> pdb=" O GLY A 96 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL A 114 " --> pdb=" O SER A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 155 removed outlier: 3.837A pdb=" N ILE A 134 " --> pdb=" O GLU A 130 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLY A 155 " --> pdb=" O VAL A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 170 Processing helix chain 'A' and resid 173 through 192 Processing helix chain 'A' and resid 200 through 217 removed outlier: 4.134A pdb=" N ARG A 207 " --> pdb=" O LEU A 203 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N PHE A 208 " --> pdb=" O ARG A 204 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N LEU A 209 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N GLN A 210 " --> pdb=" O MET A 206 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ILE A 211 " --> pdb=" O ARG A 207 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N LEU A 212 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ARG A 213 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET A 214 " --> pdb=" O GLN A 210 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N MET A 217 " --> pdb=" O ARG A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 260 removed outlier: 3.568A pdb=" N HIS A 234 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N LYS A 236 " --> pdb=" O TYR A 232 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N GLU A 237 " --> pdb=" O ALA A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 294 through 307 Processing helix chain 'A' and resid 310 through 335 Proline residue: A 314 - end of helix removed outlier: 3.527A pdb=" N LEU A 318 " --> pdb=" O ALA A 315 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS A 333 " --> pdb=" O HIS A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 356 removed outlier: 3.612A pdb=" N ILE A 346 " --> pdb=" O ALA A 343 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG A 351 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER A 354 " --> pdb=" O ARG A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 361 No H-bonds generated for 'chain 'A' and resid 359 through 361' Processing helix chain 'A' and resid 528 through 553 removed outlier: 4.182A pdb=" N LEU A 553 " --> pdb=" O PHE A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 586 Processing helix chain 'C' and resid 75 through 92 Processing helix chain 'C' and resid 96 through 120 removed outlier: 3.573A pdb=" N PHE C 110 " --> pdb=" O LEU C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 155 removed outlier: 3.837A pdb=" N ILE C 134 " --> pdb=" O GLU C 130 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLY C 155 " --> pdb=" O VAL C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 170 Processing helix chain 'C' and resid 173 through 192 Processing helix chain 'C' and resid 200 through 217 removed outlier: 4.134A pdb=" N ARG C 207 " --> pdb=" O LEU C 203 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N PHE C 208 " --> pdb=" O ARG C 204 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N LEU C 209 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N GLN C 210 " --> pdb=" O MET C 206 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ILE C 211 " --> pdb=" O ARG C 207 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N LEU C 212 " --> pdb=" O PHE C 208 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ARG C 213 " --> pdb=" O LEU C 209 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET C 214 " --> pdb=" O GLN C 210 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N MET C 217 " --> pdb=" O ARG C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 260 removed outlier: 3.568A pdb=" N HIS C 234 " --> pdb=" O VAL C 230 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N LYS C 236 " --> pdb=" O TYR C 232 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLU C 237 " --> pdb=" O ALA C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 294 through 307 Processing helix chain 'C' and resid 310 through 335 Proline residue: C 314 - end of helix removed outlier: 3.528A pdb=" N LEU C 318 " --> pdb=" O ALA C 315 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS C 333 " --> pdb=" O HIS C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 356 removed outlier: 3.611A pdb=" N ILE C 346 " --> pdb=" O ALA C 343 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG C 351 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER C 354 " --> pdb=" O ARG C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 361 No H-bonds generated for 'chain 'C' and resid 359 through 361' Processing helix chain 'C' and resid 528 through 553 removed outlier: 4.293A pdb=" N LEU C 553 " --> pdb=" O PHE C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 586 Processing helix chain 'E' and resid 75 through 91 Processing helix chain 'E' and resid 96 through 120 removed outlier: 3.668A pdb=" N SER E 111 " --> pdb=" O LEU E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 155 removed outlier: 3.837A pdb=" N ILE E 134 " --> pdb=" O GLU E 130 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLY E 155 " --> pdb=" O VAL E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 170 Processing helix chain 'E' and resid 173 through 192 Processing helix chain 'E' and resid 200 through 217 removed outlier: 4.134A pdb=" N ARG E 207 " --> pdb=" O LEU E 203 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N PHE E 208 " --> pdb=" O ARG E 204 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N LEU E 209 " --> pdb=" O SER E 205 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N GLN E 210 " --> pdb=" O MET E 206 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ILE E 211 " --> pdb=" O ARG E 207 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N LEU E 212 " --> pdb=" O PHE E 208 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ARG E 213 " --> pdb=" O LEU E 209 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N MET E 214 " --> pdb=" O GLN E 210 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N MET E 217 " --> pdb=" O ARG E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 260 removed outlier: 3.568A pdb=" N HIS E 234 " --> pdb=" O VAL E 230 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N LYS E 236 " --> pdb=" O TYR E 232 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N GLU E 237 " --> pdb=" O ALA E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 281 Processing helix chain 'E' and resid 294 through 307 Processing helix chain 'E' and resid 310 through 335 Proline residue: E 314 - end of helix removed outlier: 3.526A pdb=" N LEU E 318 " --> pdb=" O ALA E 315 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS E 333 " --> pdb=" O HIS E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 356 removed outlier: 3.611A pdb=" N ILE E 346 " --> pdb=" O ALA E 343 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG E 351 " --> pdb=" O ALA E 348 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER E 354 " --> pdb=" O ARG E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 361 No H-bonds generated for 'chain 'E' and resid 359 through 361' Processing helix chain 'E' and resid 528 through 553 removed outlier: 4.176A pdb=" N LEU E 553 " --> pdb=" O PHE E 549 " (cutoff:3.500A) Processing helix chain 'E' and resid 560 through 586 Processing helix chain 'G' and resid 75 through 92 Processing helix chain 'G' and resid 96 through 120 Processing helix chain 'G' and resid 125 through 155 removed outlier: 3.837A pdb=" N ILE G 134 " --> pdb=" O GLU G 130 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLY G 155 " --> pdb=" O VAL G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 162 through 170 Processing helix chain 'G' and resid 173 through 192 Processing helix chain 'G' and resid 200 through 217 removed outlier: 4.134A pdb=" N ARG G 207 " --> pdb=" O LEU G 203 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N PHE G 208 " --> pdb=" O ARG G 204 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N LEU G 209 " --> pdb=" O SER G 205 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N GLN G 210 " --> pdb=" O MET G 206 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ILE G 211 " --> pdb=" O ARG G 207 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N LEU G 212 " --> pdb=" O PHE G 208 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ARG G 213 " --> pdb=" O LEU G 209 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET G 214 " --> pdb=" O GLN G 210 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N MET G 217 " --> pdb=" O ARG G 213 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 260 removed outlier: 3.568A pdb=" N HIS G 234 " --> pdb=" O VAL G 230 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N LYS G 236 " --> pdb=" O TYR G 232 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLU G 237 " --> pdb=" O ALA G 233 " (cutoff:3.500A) Processing helix chain 'G' and resid 270 through 281 Processing helix chain 'G' and resid 294 through 307 Processing helix chain 'G' and resid 310 through 335 Proline residue: G 314 - end of helix removed outlier: 3.528A pdb=" N LEU G 318 " --> pdb=" O ALA G 315 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS G 333 " --> pdb=" O HIS G 330 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 356 removed outlier: 3.611A pdb=" N ILE G 346 " --> pdb=" O ALA G 343 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG G 351 " --> pdb=" O ALA G 348 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER G 354 " --> pdb=" O ARG G 351 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 361 No H-bonds generated for 'chain 'G' and resid 359 through 361' Processing helix chain 'G' and resid 528 through 553 removed outlier: 4.200A pdb=" N LEU G 553 " --> pdb=" O PHE G 549 " (cutoff:3.500A) Processing helix chain 'G' and resid 560 through 586 Processing helix chain 'B' and resid 6 through 19 removed outlier: 3.605A pdb=" N PHE B 19 " --> pdb=" O ALA B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 38 Processing helix chain 'B' and resid 45 through 54 Processing helix chain 'B' and resid 65 through 74 Processing helix chain 'B' and resid 79 through 92 removed outlier: 4.072A pdb=" N PHE B 92 " --> pdb=" O ALA B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 111 Processing helix chain 'B' and resid 118 through 127 Processing helix chain 'B' and resid 138 through 145 Processing helix chain 'D' and resid 6 through 19 removed outlier: 3.603A pdb=" N PHE D 19 " --> pdb=" O ALA D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 38 Processing helix chain 'D' and resid 45 through 54 Processing helix chain 'D' and resid 65 through 74 Processing helix chain 'D' and resid 79 through 92 removed outlier: 4.071A pdb=" N PHE D 92 " --> pdb=" O ALA D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 111 Processing helix chain 'D' and resid 118 through 127 Processing helix chain 'D' and resid 138 through 145 Processing helix chain 'F' and resid 6 through 19 removed outlier: 3.604A pdb=" N PHE F 19 " --> pdb=" O ALA F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 38 Processing helix chain 'F' and resid 45 through 54 Processing helix chain 'F' and resid 65 through 74 Processing helix chain 'F' and resid 79 through 92 removed outlier: 4.072A pdb=" N PHE F 92 " --> pdb=" O ALA F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 111 Processing helix chain 'F' and resid 118 through 127 Processing helix chain 'F' and resid 138 through 145 Processing helix chain 'H' and resid 6 through 19 removed outlier: 3.605A pdb=" N PHE H 19 " --> pdb=" O ALA H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 38 Processing helix chain 'H' and resid 45 through 54 Processing helix chain 'H' and resid 65 through 74 Processing helix chain 'H' and resid 79 through 92 removed outlier: 4.071A pdb=" N PHE H 92 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 111 Processing helix chain 'H' and resid 118 through 127 Processing helix chain 'H' and resid 138 through 145 Processing sheet with id= A, first strand: chain 'B' and resid 99 through 101 Processing sheet with id= B, first strand: chain 'D' and resid 99 through 101 Processing sheet with id= C, first strand: chain 'F' and resid 99 through 101 Processing sheet with id= D, first strand: chain 'H' and resid 99 through 101 1055 hydrogen bonds defined for protein. 2553 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: 4.55 Time building geometry restraints manager: 7.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2629 1.31 - 1.44: 4639 1.44 - 1.57: 9240 1.57 - 1.70: 18 1.70 - 1.83: 160 Bond restraints: 16686 Sorted by residual: bond pdb=" C15 FCC C 702 " pdb=" N02 FCC C 702 " ideal model delta sigma weight residual 1.415 1.512 -0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" C22 PT5 G 701 " pdb=" C23 PT5 G 701 " ideal model delta sigma weight residual 1.592 1.497 0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" C22 PT5 C 701 " pdb=" C23 PT5 C 701 " ideal model delta sigma weight residual 1.592 1.497 0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" C22 PT5 E 701 " pdb=" C23 PT5 E 701 " ideal model delta sigma weight residual 1.592 1.498 0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" C22 PT5 A 701 " pdb=" C23 PT5 A 701 " ideal model delta sigma weight residual 1.592 1.498 0.094 2.00e-02 2.50e+03 2.21e+01 ... (remaining 16681 not shown) Histogram of bond angle deviations from ideal: 99.55 - 106.48: 297 106.48 - 113.41: 9239 113.41 - 120.34: 6818 120.34 - 127.28: 6008 127.28 - 134.21: 162 Bond angle restraints: 22524 Sorted by residual: angle pdb=" C18 PT5 E 701 " pdb=" C19 PT5 E 701 " pdb=" C20 PT5 E 701 " ideal model delta sigma weight residual 85.86 125.61 -39.75 3.00e+00 1.11e-01 1.76e+02 angle pdb=" C18 PT5 C 701 " pdb=" C19 PT5 C 701 " pdb=" C20 PT5 C 701 " ideal model delta sigma weight residual 85.86 125.60 -39.74 3.00e+00 1.11e-01 1.76e+02 angle pdb=" C18 PT5 G 701 " pdb=" C19 PT5 G 701 " pdb=" C20 PT5 G 701 " ideal model delta sigma weight residual 85.86 125.60 -39.74 3.00e+00 1.11e-01 1.75e+02 angle pdb=" C18 PT5 A 701 " pdb=" C19 PT5 A 701 " pdb=" C20 PT5 A 701 " ideal model delta sigma weight residual 85.86 125.59 -39.73 3.00e+00 1.11e-01 1.75e+02 angle pdb=" C15 PT5 E 701 " pdb=" C16 PT5 E 701 " pdb=" C17 PT5 E 701 " ideal model delta sigma weight residual 152.67 125.53 27.14 3.00e+00 1.11e-01 8.18e+01 ... (remaining 22519 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.77: 9219 35.77 - 71.53: 566 71.53 - 107.30: 38 107.30 - 143.06: 11 143.06 - 178.83: 8 Dihedral angle restraints: 9842 sinusoidal: 4054 harmonic: 5788 Sorted by residual: dihedral pdb=" C13 PT5 A 701 " pdb=" C14 PT5 A 701 " pdb=" C15 PT5 A 701 " pdb=" C16 PT5 A 701 " ideal model delta sinusoidal sigma weight residual 161.05 -20.12 -178.83 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C18 PT5 E 701 " pdb=" C19 PT5 E 701 " pdb=" C20 PT5 E 701 " pdb=" C21 PT5 E 701 " ideal model delta sinusoidal sigma weight residual -7.32 169.39 -176.71 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C13 PT5 E 701 " pdb=" C14 PT5 E 701 " pdb=" C15 PT5 E 701 " pdb=" C16 PT5 E 701 " ideal model delta sinusoidal sigma weight residual 161.05 -25.40 -173.55 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 9839 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1710 0.044 - 0.089: 564 0.089 - 0.133: 130 0.133 - 0.177: 61 0.177 - 0.222: 23 Chirality restraints: 2488 Sorted by residual: chirality pdb=" CA VAL G 583 " pdb=" N VAL G 583 " pdb=" C VAL G 583 " pdb=" CB VAL G 583 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA VAL A 583 " pdb=" N VAL A 583 " pdb=" C VAL A 583 " pdb=" CB VAL A 583 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA VAL E 583 " pdb=" N VAL E 583 " pdb=" C VAL E 583 " pdb=" CB VAL E 583 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 2485 not shown) Planarity restraints: 2824 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C14 PT5 G 701 " 0.100 2.00e-02 2.50e+03 2.35e-01 5.50e+02 pdb=" C15 PT5 G 701 " -0.314 2.00e-02 2.50e+03 pdb=" C16 PT5 G 701 " 0.318 2.00e-02 2.50e+03 pdb=" C17 PT5 G 701 " -0.104 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C14 PT5 A 701 " 0.100 2.00e-02 2.50e+03 2.33e-01 5.42e+02 pdb=" C15 PT5 A 701 " -0.312 2.00e-02 2.50e+03 pdb=" C16 PT5 A 701 " 0.314 2.00e-02 2.50e+03 pdb=" C17 PT5 A 701 " -0.103 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C20 PT5 E 701 " 0.213 2.00e-02 2.50e+03 2.13e-01 4.53e+02 pdb=" C21 PT5 E 701 " -0.212 2.00e-02 2.50e+03 pdb=" C22 PT5 E 701 " -0.213 2.00e-02 2.50e+03 pdb=" C23 PT5 E 701 " 0.213 2.00e-02 2.50e+03 ... (remaining 2821 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.59: 196 2.59 - 3.23: 16971 3.23 - 3.86: 31821 3.86 - 4.50: 41611 4.50 - 5.14: 64534 Nonbonded interactions: 155133 Sorted by model distance: nonbonded pdb=" O THR G 282 " pdb=" OG1 THR G 283 " model vdw 1.949 2.440 nonbonded pdb=" O THR E 282 " pdb=" OG1 THR E 283 " model vdw 1.949 2.440 nonbonded pdb=" O THR C 282 " pdb=" OG1 THR C 283 " model vdw 1.950 2.440 nonbonded pdb=" O THR A 282 " pdb=" OG1 THR A 283 " model vdw 1.950 2.440 nonbonded pdb=" CE LYS C 78 " pdb=" OD1 ASP D 131 " model vdw 2.024 3.440 ... (remaining 155128 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 74 through 588 or resid 701)) selection = (chain 'C' and (resid 74 through 588 or resid 701)) selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } 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=0.00 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: 2.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.680 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 45.600 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5062 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 : 0.011 0.097 16686 Z= 0.730 Angle : 1.289 39.753 22524 Z= 0.688 Chirality : 0.053 0.222 2488 Planarity : 0.011 0.235 2824 Dihedral : 21.226 178.829 6106 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 24.44 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.90 % Favored : 96.90 % Rotamer: Outliers : 16.39 % Allowed : 16.21 % Favored : 67.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.17), residues: 1968 helix: -0.43 (0.11), residues: 1500 sheet: None (None), residues: 0 loop : 0.42 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 350 HIS 0.013 0.002 HIS G 569 PHE 0.012 0.002 PHE G 182 TYR 0.079 0.004 TYR E 565 ARG 0.008 0.001 ARG A 351 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 278 poor density : 268 time to evaluate : 1.831 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 136 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7720 (tp30) REVERT: A 160 TYR cc_start: 0.8229 (OUTLIER) cc_final: 0.7828 (m-80) REVERT: A 247 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8554 (mp) REVERT: A 527 MET cc_start: -0.0079 (mtp) cc_final: -0.1196 (tpt) REVERT: C 108 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7776 (tt) REVERT: C 134 ILE cc_start: 0.7536 (OUTLIER) cc_final: 0.7336 (mt) REVERT: C 145 LEU cc_start: 0.6510 (OUTLIER) cc_final: 0.6218 (mt) REVERT: C 157 CYS cc_start: 0.7895 (OUTLIER) cc_final: 0.7538 (t) REVERT: C 159 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7679 (tpt170) REVERT: C 160 TYR cc_start: 0.8290 (OUTLIER) cc_final: 0.7761 (m-80) REVERT: C 175 CYS cc_start: 0.7913 (OUTLIER) cc_final: 0.7638 (t) REVERT: C 200 THR cc_start: 0.4047 (OUTLIER) cc_final: 0.3530 (m) REVERT: C 309 SER cc_start: 0.9035 (OUTLIER) cc_final: 0.8833 (p) REVERT: E 79 ARG cc_start: 0.5884 (OUTLIER) cc_final: 0.5678 (mmm-85) REVERT: G 93 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.7833 (ptt90) REVERT: G 163 TRP cc_start: 0.6541 (p-90) cc_final: 0.6258 (p-90) REVERT: G 178 ASP cc_start: 0.8446 (t70) cc_final: 0.7985 (m-30) REVERT: G 218 ASP cc_start: 0.7546 (t0) cc_final: 0.7232 (t0) outliers start: 278 outliers final: 111 residues processed: 478 average time/residue: 0.3266 time to fit residues: 219.5471 Evaluate side-chains 306 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 181 time to evaluate : 1.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 97 TRP Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 97 TRP Chi-restraints excluded: chain C residue 99 PHE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 159 ARG Chi-restraints excluded: chain C residue 160 TYR Chi-restraints excluded: chain C residue 175 CYS Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain E residue 79 ARG Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 97 TRP Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 156 CYS Chi-restraints excluded: chain E residue 160 TYR Chi-restraints excluded: chain E residue 175 CYS Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 262 ASP Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 268 SER Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 334 HIS Chi-restraints excluded: chain E residue 335 PHE Chi-restraints excluded: chain E residue 554 ARG Chi-restraints excluded: chain E residue 558 VAL Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 93 ARG Chi-restraints excluded: chain G residue 97 TRP Chi-restraints excluded: chain G residue 99 PHE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 119 SER Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 160 TYR Chi-restraints excluded: chain G residue 188 VAL Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 229 SER Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 248 VAL Chi-restraints excluded: chain G residue 262 ASP Chi-restraints excluded: chain G residue 280 THR Chi-restraints excluded: chain G residue 308 ILE Chi-restraints excluded: chain G residue 331 ARG Chi-restraints excluded: chain G residue 335 PHE Chi-restraints excluded: chain G residue 340 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 5.9990 chunk 148 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 100 optimal weight: 8.9990 chunk 79 optimal weight: 1.9990 chunk 153 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 93 optimal weight: 0.6980 chunk 114 optimal weight: 0.9980 chunk 177 optimal weight: 10.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 HIS A 125 GLN A 329 GLN ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 HIS C 124 HIS C 125 GLN C 234 HIS C 329 GLN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 ASN E 102 HIS E 125 GLN E 329 GLN ** G 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 124 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5104 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16686 Z= 0.210 Angle : 0.633 13.110 22524 Z= 0.321 Chirality : 0.037 0.146 2488 Planarity : 0.005 0.046 2824 Dihedral : 16.032 129.339 2539 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.20 % Allowed : 0.97 % Favored : 98.83 % Rotamer: Outliers : 5.37 % Allowed : 20.52 % Favored : 74.12 % 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: 1.67 (0.19), residues: 1968 helix: 1.16 (0.13), residues: 1456 sheet: None (None), residues: 0 loop : 1.34 (0.30), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 294 HIS 0.005 0.001 HIS G 102 PHE 0.041 0.002 PHE D 12 TYR 0.010 0.001 TYR E 243 ARG 0.006 0.001 ARG F 86 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 206 time to evaluate : 2.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 TRP cc_start: 0.7173 (OUTLIER) cc_final: 0.5752 (m-90) REVERT: A 136 GLU cc_start: 0.7988 (tp30) cc_final: 0.7761 (tp30) REVERT: A 139 MET cc_start: 0.7205 (ttt) cc_final: 0.6996 (ttt) REVERT: A 148 ILE cc_start: 0.8244 (OUTLIER) cc_final: 0.7865 (tp) REVERT: A 247 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8485 (mp) REVERT: A 527 MET cc_start: -0.0347 (mtp) cc_final: -0.1721 (tpp) REVERT: C 159 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7681 (tpt170) REVERT: E 253 SER cc_start: 0.8868 (m) cc_final: 0.8548 (m) REVERT: E 340 MET cc_start: 0.6782 (tmm) cc_final: 0.6532 (tpt) REVERT: E 344 ASN cc_start: 0.4336 (OUTLIER) cc_final: 0.3977 (t0) REVERT: E 572 MET cc_start: 0.1357 (ptt) cc_final: -0.1249 (tmm) REVERT: G 92 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7787 (mm-30) REVERT: G 163 TRP cc_start: 0.6186 (p-90) cc_final: 0.5040 (p-90) REVERT: G 178 ASP cc_start: 0.8113 (t70) cc_final: 0.7754 (m-30) outliers start: 91 outliers final: 41 residues processed: 269 average time/residue: 0.2787 time to fit residues: 112.1659 Evaluate side-chains 226 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 180 time to evaluate : 1.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 97 TRP Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 97 TRP Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 159 ARG Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 175 CYS Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 206 MET Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 262 ASP Chi-restraints excluded: chain E residue 334 HIS Chi-restraints excluded: chain E residue 344 ASN Chi-restraints excluded: chain E residue 559 LYS Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 97 TRP Chi-restraints excluded: chain G residue 99 PHE Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain G residue 201 SER Chi-restraints excluded: chain G residue 205 SER Chi-restraints excluded: chain G residue 247 LEU Chi-restraints excluded: chain G residue 262 ASP Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 335 PHE Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 110 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 chunk 148 optimal weight: 0.6980 chunk 121 optimal weight: 0.9980 chunk 49 optimal weight: 0.0470 chunk 178 optimal weight: 5.9990 chunk 192 optimal weight: 4.9990 chunk 158 optimal weight: 6.9990 chunk 176 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 125 GLN H 107 HIS H 143 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5129 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16686 Z= 0.183 Angle : 0.566 12.677 22524 Z= 0.285 Chirality : 0.035 0.135 2488 Planarity : 0.004 0.035 2824 Dihedral : 13.741 125.663 2382 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.12 % Favored : 98.68 % Rotamer: Outliers : 4.19 % Allowed : 21.76 % Favored : 74.06 % 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: 2.08 (0.19), residues: 1968 helix: 1.46 (0.13), residues: 1492 sheet: None (None), residues: 0 loop : 1.48 (0.32), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 350 HIS 0.002 0.000 HIS G 102 PHE 0.040 0.001 PHE D 12 TYR 0.009 0.001 TYR E 243 ARG 0.007 0.000 ARG A 159 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 183 time to evaluate : 1.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 GLU cc_start: 0.7539 (tp30) cc_final: 0.7193 (tm-30) REVERT: A 139 MET cc_start: 0.7141 (ttt) cc_final: 0.6930 (ttt) REVERT: A 527 MET cc_start: -0.0400 (mtp) cc_final: -0.1936 (tpp) REVERT: A 572 MET cc_start: 0.1094 (tpt) cc_final: 0.0507 (tmm) REVERT: C 157 CYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7811 (t) REVERT: C 159 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7710 (tpt170) REVERT: E 130 GLU cc_start: 0.7109 (tm-30) cc_final: 0.6554 (tm-30) REVERT: E 253 SER cc_start: 0.8885 (m) cc_final: 0.8564 (m) REVERT: E 340 MET cc_start: 0.6916 (tmm) cc_final: 0.6696 (tpp) REVERT: E 344 ASN cc_start: 0.4052 (OUTLIER) cc_final: 0.3764 (t0) REVERT: E 572 MET cc_start: 0.1409 (ptt) cc_final: -0.1313 (tmm) REVERT: G 92 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7850 (mm-30) REVERT: G 163 TRP cc_start: 0.5903 (p-90) cc_final: 0.5107 (p-90) REVERT: G 178 ASP cc_start: 0.8085 (t70) cc_final: 0.7682 (m-30) REVERT: G 531 LYS cc_start: 0.4614 (tptp) cc_final: 0.4308 (tptp) REVERT: D 89 PHE cc_start: 0.5987 (OUTLIER) cc_final: 0.5440 (t80) REVERT: F 144 MET cc_start: 0.4965 (mtt) cc_final: 0.4336 (tmm) outliers start: 71 outliers final: 42 residues processed: 237 average time/residue: 0.2546 time to fit residues: 94.6694 Evaluate side-chains 216 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 170 time to evaluate : 1.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain C residue 99 PHE Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 158 CYS Chi-restraints excluded: chain C residue 159 ARG Chi-restraints excluded: chain C residue 167 PHE Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 282 THR Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 206 MET Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 334 HIS Chi-restraints excluded: chain E residue 344 ASN Chi-restraints excluded: chain G residue 97 TRP Chi-restraints excluded: chain G residue 99 PHE Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 160 TYR Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain G residue 201 SER Chi-restraints excluded: chain G residue 247 LEU Chi-restraints excluded: chain G residue 262 ASP Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 335 PHE Chi-restraints excluded: chain G residue 344 ASN Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain D residue 42 ASN Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 110 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 9.9990 chunk 134 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 chunk 178 optimal weight: 0.4980 chunk 189 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 169 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 ASN ** E 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 234 HIS H 107 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5141 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16686 Z= 0.173 Angle : 0.541 12.605 22524 Z= 0.271 Chirality : 0.034 0.140 2488 Planarity : 0.004 0.030 2824 Dihedral : 12.302 126.845 2367 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.17 % Favored : 98.63 % Rotamer: Outliers : 3.95 % Allowed : 21.46 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.19), residues: 1968 helix: 1.54 (0.13), residues: 1492 sheet: None (None), residues: 0 loop : 1.39 (0.31), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 350 HIS 0.002 0.000 HIS G 102 PHE 0.031 0.001 PHE D 68 TYR 0.014 0.001 TYR C 232 ARG 0.004 0.000 ARG E 338 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 181 time to evaluate : 2.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 TRP cc_start: 0.6934 (OUTLIER) cc_final: 0.5486 (m-90) REVERT: A 130 GLU cc_start: 0.7478 (tp30) cc_final: 0.7249 (tm-30) REVERT: A 139 MET cc_start: 0.7270 (ttt) cc_final: 0.7010 (ttt) REVERT: A 247 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8485 (mp) REVERT: A 527 MET cc_start: -0.0435 (mtp) cc_final: -0.2069 (tpt) REVERT: A 572 MET cc_start: 0.1436 (tpt) cc_final: 0.0811 (tmm) REVERT: C 157 CYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7812 (t) REVERT: C 159 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7733 (tpt170) REVERT: C 178 ASP cc_start: 0.8080 (t70) cc_final: 0.7499 (t0) REVERT: C 206 MET cc_start: 0.8001 (ttm) cc_final: 0.7567 (ppp) REVERT: E 130 GLU cc_start: 0.7234 (tm-30) cc_final: 0.6994 (mm-30) REVERT: E 253 SER cc_start: 0.8898 (m) cc_final: 0.8566 (m) REVERT: E 328 GLU cc_start: 0.7930 (tt0) cc_final: 0.7703 (tt0) REVERT: E 572 MET cc_start: 0.1513 (ptt) cc_final: -0.1173 (mmm) REVERT: G 93 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.7888 (ptt90) REVERT: G 178 ASP cc_start: 0.8080 (t70) cc_final: 0.7691 (m-30) REVERT: G 531 LYS cc_start: 0.4676 (tptp) cc_final: 0.4307 (tptp) REVERT: D 89 PHE cc_start: 0.6224 (OUTLIER) cc_final: 0.5797 (t80) REVERT: H 76 MET cc_start: 0.1569 (pmm) cc_final: -0.0987 (tpp) outliers start: 67 outliers final: 41 residues processed: 236 average time/residue: 0.2388 time to fit residues: 88.3650 Evaluate side-chains 217 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 170 time to evaluate : 2.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 TRP Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 175 CYS Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 99 PHE Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 158 CYS Chi-restraints excluded: chain C residue 159 ARG Chi-restraints excluded: chain C residue 167 PHE Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 282 THR Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 206 MET Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 334 HIS Chi-restraints excluded: chain G residue 93 ARG Chi-restraints excluded: chain G residue 97 TRP Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 160 TYR Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain G residue 201 SER Chi-restraints excluded: chain G residue 247 LEU Chi-restraints excluded: chain G residue 265 SER Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 335 PHE Chi-restraints excluded: chain G residue 344 ASN Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain H residue 14 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 0.9980 chunk 107 optimal weight: 0.1980 chunk 2 optimal weight: 0.6980 chunk 141 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 chunk 161 optimal weight: 0.4980 chunk 130 optimal weight: 0.0870 chunk 0 optimal weight: 10.0000 chunk 96 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 chunk 47 optimal weight: 0.0980 overall best weight: 0.3158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN ** G 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 GLN F 111 ASN F 143 GLN H 107 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5105 moved from start: 0.4933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16686 Z= 0.142 Angle : 0.522 12.644 22524 Z= 0.260 Chirality : 0.033 0.130 2488 Planarity : 0.004 0.030 2824 Dihedral : 11.541 130.499 2359 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.20 % Allowed : 0.71 % Favored : 99.09 % Rotamer: Outliers : 2.95 % Allowed : 22.29 % Favored : 74.76 % 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: 2.25 (0.19), residues: 1968 helix: 1.64 (0.13), residues: 1500 sheet: None (None), residues: 0 loop : 1.32 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 350 HIS 0.001 0.000 HIS E 124 PHE 0.019 0.001 PHE D 68 TYR 0.009 0.001 TYR C 353 ARG 0.003 0.000 ARG D 90 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 186 time to evaluate : 1.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8499 (mp) REVERT: A 527 MET cc_start: -0.0593 (mtp) cc_final: -0.2067 (tpt) REVERT: A 572 MET cc_start: 0.1263 (tpt) cc_final: 0.0760 (tmm) REVERT: C 157 CYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7764 (t) REVERT: C 159 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7703 (tpt170) REVERT: C 178 ASP cc_start: 0.7897 (t70) cc_final: 0.7394 (t0) REVERT: C 206 MET cc_start: 0.7831 (ttm) cc_final: 0.7517 (ppp) REVERT: E 253 SER cc_start: 0.8904 (m) cc_final: 0.8527 (m) REVERT: E 572 MET cc_start: 0.1546 (ptt) cc_final: -0.0958 (tmm) REVERT: G 93 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.7770 (ptt90) REVERT: G 178 ASP cc_start: 0.8061 (t70) cc_final: 0.7686 (m-30) REVERT: D 89 PHE cc_start: 0.6161 (OUTLIER) cc_final: 0.5727 (t80) REVERT: H 76 MET cc_start: 0.1590 (pmm) cc_final: -0.0822 (tpp) outliers start: 50 outliers final: 32 residues processed: 229 average time/residue: 0.2638 time to fit residues: 92.2689 Evaluate side-chains 208 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 171 time to evaluate : 1.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 CYS Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain C residue 99 PHE Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 156 CYS Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 159 ARG Chi-restraints excluded: chain C residue 167 PHE Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 282 THR Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 334 HIS Chi-restraints excluded: chain G residue 93 ARG Chi-restraints excluded: chain G residue 160 TYR Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain G residue 265 SER Chi-restraints excluded: chain G residue 335 PHE Chi-restraints excluded: chain G residue 344 ASN Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 143 GLN Chi-restraints excluded: chain H residue 14 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 0.0870 chunk 170 optimal weight: 0.6980 chunk 37 optimal weight: 6.9990 chunk 111 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 189 optimal weight: 5.9990 chunk 157 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 344 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 107 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5166 moved from start: 0.5139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16686 Z= 0.180 Angle : 0.561 12.422 22524 Z= 0.279 Chirality : 0.034 0.214 2488 Planarity : 0.004 0.035 2824 Dihedral : 11.048 126.536 2353 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.27 % Favored : 98.53 % Rotamer: Outliers : 3.12 % Allowed : 22.41 % Favored : 74.47 % 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: 2.25 (0.19), residues: 1968 helix: 1.67 (0.13), residues: 1496 sheet: None (None), residues: 0 loop : 1.19 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 350 HIS 0.002 0.001 HIS A 292 PHE 0.030 0.001 PHE D 12 TYR 0.010 0.001 TYR E 243 ARG 0.007 0.000 ARG H 86 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 174 time to evaluate : 1.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 TRP cc_start: 0.7120 (OUTLIER) cc_final: 0.5587 (m-90) REVERT: A 237 GLU cc_start: 0.8514 (mp0) cc_final: 0.8143 (mp0) REVERT: A 247 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8493 (mp) REVERT: A 527 MET cc_start: -0.0442 (mtp) cc_final: -0.1949 (tpt) REVERT: A 572 MET cc_start: 0.1582 (tpt) cc_final: 0.1266 (tmm) REVERT: C 139 MET cc_start: 0.7315 (tpp) cc_final: 0.7111 (mmt) REVERT: C 157 CYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7750 (t) REVERT: C 159 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7870 (tpt170) REVERT: C 178 ASP cc_start: 0.7922 (t70) cc_final: 0.7531 (t0) REVERT: C 206 MET cc_start: 0.8050 (ttm) cc_final: 0.7663 (ppp) REVERT: E 253 SER cc_start: 0.8897 (m) cc_final: 0.8438 (m) REVERT: E 572 MET cc_start: 0.1675 (ptt) cc_final: -0.1081 (mmm) REVERT: G 93 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.7892 (ptt90) REVERT: G 178 ASP cc_start: 0.8085 (t70) cc_final: 0.7686 (m-30) REVERT: D 89 PHE cc_start: 0.6159 (OUTLIER) cc_final: 0.5775 (t80) outliers start: 53 outliers final: 36 residues processed: 220 average time/residue: 0.2435 time to fit residues: 83.6953 Evaluate side-chains 205 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 163 time to evaluate : 1.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 97 TRP Chi-restraints excluded: chain A residue 175 CYS Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain C residue 99 PHE Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 156 CYS Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 158 CYS Chi-restraints excluded: chain C residue 159 ARG Chi-restraints excluded: chain C residue 167 PHE Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain E residue 156 CYS Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain G residue 93 ARG Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 160 TYR Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain G residue 247 LEU Chi-restraints excluded: chain G residue 262 ASP Chi-restraints excluded: chain G residue 265 SER Chi-restraints excluded: chain G residue 344 ASN Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain D residue 42 ASN Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain H residue 14 GLU Chi-restraints excluded: chain H residue 136 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 138 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 105 optimal weight: 20.0000 chunk 188 optimal weight: 0.9990 chunk 118 optimal weight: 0.6980 chunk 115 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 344 ASN ** G 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 41 GLN H 107 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5202 moved from start: 0.5405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16686 Z= 0.204 Angle : 0.575 12.438 22524 Z= 0.286 Chirality : 0.035 0.216 2488 Planarity : 0.004 0.035 2824 Dihedral : 10.776 125.889 2346 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.47 % Favored : 98.32 % Rotamer: Outliers : 3.77 % Allowed : 22.11 % Favored : 74.12 % 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: 2.23 (0.19), residues: 1968 helix: 1.69 (0.13), residues: 1488 sheet: None (None), residues: 0 loop : 1.08 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 350 HIS 0.002 0.001 HIS A 292 PHE 0.041 0.001 PHE B 68 TYR 0.011 0.001 TYR C 80 ARG 0.008 0.000 ARG H 86 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 173 time to evaluate : 1.898 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 TRP cc_start: 0.7191 (OUTLIER) cc_final: 0.5696 (m-90) REVERT: A 237 GLU cc_start: 0.8530 (mp0) cc_final: 0.8158 (mp0) REVERT: A 247 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8535 (mp) REVERT: A 527 MET cc_start: -0.0264 (mtp) cc_final: -0.1859 (tpt) REVERT: C 157 CYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7768 (t) REVERT: C 159 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7803 (tpt170) REVERT: C 178 ASP cc_start: 0.7985 (t70) cc_final: 0.7572 (t0) REVERT: C 206 MET cc_start: 0.8119 (ttm) cc_final: 0.7890 (tmm) REVERT: E 572 MET cc_start: 0.1305 (ptt) cc_final: -0.0705 (mmm) REVERT: G 178 ASP cc_start: 0.8089 (t70) cc_final: 0.7647 (m-30) REVERT: D 89 PHE cc_start: 0.6142 (OUTLIER) cc_final: 0.5769 (t80) outliers start: 64 outliers final: 41 residues processed: 221 average time/residue: 0.2433 time to fit residues: 83.9850 Evaluate side-chains 210 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 164 time to evaluate : 1.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 97 TRP Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 175 CYS Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 156 CYS Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 158 CYS Chi-restraints excluded: chain C residue 159 ARG Chi-restraints excluded: chain C residue 167 PHE Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 156 CYS Chi-restraints excluded: chain E residue 158 CYS Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 268 SER Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 160 TYR Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain G residue 247 LEU Chi-restraints excluded: chain G residue 262 ASP Chi-restraints excluded: chain G residue 265 SER Chi-restraints excluded: chain G residue 335 PHE Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain H residue 14 GLU Chi-restraints excluded: chain H residue 124 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 37 optimal weight: 0.0170 chunk 36 optimal weight: 0.9990 chunk 120 optimal weight: 0.6980 chunk 128 optimal weight: 0.9980 chunk 93 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 148 optimal weight: 5.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 107 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5172 moved from start: 0.5597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16686 Z= 0.160 Angle : 0.553 12.475 22524 Z= 0.276 Chirality : 0.034 0.172 2488 Planarity : 0.004 0.045 2824 Dihedral : 10.710 127.437 2346 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.27 % Favored : 98.53 % Rotamer: Outliers : 2.42 % Allowed : 23.23 % Favored : 74.35 % 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: 2.24 (0.19), residues: 1968 helix: 1.70 (0.14), residues: 1496 sheet: None (None), residues: 0 loop : 1.05 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 350 HIS 0.001 0.000 HIS E 124 PHE 0.037 0.001 PHE B 68 TYR 0.009 0.001 TYR B 138 ARG 0.008 0.000 ARG H 86 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 174 time to evaluate : 1.785 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 TRP cc_start: 0.7240 (OUTLIER) cc_final: 0.5706 (m-90) REVERT: A 247 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8507 (mp) REVERT: A 527 MET cc_start: -0.0429 (mtp) cc_final: -0.1900 (tpt) REVERT: C 157 CYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7718 (t) REVERT: C 178 ASP cc_start: 0.7869 (t70) cc_final: 0.7496 (t0) REVERT: C 206 MET cc_start: 0.8127 (ttm) cc_final: 0.7879 (tmm) REVERT: G 122 GLN cc_start: 0.8010 (OUTLIER) cc_final: 0.7787 (tp40) REVERT: G 178 ASP cc_start: 0.8094 (t70) cc_final: 0.7647 (m-30) REVERT: G 206 MET cc_start: 0.8046 (mtm) cc_final: 0.7528 (tmm) REVERT: G 527 MET cc_start: -0.0896 (ttm) cc_final: -0.1401 (tmm) REVERT: B 76 MET cc_start: 0.2640 (ptt) cc_final: 0.2307 (ptt) outliers start: 41 outliers final: 33 residues processed: 206 average time/residue: 0.2327 time to fit residues: 76.4335 Evaluate side-chains 205 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 168 time to evaluate : 1.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 TRP Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 156 CYS Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 158 CYS Chi-restraints excluded: chain C residue 167 PHE Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain G residue 122 GLN Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 156 CYS Chi-restraints excluded: chain G residue 160 TYR Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain G residue 247 LEU Chi-restraints excluded: chain G residue 265 SER Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain H residue 14 GLU Chi-restraints excluded: chain H residue 124 MET Chi-restraints excluded: chain H residue 136 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 4.9990 chunk 180 optimal weight: 8.9990 chunk 165 optimal weight: 0.0570 chunk 176 optimal weight: 9.9990 chunk 105 optimal weight: 10.0000 chunk 76 optimal weight: 0.9980 chunk 138 optimal weight: 8.9990 chunk 54 optimal weight: 0.5980 chunk 159 optimal weight: 0.9980 chunk 166 optimal weight: 4.9990 chunk 175 optimal weight: 3.9990 overall best weight: 1.3300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 89 ASN E 292 HIS ** G 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 107 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5240 moved from start: 0.5780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16686 Z= 0.234 Angle : 0.591 12.391 22524 Z= 0.294 Chirality : 0.036 0.162 2488 Planarity : 0.004 0.050 2824 Dihedral : 10.341 124.413 2342 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.68 % Favored : 98.22 % Rotamer: Outliers : 3.01 % Allowed : 22.76 % Favored : 74.23 % 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: 2.17 (0.19), residues: 1968 helix: 1.67 (0.13), residues: 1484 sheet: None (None), residues: 0 loop : 0.96 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 350 HIS 0.003 0.001 HIS E 569 PHE 0.033 0.001 PHE B 68 TYR 0.013 0.001 TYR C 80 ARG 0.008 0.000 ARG F 86 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 168 time to evaluate : 1.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 TRP cc_start: 0.7288 (OUTLIER) cc_final: 0.5934 (m-90) REVERT: A 247 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8511 (mp) REVERT: A 527 MET cc_start: 0.0067 (mtp) cc_final: -0.1589 (tpt) REVERT: C 157 CYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7660 (t) REVERT: C 178 ASP cc_start: 0.7987 (t70) cc_final: 0.7564 (t0) REVERT: G 122 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7910 (tp40) REVERT: G 178 ASP cc_start: 0.8090 (t70) cc_final: 0.7620 (m-30) REVERT: G 527 MET cc_start: -0.0864 (ttm) cc_final: -0.1729 (tmm) REVERT: B 85 ILE cc_start: 0.5685 (mt) cc_final: 0.5472 (mt) REVERT: F 28 THR cc_start: 0.5903 (p) cc_final: 0.5588 (p) outliers start: 51 outliers final: 38 residues processed: 210 average time/residue: 0.2278 time to fit residues: 76.9816 Evaluate side-chains 207 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 165 time to evaluate : 2.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 97 TRP Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 156 CYS Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 158 CYS Chi-restraints excluded: chain C residue 167 PHE Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain E residue 156 CYS Chi-restraints excluded: chain E residue 158 CYS Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 268 SER Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 122 GLN Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 160 TYR Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain G residue 247 LEU Chi-restraints excluded: chain G residue 262 ASP Chi-restraints excluded: chain G residue 265 SER Chi-restraints excluded: chain G residue 335 PHE Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain H residue 14 GLU Chi-restraints excluded: chain H residue 124 MET Chi-restraints excluded: chain H residue 136 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 1.9990 chunk 186 optimal weight: 0.9980 chunk 113 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 129 optimal weight: 0.5980 chunk 195 optimal weight: 10.0000 chunk 179 optimal weight: 0.9980 chunk 155 optimal weight: 8.9990 chunk 16 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 89 ASN ** G 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 107 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5207 moved from start: 0.5970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16686 Z= 0.184 Angle : 0.579 12.441 22524 Z= 0.287 Chirality : 0.035 0.164 2488 Planarity : 0.004 0.050 2824 Dihedral : 10.286 126.508 2342 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.32 % Favored : 98.63 % Rotamer: Outliers : 2.59 % Allowed : 23.23 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.19), residues: 1968 helix: 1.68 (0.14), residues: 1488 sheet: None (None), residues: 0 loop : 0.94 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP G 350 HIS 0.003 0.000 HIS F 107 PHE 0.035 0.001 PHE D 12 TYR 0.010 0.001 TYR C 243 ARG 0.006 0.000 ARG F 86 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 167 time to evaluate : 1.860 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 TRP cc_start: 0.7324 (OUTLIER) cc_final: 0.5800 (m-90) REVERT: A 247 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8526 (mp) REVERT: A 527 MET cc_start: 0.0055 (mtp) cc_final: -0.1539 (tpt) REVERT: A 572 MET cc_start: 0.0956 (tmm) cc_final: -0.0489 (tpt) REVERT: C 157 CYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7537 (t) REVERT: C 178 ASP cc_start: 0.7910 (t70) cc_final: 0.7511 (t0) REVERT: G 122 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7785 (tp40) REVERT: G 178 ASP cc_start: 0.8050 (t70) cc_final: 0.7591 (m-30) REVERT: G 340 MET cc_start: 0.6274 (tpp) cc_final: 0.5998 (tmm) REVERT: G 527 MET cc_start: -0.0871 (ttm) cc_final: -0.1777 (tmm) REVERT: B 85 ILE cc_start: 0.5687 (mt) cc_final: 0.5443 (mt) REVERT: D 72 MET cc_start: 0.4596 (pmm) cc_final: 0.4332 (pmm) REVERT: D 89 PHE cc_start: 0.6098 (OUTLIER) cc_final: 0.5818 (t80) outliers start: 44 outliers final: 32 residues processed: 201 average time/residue: 0.2288 time to fit residues: 74.3587 Evaluate side-chains 199 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 162 time to evaluate : 1.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 TRP Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 156 CYS Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 158 CYS Chi-restraints excluded: chain C residue 167 PHE Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain G residue 122 GLN Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 160 TYR Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain G residue 247 LEU Chi-restraints excluded: chain G residue 265 SER Chi-restraints excluded: chain G residue 335 PHE Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain H residue 124 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 0.0370 chunk 165 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 143 optimal weight: 8.9990 chunk 22 optimal weight: 0.5980 chunk 43 optimal weight: 9.9990 chunk 155 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 159 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 28 optimal weight: 6.9990 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 89 ASN ** G 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 107 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.212939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.121274 restraints weight = 25998.722| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 3.18 r_work: 0.3258 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3265 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 33 | |-----------------------------------------------------------------------------| r_final: 0.3263 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.6141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16686 Z= 0.165 Angle : 0.564 12.446 22524 Z= 0.278 Chirality : 0.034 0.183 2488 Planarity : 0.004 0.051 2824 Dihedral : 10.052 125.966 2342 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.37 % Favored : 98.58 % Rotamer: Outliers : 2.65 % Allowed : 23.17 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.19), residues: 1968 helix: 1.68 (0.14), residues: 1496 sheet: None (None), residues: 0 loop : 0.92 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP G 350 HIS 0.001 0.000 HIS G 102 PHE 0.033 0.001 PHE F 141 TYR 0.009 0.001 TYR B 138 ARG 0.007 0.000 ARG H 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3658.33 seconds wall clock time: 67 minutes 7.23 seconds (4027.23 seconds total)