Starting phenix.real_space_refine on Fri Feb 16 01:58:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ebl_9025/02_2024/6ebl_9025_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ebl_9025/02_2024/6ebl_9025.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ebl_9025/02_2024/6ebl_9025.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ebl_9025/02_2024/6ebl_9025.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ebl_9025/02_2024/6ebl_9025_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ebl_9025/02_2024/6ebl_9025_neut_updated.pdb" } resolution = 3.0 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= 0.004 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 84 5.16 5 C 8764 2.51 5 N 2388 2.21 5 O 2704 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 129": "NH1" <-> "NH2" Residue "A ASP 153": "OD1" <-> "OD2" Residue "A ARG 189": "NH1" <-> "NH2" Residue "A ARG 283": "NH1" <-> "NH2" Residue "A ARG 284": "NH1" <-> "NH2" Residue "B ARG 43": "NH1" <-> "NH2" Residue "B PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 67": "NH1" <-> "NH2" Residue "B ARG 97": "NH1" <-> "NH2" Residue "C PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 129": "NH1" <-> "NH2" Residue "C ARG 283": "NH1" <-> "NH2" Residue "C ARG 284": "NH1" <-> "NH2" Residue "D ARG 43": "NH1" <-> "NH2" Residue "D PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 67": "NH1" <-> "NH2" Residue "D ARG 97": "NH1" <-> "NH2" Residue "E ARG 129": "NH1" <-> "NH2" Residue "E ARG 283": "NH1" <-> "NH2" Residue "E ARG 284": "NH1" <-> "NH2" Residue "F GLU 33": "OE1" <-> "OE2" Residue "F ARG 43": "NH1" <-> "NH2" Residue "F PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 67": "NH1" <-> "NH2" Residue "F ARG 97": "NH1" <-> "NH2" Residue "G ARG 129": "NH1" <-> "NH2" Residue "G ARG 283": "NH1" <-> "NH2" Residue "G ARG 284": "NH1" <-> "NH2" Residue "H PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 67": "NH1" <-> "NH2" Residue "H ARG 97": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13952 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2548 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 12, 'TRANS': 312} Chain: "B" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 860 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 95} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2548 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 12, 'TRANS': 312} Chain: "D" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 860 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 95} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2548 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 12, 'TRANS': 312} Chain: "F" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 860 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 95} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2548 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 12, 'TRANS': 312} Chain: "H" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 860 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 95} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "H" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 7.82, per 1000 atoms: 0.56 Number of scatterers: 13952 At special positions: 0 Unit cell: (132.765, 132.765, 99.365, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 84 16.00 P 12 15.00 O 2704 8.00 N 2388 7.00 C 8764 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: 5.52 Conformation dependent library (CDL) restraints added in 2.3 seconds 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3144 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 84 helices and 16 sheets defined 44.9% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.77 Creating SS restraints... Processing helix chain 'A' and resid 66 through 79 removed outlier: 3.523A pdb=" N ASN A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 106 removed outlier: 6.233A pdb=" N ALA A 95 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU A 96 " --> pdb=" O GLY A 93 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL A 98 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU A 99 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE A 103 " --> pdb=" O GLY A 100 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS A 104 " --> pdb=" O ASN A 101 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LYS A 106 " --> pdb=" O ILE A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 112 No H-bonds generated for 'chain 'A' and resid 110 through 112' Processing helix chain 'A' and resid 126 through 128 No H-bonds generated for 'chain 'A' and resid 126 through 128' Processing helix chain 'A' and resid 133 through 146 removed outlier: 3.680A pdb=" N GLU A 145 " --> pdb=" O LYS A 141 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG A 146 " --> pdb=" O ALA A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 178 Processing helix chain 'A' and resid 192 through 204 removed outlier: 3.501A pdb=" N ALA A 202 " --> pdb=" O ALA A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 226 No H-bonds generated for 'chain 'A' and resid 223 through 226' Processing helix chain 'A' and resid 228 through 235 removed outlier: 3.775A pdb=" N LEU A 232 " --> pdb=" O GLN A 228 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS A 234 " --> pdb=" O PRO A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 257 removed outlier: 4.502A pdb=" N SER A 257 " --> pdb=" O LYS A 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 254 through 257' Processing helix chain 'A' and resid 264 through 266 No H-bonds generated for 'chain 'A' and resid 264 through 266' Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 280 through 298 removed outlier: 3.520A pdb=" N GLN A 285 " --> pdb=" O GLU A 281 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN A 286 " --> pdb=" O GLY A 282 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A 287 " --> pdb=" O ARG A 283 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU A 291 " --> pdb=" O ALA A 287 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 309 Processing helix chain 'A' and resid 327 through 336 removed outlier: 3.902A pdb=" N ALA A 336 " --> pdb=" O GLU A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 355 Processing helix chain 'B' and resid 48 through 53 removed outlier: 3.893A pdb=" N GLN B 53 " --> pdb=" O LYS B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 68 Processing helix chain 'B' and resid 85 through 94 removed outlier: 3.844A pdb=" N TYR B 92 " --> pdb=" O ILE B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 116 removed outlier: 3.644A pdb=" N GLU B 111 " --> pdb=" O ASP B 107 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG B 114 " --> pdb=" O SER B 110 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 130 removed outlier: 3.576A pdb=" N MET B 125 " --> pdb=" O GLU B 121 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP B 129 " --> pdb=" O MET B 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 79 removed outlier: 3.523A pdb=" N ASN C 79 " --> pdb=" O LEU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 106 removed outlier: 6.232A pdb=" N ALA C 95 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU C 96 " --> pdb=" O GLY C 93 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL C 98 " --> pdb=" O ALA C 95 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU C 99 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE C 103 " --> pdb=" O GLY C 100 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS C 104 " --> pdb=" O ASN C 101 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS C 106 " --> pdb=" O ILE C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 112 No H-bonds generated for 'chain 'C' and resid 110 through 112' Processing helix chain 'C' and resid 126 through 128 No H-bonds generated for 'chain 'C' and resid 126 through 128' Processing helix chain 'C' and resid 133 through 146 removed outlier: 3.681A pdb=" N GLU C 145 " --> pdb=" O LYS C 141 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG C 146 " --> pdb=" O ALA C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 178 Processing helix chain 'C' and resid 192 through 204 removed outlier: 3.501A pdb=" N ALA C 202 " --> pdb=" O ALA C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 226 No H-bonds generated for 'chain 'C' and resid 223 through 226' Processing helix chain 'C' and resid 228 through 235 removed outlier: 3.668A pdb=" N LEU C 232 " --> pdb=" O GLN C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 257 removed outlier: 4.502A pdb=" N SER C 257 " --> pdb=" O LYS C 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 254 through 257' Processing helix chain 'C' and resid 264 through 266 No H-bonds generated for 'chain 'C' and resid 264 through 266' Processing helix chain 'C' and resid 271 through 278 Processing helix chain 'C' and resid 280 through 298 removed outlier: 3.560A pdb=" N GLN C 285 " --> pdb=" O GLU C 281 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN C 286 " --> pdb=" O GLY C 282 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA C 287 " --> pdb=" O ARG C 283 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU C 291 " --> pdb=" O ALA C 287 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA C 294 " --> pdb=" O LYS C 290 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE C 295 " --> pdb=" O GLU C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 309 Processing helix chain 'C' and resid 327 through 336 removed outlier: 3.901A pdb=" N ALA C 336 " --> pdb=" O GLU C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 355 Processing helix chain 'D' and resid 48 through 53 removed outlier: 3.890A pdb=" N GLN D 53 " --> pdb=" O LYS D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 68 Processing helix chain 'D' and resid 85 through 94 removed outlier: 3.846A pdb=" N TYR D 92 " --> pdb=" O ILE D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 116 removed outlier: 3.640A pdb=" N GLU D 111 " --> pdb=" O ASP D 107 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG D 114 " --> pdb=" O SER D 110 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 130 removed outlier: 3.585A pdb=" N MET D 125 " --> pdb=" O GLU D 121 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP D 129 " --> pdb=" O MET D 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 79 removed outlier: 3.522A pdb=" N ASN E 79 " --> pdb=" O LEU E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 106 removed outlier: 6.233A pdb=" N ALA E 95 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU E 96 " --> pdb=" O GLY E 93 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL E 98 " --> pdb=" O ALA E 95 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU E 99 " --> pdb=" O GLU E 96 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE E 103 " --> pdb=" O GLY E 100 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS E 104 " --> pdb=" O ASN E 101 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS E 106 " --> pdb=" O ILE E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 112 No H-bonds generated for 'chain 'E' and resid 110 through 112' Processing helix chain 'E' and resid 126 through 128 No H-bonds generated for 'chain 'E' and resid 126 through 128' Processing helix chain 'E' and resid 133 through 146 removed outlier: 3.681A pdb=" N GLU E 145 " --> pdb=" O LYS E 141 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG E 146 " --> pdb=" O ALA E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 178 Processing helix chain 'E' and resid 192 through 204 Processing helix chain 'E' and resid 223 through 226 No H-bonds generated for 'chain 'E' and resid 223 through 226' Processing helix chain 'E' and resid 228 through 235 removed outlier: 3.640A pdb=" N LEU E 232 " --> pdb=" O GLN E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 257 removed outlier: 4.503A pdb=" N SER E 257 " --> pdb=" O LYS E 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 254 through 257' Processing helix chain 'E' and resid 264 through 266 No H-bonds generated for 'chain 'E' and resid 264 through 266' Processing helix chain 'E' and resid 271 through 278 Processing helix chain 'E' and resid 280 through 298 removed outlier: 3.561A pdb=" N GLN E 285 " --> pdb=" O GLU E 281 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN E 286 " --> pdb=" O GLY E 282 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA E 287 " --> pdb=" O ARG E 283 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU E 291 " --> pdb=" O ALA E 287 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA E 294 " --> pdb=" O LYS E 290 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ILE E 295 " --> pdb=" O GLU E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 309 Processing helix chain 'E' and resid 327 through 336 removed outlier: 3.901A pdb=" N ALA E 336 " --> pdb=" O GLU E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 355 Processing helix chain 'F' and resid 48 through 53 removed outlier: 3.888A pdb=" N GLN F 53 " --> pdb=" O LYS F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 68 Processing helix chain 'F' and resid 85 through 94 removed outlier: 3.845A pdb=" N TYR F 92 " --> pdb=" O ILE F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 116 removed outlier: 3.637A pdb=" N GLU F 111 " --> pdb=" O ASP F 107 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG F 114 " --> pdb=" O SER F 110 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE F 115 " --> pdb=" O GLU F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 130 removed outlier: 3.582A pdb=" N MET F 125 " --> pdb=" O GLU F 121 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP F 129 " --> pdb=" O MET F 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 79 removed outlier: 3.530A pdb=" N ASN G 79 " --> pdb=" O LEU G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 105 removed outlier: 6.232A pdb=" N ALA G 95 " --> pdb=" O ALA G 92 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU G 96 " --> pdb=" O GLY G 93 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL G 98 " --> pdb=" O ALA G 95 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU G 99 " --> pdb=" O GLU G 96 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE G 103 " --> pdb=" O GLY G 100 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS G 104 " --> pdb=" O ASN G 101 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS G 105 " --> pdb=" O ILE G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 112 No H-bonds generated for 'chain 'G' and resid 110 through 112' Processing helix chain 'G' and resid 126 through 128 No H-bonds generated for 'chain 'G' and resid 126 through 128' Processing helix chain 'G' and resid 133 through 146 removed outlier: 3.681A pdb=" N GLU G 145 " --> pdb=" O LYS G 141 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG G 146 " --> pdb=" O ALA G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 178 Processing helix chain 'G' and resid 192 through 204 removed outlier: 3.501A pdb=" N ALA G 202 " --> pdb=" O ALA G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 223 through 226 No H-bonds generated for 'chain 'G' and resid 223 through 226' Processing helix chain 'G' and resid 228 through 235 removed outlier: 3.666A pdb=" N LEU G 232 " --> pdb=" O GLN G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 254 through 257 removed outlier: 4.499A pdb=" N SER G 257 " --> pdb=" O LYS G 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 254 through 257' Processing helix chain 'G' and resid 264 through 266 No H-bonds generated for 'chain 'G' and resid 264 through 266' Processing helix chain 'G' and resid 271 through 278 Processing helix chain 'G' and resid 280 through 298 removed outlier: 3.521A pdb=" N GLN G 285 " --> pdb=" O GLU G 281 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN G 286 " --> pdb=" O GLY G 282 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA G 287 " --> pdb=" O ARG G 283 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU G 291 " --> pdb=" O ALA G 287 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA G 294 " --> pdb=" O LYS G 290 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE G 295 " --> pdb=" O GLU G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 303 through 309 Processing helix chain 'G' and resid 327 through 336 removed outlier: 3.901A pdb=" N ALA G 336 " --> pdb=" O GLU G 332 " (cutoff:3.500A) Processing helix chain 'G' and resid 345 through 355 Processing helix chain 'H' and resid 48 through 53 removed outlier: 3.889A pdb=" N GLN H 53 " --> pdb=" O LYS H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 68 Processing helix chain 'H' and resid 85 through 94 removed outlier: 3.844A pdb=" N TYR H 92 " --> pdb=" O ILE H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 116 removed outlier: 3.638A pdb=" N GLU H 111 " --> pdb=" O ASP H 107 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE H 115 " --> pdb=" O GLU H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 130 removed outlier: 3.583A pdb=" N MET H 125 " --> pdb=" O GLU H 121 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP H 129 " --> pdb=" O MET H 125 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 39 through 41 Processing sheet with id= B, first strand: chain 'A' and resid 52 through 54 removed outlier: 7.752A pdb=" N GLY A 53 " --> pdb=" O SER A 318 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL A 320 " --> pdb=" O GLY A 53 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ALA A 240 " --> pdb=" O SER A 318 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL A 320 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THR A 242 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N LEU A 322 " --> pdb=" O THR A 242 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.633A pdb=" N VAL A 114 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL A 154 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N TYR A 184 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N ALA A 157 " --> pdb=" O TYR A 184 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N GLY A 186 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N CYS A 212 " --> pdb=" O THR A 187 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 42 through 47 removed outlier: 3.504A pdb=" N ILE B 37 " --> pdb=" O PHE B 44 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N TYR B 76 " --> pdb=" O ASN B 38 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 39 through 41 Processing sheet with id= F, first strand: chain 'C' and resid 52 through 54 removed outlier: 7.755A pdb=" N GLY C 53 " --> pdb=" O SER C 318 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N VAL C 320 " --> pdb=" O GLY C 53 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ALA C 240 " --> pdb=" O SER C 318 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N VAL C 320 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THR C 242 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N LEU C 322 " --> pdb=" O THR C 242 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.634A pdb=" N VAL C 114 " --> pdb=" O PHE C 84 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL C 154 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TYR C 184 " --> pdb=" O VAL C 155 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N ALA C 157 " --> pdb=" O TYR C 184 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N GLY C 186 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N CYS C 212 " --> pdb=" O THR C 187 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'D' and resid 42 through 47 removed outlier: 6.118A pdb=" N TYR D 76 " --> pdb=" O ASN D 38 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 39 through 41 Processing sheet with id= J, first strand: chain 'E' and resid 52 through 54 removed outlier: 7.755A pdb=" N GLY E 53 " --> pdb=" O SER E 318 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N VAL E 320 " --> pdb=" O GLY E 53 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ALA E 240 " --> pdb=" O SER E 318 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL E 320 " --> pdb=" O ALA E 240 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR E 242 " --> pdb=" O VAL E 320 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N LEU E 322 " --> pdb=" O THR E 242 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'E' and resid 83 through 85 removed outlier: 6.634A pdb=" N VAL E 114 " --> pdb=" O PHE E 84 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL E 154 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N ILE E 119 " --> pdb=" O VAL E 154 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N PHE E 156 " --> pdb=" O ILE E 119 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N TYR E 184 " --> pdb=" O VAL E 155 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N ALA E 157 " --> pdb=" O TYR E 184 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N GLY E 186 " --> pdb=" O ALA E 157 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N CYS E 212 " --> pdb=" O THR E 187 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'F' and resid 42 through 47 removed outlier: 6.117A pdb=" N TYR F 76 " --> pdb=" O ASN F 38 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 39 through 41 Processing sheet with id= N, first strand: chain 'G' and resid 52 through 54 removed outlier: 7.755A pdb=" N GLY G 53 " --> pdb=" O SER G 318 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL G 320 " --> pdb=" O GLY G 53 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ALA G 240 " --> pdb=" O SER G 318 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL G 320 " --> pdb=" O ALA G 240 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N THR G 242 " --> pdb=" O VAL G 320 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N LEU G 322 " --> pdb=" O THR G 242 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'G' and resid 83 through 85 removed outlier: 6.641A pdb=" N VAL G 114 " --> pdb=" O PHE G 84 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL G 154 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ILE G 119 " --> pdb=" O VAL G 154 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N PHE G 156 " --> pdb=" O ILE G 119 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N TYR G 184 " --> pdb=" O VAL G 155 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N ALA G 157 " --> pdb=" O TYR G 184 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N GLY G 186 " --> pdb=" O ALA G 157 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N CYS G 212 " --> pdb=" O THR G 187 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'H' and resid 42 through 47 removed outlier: 6.120A pdb=" N TYR H 76 " --> pdb=" O ASN H 38 " (cutoff:3.500A) 378 hydrogen bonds defined for protein. 1029 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.55 Time building geometry restraints manager: 5.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2858 1.32 - 1.45: 3316 1.45 - 1.57: 7782 1.57 - 1.69: 28 1.69 - 1.81: 144 Bond restraints: 14128 Sorted by residual: bond pdb=" O2B NAP A1001 " pdb=" P2B NAP A1001 " ideal model delta sigma weight residual 1.736 1.613 0.123 2.00e-02 2.50e+03 3.80e+01 bond pdb=" O2B NAP E1001 " pdb=" P2B NAP E1001 " ideal model delta sigma weight residual 1.736 1.613 0.123 2.00e-02 2.50e+03 3.79e+01 bond pdb=" O2B NAP C1001 " pdb=" P2B NAP C1001 " ideal model delta sigma weight residual 1.736 1.614 0.122 2.00e-02 2.50e+03 3.74e+01 bond pdb=" O2B NAP G1001 " pdb=" P2B NAP G1001 " ideal model delta sigma weight residual 1.736 1.614 0.122 2.00e-02 2.50e+03 3.71e+01 bond pdb=" O3 NAP A1001 " pdb=" PN NAP A1001 " ideal model delta sigma weight residual 1.643 1.745 -0.102 2.00e-02 2.50e+03 2.59e+01 ... (remaining 14123 not shown) Histogram of bond angle deviations from ideal: 75.54 - 87.47: 8 87.47 - 99.40: 4 99.40 - 111.33: 5876 111.33 - 123.26: 12534 123.26 - 135.19: 682 Bond angle restraints: 19104 Sorted by residual: angle pdb=" O1A NAP G1001 " pdb=" PA NAP G1001 " pdb=" O3 NAP G1001 " ideal model delta sigma weight residual 111.13 75.54 35.59 3.00e+00 1.11e-01 1.41e+02 angle pdb=" O1A NAP A1001 " pdb=" PA NAP A1001 " pdb=" O3 NAP A1001 " ideal model delta sigma weight residual 111.13 75.55 35.58 3.00e+00 1.11e-01 1.41e+02 angle pdb=" O1A NAP C1001 " pdb=" PA NAP C1001 " pdb=" O3 NAP C1001 " ideal model delta sigma weight residual 111.13 75.61 35.52 3.00e+00 1.11e-01 1.40e+02 angle pdb=" O1A NAP E1001 " pdb=" PA NAP E1001 " pdb=" O3 NAP E1001 " ideal model delta sigma weight residual 111.13 75.65 35.48 3.00e+00 1.11e-01 1.40e+02 angle pdb=" N ILE A 119 " pdb=" CA ILE A 119 " pdb=" C ILE A 119 " ideal model delta sigma weight residual 112.17 122.69 -10.52 9.50e-01 1.11e+00 1.23e+02 ... (remaining 19099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.90: 8016 14.90 - 29.79: 458 29.79 - 44.69: 138 44.69 - 59.58: 36 59.58 - 74.48: 16 Dihedral angle restraints: 8664 sinusoidal: 3752 harmonic: 4912 Sorted by residual: dihedral pdb=" N PHE A 120 " pdb=" C PHE A 120 " pdb=" CA PHE A 120 " pdb=" CB PHE A 120 " ideal model delta harmonic sigma weight residual 122.80 133.54 -10.74 0 2.50e+00 1.60e-01 1.84e+01 dihedral pdb=" C PHE A 120 " pdb=" N PHE A 120 " pdb=" CA PHE A 120 " pdb=" CB PHE A 120 " ideal model delta harmonic sigma weight residual -122.60 -132.74 10.14 0 2.50e+00 1.60e-01 1.64e+01 dihedral pdb=" N VAL E 58 " pdb=" C VAL E 58 " pdb=" CA VAL E 58 " pdb=" CB VAL E 58 " ideal model delta harmonic sigma weight residual 123.40 133.07 -9.67 0 2.50e+00 1.60e-01 1.49e+01 ... (remaining 8661 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.154: 1992 0.154 - 0.307: 40 0.307 - 0.461: 15 0.461 - 0.614: 1 0.614 - 0.768: 4 Chirality restraints: 2052 Sorted by residual: chirality pdb=" C2B NAP E1001 " pdb=" C1B NAP E1001 " pdb=" C3B NAP E1001 " pdb=" O2B NAP E1001 " both_signs ideal model delta sigma weight residual False -2.75 -1.99 -0.77 2.00e-01 2.50e+01 1.47e+01 chirality pdb=" C2B NAP A1001 " pdb=" C1B NAP A1001 " pdb=" C3B NAP A1001 " pdb=" O2B NAP A1001 " both_signs ideal model delta sigma weight residual False -2.75 -1.99 -0.76 2.00e-01 2.50e+01 1.45e+01 chirality pdb=" C2B NAP C1001 " pdb=" C1B NAP C1001 " pdb=" C3B NAP C1001 " pdb=" O2B NAP C1001 " both_signs ideal model delta sigma weight residual False -2.75 -1.99 -0.76 2.00e-01 2.50e+01 1.45e+01 ... (remaining 2049 not shown) Planarity restraints: 2436 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE G 103 " -0.019 2.00e-02 2.50e+03 3.79e-02 1.43e+01 pdb=" C ILE G 103 " 0.065 2.00e-02 2.50e+03 pdb=" O ILE G 103 " -0.025 2.00e-02 2.50e+03 pdb=" N LYS G 104 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 136 " -0.014 2.00e-02 2.50e+03 2.80e-02 7.85e+00 pdb=" C ILE C 136 " 0.048 2.00e-02 2.50e+03 pdb=" O ILE C 136 " -0.018 2.00e-02 2.50e+03 pdb=" N ILE C 137 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU E 340 " 0.045 5.00e-02 4.00e+02 6.81e-02 7.41e+00 pdb=" N PRO E 341 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO E 341 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 341 " 0.039 5.00e-02 4.00e+02 ... (remaining 2433 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 184 2.61 - 3.18: 11593 3.18 - 3.75: 21674 3.75 - 4.33: 33438 4.33 - 4.90: 53074 Nonbonded interactions: 119963 Sorted by model distance: nonbonded pdb=" OH TYR E 199 " pdb=" O PRO F 71 " model vdw 2.034 2.440 nonbonded pdb=" ND2 ASN D 81 " pdb=" OG SER D 84 " model vdw 2.126 2.520 nonbonded pdb=" OH TYR G 199 " pdb=" O PRO H 71 " model vdw 2.195 2.440 nonbonded pdb=" OH TYR C 199 " pdb=" O PRO D 71 " model vdw 2.196 2.440 nonbonded pdb=" OG SER C 191 " pdb=" O HOH C1101 " model vdw 2.198 2.440 ... (remaining 119958 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 2.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 12.610 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 37.950 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 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 0.123 14128 Z= 0.729 Angle : 1.409 35.593 19104 Z= 0.678 Chirality : 0.077 0.768 2052 Planarity : 0.007 0.068 2436 Dihedral : 11.599 74.476 5520 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.21 % Allowed : 1.65 % Favored : 98.15 % 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: -4.53 (0.15), residues: 1692 helix: -4.14 (0.09), residues: 808 sheet: -0.54 (0.38), residues: 176 loop : -1.99 (0.18), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.004 TRP G 185 HIS 0.008 0.003 HIS C 71 PHE 0.031 0.004 PHE E 84 TYR 0.045 0.004 TYR D 116 ARG 0.022 0.002 ARG F 80 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 394 time to evaluate : 1.676 Fit side-chains revert: symmetry clash REVERT: A 75 LEU cc_start: 0.8575 (tp) cc_final: 0.8148 (mt) REVERT: A 148 GLN cc_start: 0.8616 (mt0) cc_final: 0.8207 (mt0) REVERT: A 301 CYS cc_start: 0.7705 (p) cc_final: 0.7392 (p) REVERT: B 97 ARG cc_start: 0.7999 (mtm180) cc_final: 0.7116 (ttt90) REVERT: C 75 LEU cc_start: 0.8587 (tp) cc_final: 0.8164 (mt) REVERT: C 148 GLN cc_start: 0.8588 (mt0) cc_final: 0.8127 (mt0) REVERT: C 301 CYS cc_start: 0.7685 (p) cc_final: 0.7390 (p) REVERT: D 97 ARG cc_start: 0.7972 (mtm180) cc_final: 0.7080 (ttt90) REVERT: E 75 LEU cc_start: 0.8594 (tp) cc_final: 0.8173 (mt) REVERT: E 148 GLN cc_start: 0.8622 (mt0) cc_final: 0.8160 (mt0) REVERT: E 301 CYS cc_start: 0.7666 (p) cc_final: 0.7363 (p) REVERT: F 97 ARG cc_start: 0.7992 (mtm180) cc_final: 0.7096 (ttt90) REVERT: G 75 LEU cc_start: 0.8590 (tp) cc_final: 0.8173 (mt) REVERT: G 148 GLN cc_start: 0.8635 (mt0) cc_final: 0.8161 (mt0) REVERT: H 97 ARG cc_start: 0.7978 (mtm180) cc_final: 0.7098 (ttt90) outliers start: 3 outliers final: 1 residues processed: 397 average time/residue: 1.8061 time to fit residues: 764.1743 Evaluate side-chains 280 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 279 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 85 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 131 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 98 optimal weight: 0.6980 chunk 152 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN A 135 HIS A 175 HIS A 333 ASN C 135 HIS C 175 HIS C 333 ASN D 81 ASN E 135 HIS E 175 HIS G 135 HIS G 175 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14128 Z= 0.214 Angle : 0.620 7.396 19104 Z= 0.305 Chirality : 0.044 0.253 2052 Planarity : 0.005 0.034 2436 Dihedral : 10.482 63.317 2153 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.40 % Allowed : 10.16 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.17), residues: 1692 helix: -2.24 (0.14), residues: 780 sheet: -0.47 (0.38), residues: 176 loop : -1.37 (0.20), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 185 HIS 0.005 0.001 HIS C 135 PHE 0.017 0.002 PHE B 115 TYR 0.017 0.001 TYR D 116 ARG 0.006 0.000 ARG F 43 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 294 time to evaluate : 1.712 Fit side-chains REVERT: A 148 GLN cc_start: 0.8587 (mt0) cc_final: 0.8082 (mt0) REVERT: B 33 GLU cc_start: 0.6957 (tt0) cc_final: 0.6517 (tt0) REVERT: B 97 ARG cc_start: 0.7832 (mtm180) cc_final: 0.6932 (tpt170) REVERT: C 148 GLN cc_start: 0.8578 (mt0) cc_final: 0.8114 (mt0) REVERT: C 314 ASN cc_start: 0.7982 (m-40) cc_final: 0.7508 (p0) REVERT: D 43 ARG cc_start: 0.7680 (mtp-110) cc_final: 0.7402 (mtt90) REVERT: D 47 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.7574 (mt0) REVERT: D 97 ARG cc_start: 0.7833 (mtm180) cc_final: 0.6911 (ttt90) REVERT: E 148 GLN cc_start: 0.8579 (mt0) cc_final: 0.8124 (mt0) REVERT: E 314 ASN cc_start: 0.7999 (m-40) cc_final: 0.7519 (p0) REVERT: F 43 ARG cc_start: 0.7697 (mtp-110) cc_final: 0.7460 (mtt90) REVERT: F 47 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7554 (mt0) REVERT: F 97 ARG cc_start: 0.7836 (mtm180) cc_final: 0.6922 (tpt170) REVERT: G 148 GLN cc_start: 0.8571 (mt0) cc_final: 0.8072 (mt0) REVERT: H 43 ARG cc_start: 0.7705 (mtp-110) cc_final: 0.7390 (mtt90) REVERT: H 47 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7550 (mt0) REVERT: H 97 ARG cc_start: 0.7822 (mtm180) cc_final: 0.6918 (ttt90) outliers start: 35 outliers final: 13 residues processed: 304 average time/residue: 1.6062 time to fit residues: 523.7223 Evaluate side-chains 280 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 264 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain F residue 47 GLN Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain G residue 200 SER Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 98 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 4.9990 chunk 47 optimal weight: 0.0000 chunk 126 optimal weight: 3.9990 chunk 103 optimal weight: 0.1980 chunk 42 optimal weight: 4.9990 chunk 152 optimal weight: 0.9980 chunk 165 optimal weight: 0.6980 chunk 136 optimal weight: 4.9990 chunk 151 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 122 optimal weight: 2.9990 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN E 333 ASN F 93 GLN G 333 ASN H 93 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 14128 Z= 0.159 Angle : 0.525 6.478 19104 Z= 0.255 Chirality : 0.041 0.226 2052 Planarity : 0.003 0.029 2436 Dihedral : 8.658 58.676 2152 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.20 % Allowed : 13.74 % Favored : 84.07 % 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: -1.56 (0.18), residues: 1692 helix: -1.05 (0.16), residues: 788 sheet: -0.62 (0.49), residues: 116 loop : -0.92 (0.20), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 185 HIS 0.004 0.001 HIS C 135 PHE 0.013 0.001 PHE H 115 TYR 0.012 0.001 TYR H 116 ARG 0.006 0.000 ARG A 284 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 273 time to evaluate : 1.458 Fit side-chains REVERT: A 148 GLN cc_start: 0.8570 (mt0) cc_final: 0.8106 (mt0) REVERT: A 314 ASN cc_start: 0.7985 (m-40) cc_final: 0.7461 (p0) REVERT: A 350 GLU cc_start: 0.7611 (tp30) cc_final: 0.7357 (tp30) REVERT: B 47 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7578 (mt0) REVERT: B 99 ARG cc_start: 0.8169 (ptm160) cc_final: 0.7885 (ptp-110) REVERT: B 111 GLU cc_start: 0.6811 (tp30) cc_final: 0.6345 (tp30) REVERT: B 112 GLU cc_start: 0.7767 (tp30) cc_final: 0.7497 (mm-30) REVERT: B 116 TYR cc_start: 0.8651 (m-80) cc_final: 0.8401 (m-80) REVERT: C 75 LEU cc_start: 0.8590 (tp) cc_final: 0.8326 (tm) REVERT: C 148 GLN cc_start: 0.8550 (mt0) cc_final: 0.8050 (mt0) REVERT: C 314 ASN cc_start: 0.7997 (m-40) cc_final: 0.7496 (p0) REVERT: C 315 GLU cc_start: 0.6955 (pt0) cc_final: 0.6716 (pt0) REVERT: C 350 GLU cc_start: 0.7571 (tp30) cc_final: 0.7260 (tp30) REVERT: D 97 ARG cc_start: 0.7815 (mtm180) cc_final: 0.6859 (ttt90) REVERT: D 116 TYR cc_start: 0.8635 (m-80) cc_final: 0.8405 (m-80) REVERT: E 75 LEU cc_start: 0.8544 (tp) cc_final: 0.8274 (tm) REVERT: E 148 GLN cc_start: 0.8583 (mt0) cc_final: 0.8086 (mt0) REVERT: E 314 ASN cc_start: 0.8017 (m-40) cc_final: 0.7518 (p0) REVERT: E 315 GLU cc_start: 0.6961 (pt0) cc_final: 0.6722 (pt0) REVERT: F 70 ASP cc_start: 0.8180 (t0) cc_final: 0.7966 (t0) REVERT: F 99 ARG cc_start: 0.8162 (ptm160) cc_final: 0.7896 (ptp-110) REVERT: G 75 LEU cc_start: 0.8536 (tp) cc_final: 0.8260 (tm) REVERT: G 148 GLN cc_start: 0.8576 (mt0) cc_final: 0.8035 (mt0) REVERT: G 314 ASN cc_start: 0.7967 (m-40) cc_final: 0.7443 (p0) REVERT: G 350 GLU cc_start: 0.7601 (tp30) cc_final: 0.7339 (tp30) REVERT: H 97 ARG cc_start: 0.7818 (mtm180) cc_final: 0.6884 (ttt90) REVERT: H 116 TYR cc_start: 0.8651 (m-80) cc_final: 0.8416 (m-80) outliers start: 32 outliers final: 12 residues processed: 284 average time/residue: 1.6948 time to fit residues: 514.6824 Evaluate side-chains 268 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 255 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 200 SER Chi-restraints excluded: chain G residue 325 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 0.8980 chunk 114 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 153 optimal weight: 0.5980 chunk 162 optimal weight: 0.3980 chunk 80 optimal weight: 2.9990 chunk 145 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN D 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14128 Z= 0.229 Angle : 0.550 6.516 19104 Z= 0.268 Chirality : 0.042 0.230 2052 Planarity : 0.003 0.032 2436 Dihedral : 7.494 56.721 2152 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.09 % Allowed : 13.32 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.19), residues: 1692 helix: -0.33 (0.17), residues: 788 sheet: -0.50 (0.48), residues: 116 loop : -0.58 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 185 HIS 0.007 0.001 HIS A 135 PHE 0.012 0.002 PHE F 115 TYR 0.018 0.001 TYR H 116 ARG 0.008 0.001 ARG F 43 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 251 time to evaluate : 1.607 Fit side-chains REVERT: A 148 GLN cc_start: 0.8550 (mt0) cc_final: 0.8045 (mt0) REVERT: A 314 ASN cc_start: 0.7998 (m-40) cc_final: 0.7484 (OUTLIER) REVERT: A 350 GLU cc_start: 0.7605 (tp30) cc_final: 0.7402 (tp30) REVERT: B 47 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7678 (mt0) REVERT: B 99 ARG cc_start: 0.8227 (ptm160) cc_final: 0.7901 (ptp-170) REVERT: B 111 GLU cc_start: 0.6793 (tp30) cc_final: 0.6422 (tp30) REVERT: C 148 GLN cc_start: 0.8547 (mt0) cc_final: 0.8028 (mt0) REVERT: C 314 ASN cc_start: 0.7991 (m-40) cc_final: 0.7486 (OUTLIER) REVERT: C 315 GLU cc_start: 0.6985 (pt0) cc_final: 0.6746 (pt0) REVERT: C 350 GLU cc_start: 0.7556 (tp30) cc_final: 0.7342 (tp30) REVERT: D 47 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.8064 (mp10) REVERT: D 97 ARG cc_start: 0.7831 (mtm180) cc_final: 0.6878 (ttt90) REVERT: E 148 GLN cc_start: 0.8560 (mt0) cc_final: 0.8045 (mt0) REVERT: E 314 ASN cc_start: 0.7978 (m-40) cc_final: 0.7485 (OUTLIER) REVERT: E 315 GLU cc_start: 0.6937 (pt0) cc_final: 0.6696 (pt0) REVERT: E 350 GLU cc_start: 0.7636 (tp30) cc_final: 0.7297 (tp30) REVERT: F 70 ASP cc_start: 0.8215 (t0) cc_final: 0.7998 (t0) REVERT: F 99 ARG cc_start: 0.8178 (ptm160) cc_final: 0.7866 (ptp-170) REVERT: G 148 GLN cc_start: 0.8556 (mt0) cc_final: 0.8033 (mt0) REVERT: G 314 ASN cc_start: 0.7975 (m-40) cc_final: 0.7460 (OUTLIER) REVERT: G 350 GLU cc_start: 0.7570 (tp30) cc_final: 0.7364 (tp30) REVERT: H 97 ARG cc_start: 0.7866 (mtm180) cc_final: 0.6888 (tpt170) outliers start: 45 outliers final: 15 residues processed: 272 average time/residue: 1.7545 time to fit residues: 509.4336 Evaluate side-chains 253 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 240 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 98 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 138 optimal weight: 0.6980 chunk 112 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 145 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN B 81 ASN B 93 GLN E 204 GLN F 93 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 14128 Z= 0.248 Angle : 0.551 6.454 19104 Z= 0.268 Chirality : 0.042 0.228 2052 Planarity : 0.004 0.064 2436 Dihedral : 7.410 55.629 2152 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.82 % Allowed : 14.84 % Favored : 82.35 % 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: -0.31 (0.20), residues: 1692 helix: 0.15 (0.18), residues: 776 sheet: -0.75 (0.44), residues: 136 loop : -0.31 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 185 HIS 0.007 0.001 HIS C 135 PHE 0.011 0.002 PHE C 84 TYR 0.016 0.001 TYR H 116 ARG 0.007 0.001 ARG D 73 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 255 time to evaluate : 1.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 GLN cc_start: 0.8517 (mt0) cc_final: 0.7993 (mt0) REVERT: A 314 ASN cc_start: 0.8036 (m-40) cc_final: 0.7481 (OUTLIER) REVERT: A 350 GLU cc_start: 0.7615 (tp30) cc_final: 0.7398 (tp30) REVERT: B 70 ASP cc_start: 0.8228 (t0) cc_final: 0.7961 (t0) REVERT: B 111 GLU cc_start: 0.6796 (tp30) cc_final: 0.6448 (tp30) REVERT: C 148 GLN cc_start: 0.8533 (mt0) cc_final: 0.7998 (mt0) REVERT: C 314 ASN cc_start: 0.8045 (m-40) cc_final: 0.7503 (OUTLIER) REVERT: C 315 GLU cc_start: 0.6956 (pt0) cc_final: 0.6701 (pt0) REVERT: C 350 GLU cc_start: 0.7538 (tp30) cc_final: 0.7316 (tp30) REVERT: E 148 GLN cc_start: 0.8556 (mt0) cc_final: 0.8023 (mt0) REVERT: E 314 ASN cc_start: 0.8041 (m-40) cc_final: 0.7496 (OUTLIER) REVERT: E 315 GLU cc_start: 0.6964 (pt0) cc_final: 0.6707 (pt0) REVERT: E 350 GLU cc_start: 0.7586 (tp30) cc_final: 0.7298 (tp30) REVERT: F 99 ARG cc_start: 0.8215 (ptm160) cc_final: 0.7921 (ptp-170) REVERT: G 148 GLN cc_start: 0.8569 (mt0) cc_final: 0.8031 (mt0) REVERT: G 314 ASN cc_start: 0.8011 (m-40) cc_final: 0.7470 (OUTLIER) REVERT: G 350 GLU cc_start: 0.7570 (tp30) cc_final: 0.7349 (tp30) REVERT: H 70 ASP cc_start: 0.8277 (t0) cc_final: 0.8073 (t0) outliers start: 41 outliers final: 24 residues processed: 274 average time/residue: 1.6333 time to fit residues: 480.0257 Evaluate side-chains 269 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 249 time to evaluate : 1.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 114 ARG Chi-restraints excluded: chain E residue 68 MET Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 114 ARG Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 200 SER Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 114 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 162 optimal weight: 0.6980 chunk 134 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN B 93 GLN D 81 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 14128 Z= 0.287 Angle : 0.576 7.269 19104 Z= 0.281 Chirality : 0.043 0.232 2052 Planarity : 0.003 0.032 2436 Dihedral : 7.575 49.602 2152 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.02 % Allowed : 15.04 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.20), residues: 1692 helix: 0.31 (0.18), residues: 776 sheet: -0.70 (0.44), residues: 136 loop : -0.24 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 185 HIS 0.007 0.001 HIS A 135 PHE 0.013 0.002 PHE C 84 TYR 0.018 0.001 TYR D 116 ARG 0.007 0.001 ARG F 43 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 252 time to evaluate : 1.623 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 148 GLN cc_start: 0.8542 (mt0) cc_final: 0.7995 (mt0) REVERT: A 314 ASN cc_start: 0.8067 (m-40) cc_final: 0.7484 (OUTLIER) REVERT: A 350 GLU cc_start: 0.7564 (tp30) cc_final: 0.7341 (tp30) REVERT: B 47 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.7776 (mt0) REVERT: B 97 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7366 (ptp-170) REVERT: B 111 GLU cc_start: 0.6753 (tp30) cc_final: 0.6438 (tp30) REVERT: B 114 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.7593 (mtm180) REVERT: C 148 GLN cc_start: 0.8552 (mt0) cc_final: 0.8013 (mt0) REVERT: C 314 ASN cc_start: 0.8049 (m-40) cc_final: 0.7502 (OUTLIER) REVERT: C 315 GLU cc_start: 0.6898 (pt0) cc_final: 0.6642 (pt0) REVERT: C 350 GLU cc_start: 0.7513 (tp30) cc_final: 0.7297 (tp30) REVERT: D 33 GLU cc_start: 0.7079 (pm20) cc_final: 0.6734 (pt0) REVERT: D 47 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.7623 (mt0) REVERT: D 73 ARG cc_start: 0.8007 (mtp-110) cc_final: 0.7522 (mtm-85) REVERT: D 99 ARG cc_start: 0.8181 (ptm160) cc_final: 0.7913 (ptp-170) REVERT: E 148 GLN cc_start: 0.8582 (mt0) cc_final: 0.8041 (mt0) REVERT: E 314 ASN cc_start: 0.8139 (m-40) cc_final: 0.7489 (OUTLIER) REVERT: E 315 GLU cc_start: 0.6940 (pt0) cc_final: 0.6682 (pt0) REVERT: E 350 GLU cc_start: 0.7575 (tp30) cc_final: 0.7318 (tp30) REVERT: F 70 ASP cc_start: 0.8265 (t0) cc_final: 0.7902 (t0) REVERT: F 97 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7243 (ptp-170) REVERT: F 99 ARG cc_start: 0.8242 (ptm160) cc_final: 0.7942 (ptp-170) REVERT: G 75 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8237 (tp) REVERT: G 148 GLN cc_start: 0.8562 (mt0) cc_final: 0.8015 (mt0) REVERT: G 314 ASN cc_start: 0.8058 (m-40) cc_final: 0.7484 (OUTLIER) REVERT: G 350 GLU cc_start: 0.7550 (tp30) cc_final: 0.7327 (tp30) REVERT: H 70 ASP cc_start: 0.8321 (t0) cc_final: 0.8056 (t0) REVERT: H 73 ARG cc_start: 0.8071 (mtp-110) cc_final: 0.7539 (mtm-85) REVERT: H 99 ARG cc_start: 0.8173 (ptm160) cc_final: 0.7903 (ptp-170) outliers start: 44 outliers final: 27 residues processed: 272 average time/residue: 1.6915 time to fit residues: 492.4164 Evaluate side-chains 272 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 243 time to evaluate : 1.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 114 ARG Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 114 ARG Chi-restraints excluded: chain E residue 68 MET Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 97 ARG Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 315 GLU Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 114 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 136 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN B 93 GLN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 GLN H 93 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14128 Z= 0.214 Angle : 0.549 9.135 19104 Z= 0.264 Chirality : 0.041 0.209 2052 Planarity : 0.003 0.031 2436 Dihedral : 7.341 50.931 2152 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.20 % Allowed : 16.62 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.20), residues: 1692 helix: 0.54 (0.19), residues: 776 sheet: -0.65 (0.45), residues: 136 loop : -0.14 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 185 HIS 0.006 0.001 HIS A 135 PHE 0.011 0.001 PHE A 84 TYR 0.013 0.001 TYR H 116 ARG 0.009 0.000 ARG F 43 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 251 time to evaluate : 1.683 Fit side-chains revert: symmetry clash REVERT: A 148 GLN cc_start: 0.8505 (mt0) cc_final: 0.7948 (mt0) REVERT: A 314 ASN cc_start: 0.8061 (m-40) cc_final: 0.7483 (OUTLIER) REVERT: B 47 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.7752 (mt0) REVERT: B 97 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.7231 (ptp-170) REVERT: B 111 GLU cc_start: 0.6651 (tp30) cc_final: 0.6254 (tp30) REVERT: C 148 GLN cc_start: 0.8521 (mt0) cc_final: 0.7962 (mt0) REVERT: C 314 ASN cc_start: 0.8132 (m-40) cc_final: 0.7478 (OUTLIER) REVERT: C 315 GLU cc_start: 0.6885 (pt0) cc_final: 0.6639 (pt0) REVERT: D 33 GLU cc_start: 0.7011 (pm20) cc_final: 0.6781 (pt0) REVERT: D 47 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.7596 (mt0) REVERT: D 73 ARG cc_start: 0.7983 (mtp-110) cc_final: 0.7504 (mtm-85) REVERT: D 99 ARG cc_start: 0.8155 (ptm160) cc_final: 0.7907 (ptp-170) REVERT: E 148 GLN cc_start: 0.8554 (mt0) cc_final: 0.8016 (mt0) REVERT: E 314 ASN cc_start: 0.8135 (m-40) cc_final: 0.7476 (OUTLIER) REVERT: E 315 GLU cc_start: 0.6891 (pt0) cc_final: 0.6643 (pt0) REVERT: E 350 GLU cc_start: 0.7522 (tp30) cc_final: 0.7312 (tp30) REVERT: F 47 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.7631 (mt0) REVERT: F 70 ASP cc_start: 0.8379 (t0) cc_final: 0.8098 (t0) REVERT: F 97 ARG cc_start: 0.7762 (OUTLIER) cc_final: 0.7133 (ptp-170) REVERT: F 99 ARG cc_start: 0.8228 (ptm160) cc_final: 0.7924 (ptp-170) REVERT: G 148 GLN cc_start: 0.8536 (mt0) cc_final: 0.7971 (mt0) REVERT: G 314 ASN cc_start: 0.8048 (m-40) cc_final: 0.7475 (OUTLIER) REVERT: H 70 ASP cc_start: 0.8310 (t0) cc_final: 0.8095 (t0) REVERT: H 99 ARG cc_start: 0.8150 (ptm160) cc_final: 0.7897 (ptp-170) outliers start: 32 outliers final: 20 residues processed: 268 average time/residue: 1.6121 time to fit residues: 464.0494 Evaluate side-chains 259 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 238 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 114 ARG Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 49 LYS Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 47 GLN Chi-restraints excluded: chain F residue 97 ARG Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 98 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 0.5980 chunk 64 optimal weight: 7.9990 chunk 96 optimal weight: 0.0470 chunk 48 optimal weight: 2.9990 chunk 31 optimal weight: 0.0770 chunk 102 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 147 optimal weight: 0.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN B 93 GLN C 79 ASN D 93 GLN E 79 ASN G 79 ASN H 93 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14128 Z= 0.158 Angle : 0.544 9.861 19104 Z= 0.262 Chirality : 0.040 0.186 2052 Planarity : 0.003 0.044 2436 Dihedral : 7.036 54.123 2152 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.06 % Allowed : 17.24 % Favored : 80.70 % 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: 0.33 (0.21), residues: 1692 helix: 0.78 (0.19), residues: 780 sheet: -0.60 (0.45), residues: 136 loop : -0.05 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 185 HIS 0.005 0.001 HIS A 135 PHE 0.018 0.001 PHE D 54 TYR 0.008 0.001 TYR B 116 ARG 0.008 0.000 ARG F 43 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 242 time to evaluate : 1.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 GLN cc_start: 0.8469 (mt0) cc_final: 0.7898 (mt0) REVERT: A 314 ASN cc_start: 0.8053 (m-40) cc_final: 0.7457 (OUTLIER) REVERT: B 97 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.7100 (ptp-170) REVERT: C 148 GLN cc_start: 0.8491 (mt0) cc_final: 0.7932 (mt0) REVERT: C 314 ASN cc_start: 0.8115 (m-40) cc_final: 0.7465 (OUTLIER) REVERT: C 315 GLU cc_start: 0.6855 (pt0) cc_final: 0.6612 (pt0) REVERT: D 33 GLU cc_start: 0.7062 (pm20) cc_final: 0.6797 (pt0) REVERT: D 73 ARG cc_start: 0.7903 (mtp-110) cc_final: 0.7427 (mtm-85) REVERT: D 99 ARG cc_start: 0.8161 (ptm160) cc_final: 0.7929 (ptp-170) REVERT: E 148 GLN cc_start: 0.8505 (mt0) cc_final: 0.7949 (mt0) REVERT: E 314 ASN cc_start: 0.8126 (m-40) cc_final: 0.7473 (OUTLIER) REVERT: E 315 GLU cc_start: 0.6901 (pt0) cc_final: 0.6650 (pt0) REVERT: F 47 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.7575 (mt0) REVERT: F 70 ASP cc_start: 0.8384 (t0) cc_final: 0.8097 (t0) REVERT: F 97 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.7058 (ptp-170) REVERT: F 99 ARG cc_start: 0.8204 (ptm160) cc_final: 0.7919 (ptp-170) REVERT: F 130 GLU cc_start: 0.6145 (tm-30) cc_final: 0.5911 (tm-30) REVERT: G 148 GLN cc_start: 0.8492 (mt0) cc_final: 0.7922 (mt0) REVERT: G 314 ASN cc_start: 0.8043 (m-40) cc_final: 0.7452 (OUTLIER) REVERT: H 33 GLU cc_start: 0.6988 (pm20) cc_final: 0.6757 (pt0) REVERT: H 47 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.7587 (mt0) REVERT: H 70 ASP cc_start: 0.8356 (t0) cc_final: 0.8151 (t0) REVERT: H 99 ARG cc_start: 0.8147 (ptm160) cc_final: 0.7919 (ptp-170) outliers start: 30 outliers final: 20 residues processed: 257 average time/residue: 1.7029 time to fit residues: 469.0865 Evaluate side-chains 251 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 231 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 114 ARG Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 114 ARG Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain F residue 47 GLN Chi-restraints excluded: chain F residue 49 LYS Chi-restraints excluded: chain F residue 97 ARG Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 114 ARG Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 114 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 3.9990 chunk 141 optimal weight: 0.9980 chunk 150 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 118 optimal weight: 0.0040 chunk 46 optimal weight: 3.9990 chunk 136 optimal weight: 0.8980 chunk 142 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 GLN ** F 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14128 Z= 0.260 Angle : 0.598 10.951 19104 Z= 0.287 Chirality : 0.042 0.212 2052 Planarity : 0.004 0.036 2436 Dihedral : 7.271 50.090 2152 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.13 % Allowed : 17.99 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.20), residues: 1692 helix: 0.86 (0.19), residues: 764 sheet: -0.64 (0.45), residues: 136 loop : -0.11 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 185 HIS 0.007 0.001 HIS A 135 PHE 0.020 0.002 PHE B 54 TYR 0.015 0.001 TYR B 116 ARG 0.007 0.001 ARG D 43 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 245 time to evaluate : 3.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 GLN cc_start: 0.8497 (mt0) cc_final: 0.7926 (mt0) REVERT: A 314 ASN cc_start: 0.8057 (m-40) cc_final: 0.7461 (OUTLIER) REVERT: B 97 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.7050 (ptp-170) REVERT: B 114 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7556 (mtm180) REVERT: C 148 GLN cc_start: 0.8516 (mt0) cc_final: 0.7954 (mt0) REVERT: C 314 ASN cc_start: 0.8135 (m-40) cc_final: 0.7478 (OUTLIER) REVERT: C 315 GLU cc_start: 0.6878 (pt0) cc_final: 0.6627 (pt0) REVERT: D 33 GLU cc_start: 0.7089 (pm20) cc_final: 0.6841 (pt0) REVERT: D 73 ARG cc_start: 0.7948 (mtp-110) cc_final: 0.7442 (mtm-85) REVERT: D 99 ARG cc_start: 0.8213 (ptm160) cc_final: 0.7968 (ptp-170) REVERT: D 112 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7057 (mp0) REVERT: E 148 GLN cc_start: 0.8519 (mt0) cc_final: 0.7953 (mt0) REVERT: E 314 ASN cc_start: 0.8137 (m-40) cc_final: 0.7479 (OUTLIER) REVERT: E 315 GLU cc_start: 0.6882 (pt0) cc_final: 0.6631 (pt0) REVERT: F 97 ARG cc_start: 0.7619 (OUTLIER) cc_final: 0.7037 (ptp-170) REVERT: F 99 ARG cc_start: 0.8210 (ptm160) cc_final: 0.7941 (ptp-170) REVERT: G 148 GLN cc_start: 0.8509 (mt0) cc_final: 0.7935 (mt0) REVERT: G 314 ASN cc_start: 0.8142 (m-40) cc_final: 0.7445 (OUTLIER) REVERT: H 70 ASP cc_start: 0.8363 (t0) cc_final: 0.8010 (t0) REVERT: H 73 ARG cc_start: 0.7965 (mtp-110) cc_final: 0.7407 (mtm-85) REVERT: H 99 ARG cc_start: 0.8216 (ptm160) cc_final: 0.7968 (ptp-170) outliers start: 31 outliers final: 18 residues processed: 262 average time/residue: 1.6775 time to fit residues: 471.4917 Evaluate side-chains 250 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 232 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 114 ARG Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 112 GLU Chi-restraints excluded: chain D residue 114 ARG Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain F residue 49 LYS Chi-restraints excluded: chain F residue 97 ARG Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 114 ARG Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 49 LYS Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 114 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 167 optimal weight: 0.2980 chunk 154 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 81 optimal weight: 0.0970 chunk 105 optimal weight: 0.3980 chunk 141 optimal weight: 2.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14128 Z= 0.166 Angle : 0.564 11.255 19104 Z= 0.270 Chirality : 0.040 0.173 2052 Planarity : 0.003 0.036 2436 Dihedral : 6.919 54.699 2152 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.37 % Allowed : 18.54 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.20), residues: 1692 helix: 1.03 (0.19), residues: 768 sheet: -0.54 (0.45), residues: 136 loop : -0.04 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 185 HIS 0.005 0.001 HIS A 135 PHE 0.018 0.001 PHE F 54 TYR 0.009 0.001 TYR F 92 ARG 0.009 0.000 ARG F 43 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 245 time to evaluate : 1.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 GLN cc_start: 0.8437 (mt0) cc_final: 0.7867 (mt0) REVERT: A 314 ASN cc_start: 0.8139 (m-40) cc_final: 0.7439 (OUTLIER) REVERT: B 97 ARG cc_start: 0.7538 (OUTLIER) cc_final: 0.6980 (ptp-170) REVERT: C 148 GLN cc_start: 0.8478 (mt0) cc_final: 0.7910 (mt0) REVERT: C 314 ASN cc_start: 0.8117 (m-40) cc_final: 0.7454 (OUTLIER) REVERT: C 315 GLU cc_start: 0.6847 (pt0) cc_final: 0.6597 (pt0) REVERT: D 33 GLU cc_start: 0.7107 (pm20) cc_final: 0.6863 (pt0) REVERT: D 73 ARG cc_start: 0.7855 (mtp-110) cc_final: 0.7305 (mtm-85) REVERT: D 99 ARG cc_start: 0.8196 (ptm160) cc_final: 0.7966 (ptp-170) REVERT: E 148 GLN cc_start: 0.8484 (mt0) cc_final: 0.7918 (mt0) REVERT: E 314 ASN cc_start: 0.8131 (m-40) cc_final: 0.7466 (OUTLIER) REVERT: E 315 GLU cc_start: 0.6850 (pt0) cc_final: 0.6604 (pt0) REVERT: F 97 ARG cc_start: 0.7531 (OUTLIER) cc_final: 0.6957 (ptp-170) REVERT: F 99 ARG cc_start: 0.8190 (ptm160) cc_final: 0.7916 (ptp-170) REVERT: F 130 GLU cc_start: 0.6013 (tm-30) cc_final: 0.5801 (tm-30) REVERT: G 148 GLN cc_start: 0.8457 (mt0) cc_final: 0.7885 (mt0) REVERT: G 314 ASN cc_start: 0.8138 (m-40) cc_final: 0.7438 (OUTLIER) REVERT: H 33 GLU cc_start: 0.7114 (pm20) cc_final: 0.6858 (pt0) REVERT: H 70 ASP cc_start: 0.8399 (t0) cc_final: 0.8091 (t0) REVERT: H 73 ARG cc_start: 0.7937 (mtp-110) cc_final: 0.7341 (mtm-85) REVERT: H 99 ARG cc_start: 0.8193 (ptm160) cc_final: 0.7978 (ptp-170) outliers start: 20 outliers final: 19 residues processed: 257 average time/residue: 1.6806 time to fit residues: 462.6110 Evaluate side-chains 247 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 230 time to evaluate : 1.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 114 ARG Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 97 ARG Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 114 ARG Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 98 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 0.3980 chunk 133 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 137 optimal weight: 0.5980 chunk 16 optimal weight: 0.1980 chunk 24 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN C 271 GLN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 GLN E 271 GLN G 271 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.138447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.114102 restraints weight = 16414.420| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.66 r_work: 0.3151 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14128 Z= 0.174 Angle : 0.549 11.508 19104 Z= 0.263 Chirality : 0.040 0.175 2052 Planarity : 0.003 0.038 2436 Dihedral : 6.852 54.633 2152 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.58 % Allowed : 18.27 % Favored : 80.15 % 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: 0.62 (0.20), residues: 1692 helix: 1.17 (0.19), residues: 764 sheet: -0.55 (0.45), residues: 136 loop : -0.05 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 185 HIS 0.006 0.001 HIS A 135 PHE 0.017 0.001 PHE D 54 TYR 0.010 0.001 TYR F 92 ARG 0.008 0.000 ARG F 43 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7355.49 seconds wall clock time: 130 minutes 52.48 seconds (7852.48 seconds total)