Starting phenix.real_space_refine (version: dev) on Sun Feb 26 22:40:12 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pif_20349/02_2023/6pif_20349.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pif_20349/02_2023/6pif_20349.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pif_20349/02_2023/6pif_20349.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pif_20349/02_2023/6pif_20349.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pif_20349/02_2023/6pif_20349.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pif_20349/02_2023/6pif_20349.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.005 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 Process input model Symmetric amino acids flipped Residue "A ARG 37": "NH1" <-> "NH2" Residue "A ARG 178": "NH1" <-> "NH2" Residue "A ARG 210": "NH1" <-> "NH2" Residue "A GLU 280": "OE1" <-> "OE2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "B ARG 37": "NH1" <-> "NH2" Residue "B GLU 164": "OE1" <-> "OE2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B ARG 178": "NH1" <-> "NH2" Residue "B GLU 192": "OE1" <-> "OE2" Residue "B PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 210": "NH1" <-> "NH2" Residue "B GLU 329": "OE1" <-> "OE2" Residue "C TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 37": "NH1" <-> "NH2" Residue "C GLU 63": "OE1" <-> "OE2" Residue "C GLU 86": "OE1" <-> "OE2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "C GLU 127": "OE1" <-> "OE2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C ARG 178": "NH1" <-> "NH2" Residue "C ARG 210": "NH1" <-> "NH2" Residue "C GLU 254": "OE1" <-> "OE2" Residue "D ARG 37": "NH1" <-> "NH2" Residue "D GLU 44": "OE1" <-> "OE2" Residue "D GLU 63": "OE1" <-> "OE2" Residue "D GLU 164": "OE1" <-> "OE2" Residue "D ARG 178": "NH1" <-> "NH2" Residue "D ARG 210": "NH1" <-> "NH2" Residue "D GLU 254": "OE1" <-> "OE2" Residue "D GLU 292": "OE1" <-> "OE2" Residue "E ARG 37": "NH1" <-> "NH2" Residue "E GLU 44": "OE1" <-> "OE2" Residue "E GLU 96": "OE1" <-> "OE2" Residue "E GLU 169": "OE1" <-> "OE2" Residue "E ARG 178": "NH1" <-> "NH2" Residue "E ARG 210": "NH1" <-> "NH2" Residue "E GLU 229": "OE1" <-> "OE2" Residue "E GLU 254": "OE1" <-> "OE2" Residue "E GLU 277": "OE1" <-> "OE2" Residue "F TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 37": "NH1" <-> "NH2" Residue "F ARG 178": "NH1" <-> "NH2" Residue "F ARG 210": "NH1" <-> "NH2" Residue "F GLU 229": "OE1" <-> "OE2" Residue "F GLU 314": "OE1" <-> "OE2" Residue "G ARG 21": "NH1" <-> "NH2" Residue "G ARG 24": "NH1" <-> "NH2" Residue "G ARG 67": "NH1" <-> "NH2" Residue "G ARG 82": "NH1" <-> "NH2" Residue "G ARG 93": "NH1" <-> "NH2" Residue "G GLU 105": "OE1" <-> "OE2" Residue "G TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 145": "OE1" <-> "OE2" Residue "G ARG 228": "NH1" <-> "NH2" Residue "G ARG 234": "NH1" <-> "NH2" Residue "G ARG 259": "NH1" <-> "NH2" Residue "G GLU 436": "OE1" <-> "OE2" Residue "G ARG 503": "NH1" <-> "NH2" Residue "G GLU 526": "OE1" <-> "OE2" Residue "G ARG 584": "NH1" <-> "NH2" Residue "G GLU 592": "OE1" <-> "OE2" Residue "G GLU 606": "OE1" <-> "OE2" Residue "G ARG 628": "NH1" <-> "NH2" Residue "H GLU 13": "OE1" <-> "OE2" Residue "H GLU 36": "OE1" <-> "OE2" Residue "H GLU 94": "OE1" <-> "OE2" Residue "H ARG 103": "NH1" <-> "NH2" Residue "H ARG 117": "NH1" <-> "NH2" Residue "H ARG 120": "NH1" <-> "NH2" Residue "H ARG 121": "NH1" <-> "NH2" Residue "H ARG 125": "NH1" <-> "NH2" Residue "H GLU 131": "OE1" <-> "OE2" Residue "H ARG 168": "NH1" <-> "NH2" Residue "I ARG 5": "NH1" <-> "NH2" Residue "I GLU 35": "OE1" <-> "OE2" Residue "I TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 148": "OE1" <-> "OE2" Residue "I ARG 249": "NH1" <-> "NH2" Residue "I GLU 256": "OE1" <-> "OE2" Residue "I GLU 260": "OE1" <-> "OE2" Residue "I GLU 264": "OE1" <-> "OE2" Residue "I ARG 281": "NH1" <-> "NH2" Residue "I GLU 302": "OE1" <-> "OE2" Residue "I ARG 310": "NH1" <-> "NH2" Residue "I GLU 344": "OE1" <-> "OE2" Residue "I ARG 346": "NH1" <-> "NH2" Residue "I GLU 384": "OE1" <-> "OE2" Residue "I ARG 387": "NH1" <-> "NH2" Residue "J ARG 20": "NH1" <-> "NH2" Residue "J ARG 32": "NH1" <-> "NH2" Residue "J GLU 35": "OE1" <-> "OE2" Residue "J GLU 88": "OE1" <-> "OE2" Residue "J ARG 121": "NH1" <-> "NH2" Residue "J GLU 148": "OE1" <-> "OE2" Residue "J ARG 220": "NH1" <-> "NH2" Residue "J GLU 256": "OE1" <-> "OE2" Residue "J GLU 258": "OE1" <-> "OE2" Residue "J ARG 274": "NH1" <-> "NH2" Residue "J ARG 281": "NH1" <-> "NH2" Residue "J GLU 291": "OE1" <-> "OE2" Residue "J GLU 308": "OE1" <-> "OE2" Residue "J ARG 310": "NH1" <-> "NH2" Residue "J GLU 327": "OE1" <-> "OE2" Residue "J ARG 346": "NH1" <-> "NH2" Residue "J GLU 384": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 28954 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2742 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 323} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2714 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 317} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 2705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2705 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 317} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 2705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2705 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 317} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 2705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2705 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 317} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 2509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2509 Classifications: {'peptide': 310} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 291} Chain breaks: 2 Chain: "G" Number of atoms: 4093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 4093 Classifications: {'peptide': 521} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 21, 'TRANS': 495} Chain breaks: 1 Chain: "H" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1619 Classifications: {'peptide': 198} Link IDs: {'CIS': 2, 'PTRANS': 7, 'TRANS': 188} Chain breaks: 1 Chain: "I" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2909 Classifications: {'peptide': 355} Link IDs: {'CIS': 5, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 332} Chain breaks: 3 Chain: "J" Number of atoms: 2982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2982 Classifications: {'peptide': 368} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 347} Chain breaks: 2 Chain: "1" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1271 Classifications: {'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 14, 'rna3p_pur': 20, 'rna3p_pyr': 17} Link IDs: {'rna2p': 23, 'rna3p': 36} Time building chain proxies: 15.26, per 1000 atoms: 0.53 Number of scatterers: 28954 At special positions: 0 Unit cell: (133, 164.35, 184.3, 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 142 16.00 P 59 15.00 O 5556 8.00 N 5003 7.00 C 18194 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: 12.01 Conformation dependent library (CDL) restraints added in 4.1 seconds 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6572 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 38 sheets defined 26.0% alpha, 13.0% beta 6 base pairs and 23 stacking pairs defined. Time for finding SS restraints: 7.05 Creating SS restraints... Processing helix chain 'A' and resid 45 through 50 removed outlier: 4.535A pdb=" N ALA A 49 " --> pdb=" O ALA A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 123 Processing helix chain 'A' and resid 125 through 134 Processing helix chain 'A' and resid 139 through 143 removed outlier: 3.591A pdb=" N LEU A 142 " --> pdb=" O GLY A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 182 removed outlier: 3.903A pdb=" N PHE A 181 " --> pdb=" O SER A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 200 removed outlier: 3.661A pdb=" N ILE A 190 " --> pdb=" O ASN A 186 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE A 194 " --> pdb=" O ILE A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 268 Processing helix chain 'A' and resid 309 through 311 No H-bonds generated for 'chain 'A' and resid 309 through 311' Processing helix chain 'A' and resid 312 through 321 removed outlier: 3.946A pdb=" N GLU A 318 " --> pdb=" O GLU A 314 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 319 " --> pdb=" O HIS A 315 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU A 320 " --> pdb=" O TYR A 316 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER A 321 " --> pdb=" O ILE A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 342 Processing helix chain 'B' and resid 107 through 123 Processing helix chain 'B' and resid 125 through 135 removed outlier: 4.007A pdb=" N ASN B 135 " --> pdb=" O ARG B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 200 Processing helix chain 'B' and resid 264 through 269 removed outlier: 3.873A pdb=" N ILE B 268 " --> pdb=" O THR B 264 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA B 269 " --> pdb=" O GLY B 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 264 through 269' Processing helix chain 'B' and resid 309 through 311 No H-bonds generated for 'chain 'B' and resid 309 through 311' Processing helix chain 'B' and resid 312 through 319 Processing helix chain 'B' and resid 330 through 343 removed outlier: 3.675A pdb=" N LYS B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 49 removed outlier: 3.973A pdb=" N ALA C 49 " --> pdb=" O LYS C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 123 removed outlier: 3.712A pdb=" N THR C 111 " --> pdb=" O LYS C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 134 Processing helix chain 'C' and resid 139 through 143 removed outlier: 3.569A pdb=" N LEU C 142 " --> pdb=" O GLY C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 182 removed outlier: 3.634A pdb=" N PHE C 181 " --> pdb=" O SER C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 192 removed outlier: 3.776A pdb=" N ILE C 190 " --> pdb=" O ASN C 186 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU C 192 " --> pdb=" O SER C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 200 removed outlier: 3.932A pdb=" N SER C 200 " --> pdb=" O THR C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 269 removed outlier: 3.898A pdb=" N ILE C 268 " --> pdb=" O THR C 264 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA C 269 " --> pdb=" O GLY C 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 264 through 269' Processing helix chain 'C' and resid 305 through 311 Processing helix chain 'C' and resid 330 through 344 removed outlier: 3.686A pdb=" N PHE C 336 " --> pdb=" O ASN C 332 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS C 343 " --> pdb=" O ALA C 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 49 Processing helix chain 'D' and resid 107 through 123 removed outlier: 3.803A pdb=" N THR D 111 " --> pdb=" O LYS D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 138 removed outlier: 3.842A pdb=" N ASN D 135 " --> pdb=" O ARG D 131 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE D 136 " --> pdb=" O TYR D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 143 Processing helix chain 'D' and resid 177 through 182 Processing helix chain 'D' and resid 194 through 199 Processing helix chain 'D' and resid 264 through 269 removed outlier: 3.897A pdb=" N ILE D 268 " --> pdb=" O THR D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 311 removed outlier: 3.708A pdb=" N GLN D 311 " --> pdb=" O PHE D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 319 removed outlier: 3.670A pdb=" N GLU D 318 " --> pdb=" O GLU D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 344 removed outlier: 3.504A pdb=" N PHE D 336 " --> pdb=" O ASN D 332 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS D 343 " --> pdb=" O ALA D 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 49 removed outlier: 3.846A pdb=" N LEU E 48 " --> pdb=" O ALA E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 123 Processing helix chain 'E' and resid 125 through 135 removed outlier: 3.519A pdb=" N ASN E 135 " --> pdb=" O ARG E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 143 removed outlier: 3.648A pdb=" N LEU E 142 " --> pdb=" O GLY E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 182 removed outlier: 4.003A pdb=" N PHE E 181 " --> pdb=" O SER E 177 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS E 182 " --> pdb=" O ARG E 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 177 through 182' Processing helix chain 'E' and resid 183 through 187 removed outlier: 3.906A pdb=" N ASN E 186 " --> pdb=" O ASN E 183 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TRP E 187 " --> pdb=" O ASN E 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 183 through 187' Processing helix chain 'E' and resid 194 through 199 Processing helix chain 'E' and resid 305 through 311 Processing helix chain 'E' and resid 312 through 320 removed outlier: 3.600A pdb=" N ILE E 317 " --> pdb=" O ALA E 313 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU E 318 " --> pdb=" O GLU E 314 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL E 319 " --> pdb=" O HIS E 315 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU E 320 " --> pdb=" O TYR E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 342 removed outlier: 3.700A pdb=" N PHE E 336 " --> pdb=" O ASN E 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 123 Processing helix chain 'F' and resid 125 through 135 removed outlier: 4.068A pdb=" N ASN F 135 " --> pdb=" O ARG F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 182 removed outlier: 3.913A pdb=" N PHE F 181 " --> pdb=" O SER F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 200 Processing helix chain 'F' and resid 264 through 269 removed outlier: 4.021A pdb=" N ILE F 268 " --> pdb=" O THR F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 311 No H-bonds generated for 'chain 'F' and resid 309 through 311' Processing helix chain 'F' and resid 312 through 320 removed outlier: 3.682A pdb=" N GLU F 318 " --> pdb=" O GLU F 314 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU F 320 " --> pdb=" O TYR F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 344 removed outlier: 3.852A pdb=" N LYS F 343 " --> pdb=" O ALA F 339 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 10 Processing helix chain 'G' and resid 18 through 24 removed outlier: 4.050A pdb=" N PHE G 23 " --> pdb=" O LEU G 19 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 45 removed outlier: 3.516A pdb=" N VAL G 44 " --> pdb=" O LEU G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 76 Processing helix chain 'G' and resid 77 through 79 No H-bonds generated for 'chain 'G' and resid 77 through 79' Processing helix chain 'G' and resid 130 through 134 Processing helix chain 'G' and resid 160 through 167 removed outlier: 3.501A pdb=" N LEU G 167 " --> pdb=" O THR G 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 181 Processing helix chain 'G' and resid 219 through 228 removed outlier: 3.733A pdb=" N SER G 223 " --> pdb=" O LEU G 219 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N HIS G 224 " --> pdb=" O SER G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 253 removed outlier: 3.538A pdb=" N MET G 252 " --> pdb=" O GLY G 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 411 through 427 removed outlier: 3.829A pdb=" N PHE G 415 " --> pdb=" O SER G 411 " (cutoff:3.500A) Processing helix chain 'G' and resid 493 through 499 removed outlier: 3.684A pdb=" N VAL G 497 " --> pdb=" O GLN G 493 " (cutoff:3.500A) Processing helix chain 'G' and resid 525 through 530 removed outlier: 3.713A pdb=" N GLU G 530 " --> pdb=" O GLU G 526 " (cutoff:3.500A) Processing helix chain 'G' and resid 549 through 558 removed outlier: 3.649A pdb=" N LEU G 553 " --> pdb=" O ASN G 549 " (cutoff:3.500A) Processing helix chain 'H' and resid 16 through 31 removed outlier: 3.822A pdb=" N LYS H 23 " --> pdb=" O SER H 19 " (cutoff:3.500A) Processing helix chain 'H' and resid 66 through 71 Processing helix chain 'H' and resid 76 through 81 removed outlier: 3.693A pdb=" N LEU H 81 " --> pdb=" O GLN H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 125 Processing helix chain 'I' and resid 14 through 22 Processing helix chain 'I' and resid 30 through 45 removed outlier: 4.242A pdb=" N LEU I 34 " --> pdb=" O VAL I 30 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU I 35 " --> pdb=" O HIS I 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 68 through 82 removed outlier: 3.695A pdb=" N THR I 72 " --> pdb=" O SER I 68 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU I 81 " --> pdb=" O LYS I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 196 through 206 Processing helix chain 'I' and resid 218 through 228 removed outlier: 3.693A pdb=" N GLY I 222 " --> pdb=" O SER I 218 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET I 228 " --> pdb=" O VAL I 224 " (cutoff:3.500A) Processing helix chain 'I' and resid 240 through 245 Processing helix chain 'I' and resid 246 through 248 No H-bonds generated for 'chain 'I' and resid 246 through 248' Processing helix chain 'I' and resid 249 through 265 removed outlier: 3.969A pdb=" N SER I 253 " --> pdb=" O ARG I 249 " (cutoff:3.500A) Processing helix chain 'I' and resid 297 through 310 removed outlier: 4.250A pdb=" N GLY I 301 " --> pdb=" O ASN I 297 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU I 302 " --> pdb=" O ILE I 298 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU I 303 " --> pdb=" O ILE I 299 " (cutoff:3.500A) Processing helix chain 'I' and resid 327 through 332 Processing helix chain 'I' and resid 337 through 345 Processing helix chain 'I' and resid 369 through 379 Processing helix chain 'J' and resid 14 through 23 removed outlier: 3.628A pdb=" N PHE J 18 " --> pdb=" O LEU J 14 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 43 Processing helix chain 'J' and resid 67 through 81 removed outlier: 3.723A pdb=" N ALA J 73 " --> pdb=" O SER J 69 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU J 81 " --> pdb=" O LYS J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 196 through 207 removed outlier: 3.622A pdb=" N GLY J 206 " --> pdb=" O ASN J 202 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N HIS J 207 " --> pdb=" O TRP J 203 " (cutoff:3.500A) Processing helix chain 'J' and resid 216 through 231 removed outlier: 3.607A pdb=" N ARG J 220 " --> pdb=" O PRO J 216 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N TRP J 221 " --> pdb=" O LYS J 217 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLY J 222 " --> pdb=" O SER J 218 " (cutoff:3.500A) Processing helix chain 'J' and resid 237 through 242 Processing helix chain 'J' and resid 246 through 261 removed outlier: 3.513A pdb=" N PHE J 251 " --> pdb=" O TRP J 247 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N HIS J 252 " --> pdb=" O PRO J 248 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE J 261 " --> pdb=" O ASP J 257 " (cutoff:3.500A) Processing helix chain 'J' and resid 297 through 310 removed outlier: 3.657A pdb=" N LEU J 303 " --> pdb=" O ILE J 299 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG J 310 " --> pdb=" O TYR J 306 " (cutoff:3.500A) Processing helix chain 'J' and resid 327 through 333 removed outlier: 3.739A pdb=" N MET J 331 " --> pdb=" O GLU J 327 " (cutoff:3.500A) Processing helix chain 'J' and resid 337 through 345 Processing helix chain 'J' and resid 369 through 380 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.597A pdb=" N SER A 88 " --> pdb=" O CYS A 19 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N HIS A 84 " --> pdb=" O VAL A 23 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N CYS A 151 " --> pdb=" O HIS A 214 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL A 166 " --> pdb=" O LEU A 156 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 34 through 41 removed outlier: 3.500A pdb=" N VAL A 73 " --> pdb=" O ARG A 37 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 248 through 251 removed outlier: 4.081A pdb=" N GLU A 254 " --> pdb=" O ILE A 251 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 13 through 15 Processing sheet with id=AA5, first strand: chain 'B' and resid 13 through 15 removed outlier: 3.733A pdb=" N CYS B 151 " --> pdb=" O HIS B 214 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 35 through 42 Processing sheet with id=AA7, first strand: chain 'B' and resid 248 through 251 Processing sheet with id=AA8, first strand: chain 'C' and resid 13 through 14 Processing sheet with id=AA9, first strand: chain 'C' and resid 13 through 14 removed outlier: 3.830A pdb=" N CYS C 151 " --> pdb=" O HIS C 214 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 35 through 40 Processing sheet with id=AB2, first strand: chain 'C' and resid 248 through 251 Processing sheet with id=AB3, first strand: chain 'D' and resid 13 through 14 Processing sheet with id=AB4, first strand: chain 'D' and resid 13 through 14 removed outlier: 3.795A pdb=" N CYS D 151 " --> pdb=" O HIS D 214 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 35 through 41 Processing sheet with id=AB6, first strand: chain 'D' and resid 248 through 251 Processing sheet with id=AB7, first strand: chain 'D' and resid 270 through 272 Processing sheet with id=AB8, first strand: chain 'E' and resid 13 through 14 Processing sheet with id=AB9, first strand: chain 'E' and resid 13 through 14 removed outlier: 3.781A pdb=" N CYS E 151 " --> pdb=" O HIS E 214 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 35 through 41 Processing sheet with id=AC2, first strand: chain 'E' and resid 248 through 251 Processing sheet with id=AC3, first strand: chain 'E' and resid 270 through 272 Processing sheet with id=AC4, first strand: chain 'F' and resid 13 through 14 Processing sheet with id=AC5, first strand: chain 'F' and resid 13 through 14 removed outlier: 3.891A pdb=" N CYS F 151 " --> pdb=" O HIS F 214 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 72 through 75 removed outlier: 7.394A pdb=" N ILE H 146 " --> pdb=" O SER F 36 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N THR F 38 " --> pdb=" O ILE H 146 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 248 through 251 Processing sheet with id=AC8, first strand: chain 'F' and resid 270 through 272 Processing sheet with id=AC9, first strand: chain 'G' and resid 85 through 86 Processing sheet with id=AD1, first strand: chain 'G' and resid 201 through 204 removed outlier: 3.726A pdb=" N GLY G 569 " --> pdb=" O ILE G 594 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 438 through 444 removed outlier: 6.560A pdb=" N VAL G 478 " --> pdb=" O HIS G 443 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU G 481 " --> pdb=" O PRO G 391 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LEU G 483 " --> pdb=" O VAL G 389 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N VAL G 389 " --> pdb=" O LEU G 483 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 398 through 399 Processing sheet with id=AD4, first strand: chain 'G' and resid 457 through 458 Processing sheet with id=AD5, first strand: chain 'G' and resid 539 through 542 Processing sheet with id=AD6, first strand: chain 'G' and resid 615 through 616 Processing sheet with id=AD7, first strand: chain 'H' and resid 4 through 5 removed outlier: 3.664A pdb=" N VAL H 90 " --> pdb=" O TYR H 5 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 7 through 9 Processing sheet with id=AD9, first strand: chain 'H' and resid 102 through 103 removed outlier: 3.599A pdb=" N ARG H 102 " --> pdb=" O ARG H 168 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 322 through 323 removed outlier: 3.585A pdb=" N PHE I 367 " --> pdb=" O MET I 323 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 322 through 324 748 hydrogen bonds defined for protein. 2067 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 15 hydrogen bonds 22 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 23 stacking parallelities Total time for adding SS restraints: 8.43 Time building geometry restraints manager: 12.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5575 1.34 - 1.46: 7880 1.46 - 1.58: 16036 1.58 - 1.70: 118 1.70 - 1.82: 205 Bond restraints: 29814 Sorted by residual: bond pdb=" CD GLU D 127 " pdb=" OE1 GLU D 127 " ideal model delta sigma weight residual 1.249 1.415 -0.166 1.90e-02 2.77e+03 7.61e+01 bond pdb=" CD GLU D 127 " pdb=" OE2 GLU D 127 " ideal model delta sigma weight residual 1.249 1.378 -0.129 1.90e-02 2.77e+03 4.62e+01 bond pdb=" N GLY D 285 " pdb=" CA GLY D 285 " ideal model delta sigma weight residual 1.442 1.476 -0.034 7.70e-03 1.69e+04 1.98e+01 bond pdb=" N ILE B 258 " pdb=" CA ILE B 258 " ideal model delta sigma weight residual 1.460 1.497 -0.037 8.60e-03 1.35e+04 1.81e+01 bond pdb=" N ILE J 347 " pdb=" CA ILE J 347 " ideal model delta sigma weight residual 1.458 1.496 -0.038 9.00e-03 1.23e+04 1.80e+01 ... (remaining 29809 not shown) Histogram of bond angle deviations from ideal: 97.27 - 104.73: 813 104.73 - 112.18: 13306 112.18 - 119.63: 14352 119.63 - 127.09: 11731 127.09 - 134.54: 540 Bond angle restraints: 40742 Sorted by residual: angle pdb=" N PRO I 86 " pdb=" CA PRO I 86 " pdb=" CB PRO I 86 " ideal model delta sigma weight residual 103.08 97.36 5.72 9.70e-01 1.06e+00 3.48e+01 angle pdb=" N PRO G 533 " pdb=" CA PRO G 533 " pdb=" CB PRO G 533 " ideal model delta sigma weight residual 103.25 97.27 5.98 1.05e+00 9.07e-01 3.24e+01 angle pdb=" C CYS I 131 " pdb=" CA CYS I 131 " pdb=" CB CYS I 131 " ideal model delta sigma weight residual 117.23 109.68 7.55 1.36e+00 5.41e-01 3.08e+01 angle pdb=" CA GLY H 177 " pdb=" C GLY H 177 " pdb=" O GLY H 177 " ideal model delta sigma weight residual 122.33 117.88 4.45 8.10e-01 1.52e+00 3.02e+01 angle pdb=" N PRO D 276 " pdb=" CA PRO D 276 " pdb=" CB PRO D 276 " ideal model delta sigma weight residual 103.25 97.79 5.46 1.05e+00 9.07e-01 2.70e+01 ... (remaining 40737 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.78: 17156 35.78 - 71.56: 413 71.56 - 107.34: 30 107.34 - 143.12: 4 143.12 - 178.90: 3 Dihedral angle restraints: 17606 sinusoidal: 7492 harmonic: 10114 Sorted by residual: dihedral pdb=" CA LYS G 49 " pdb=" C LYS G 49 " pdb=" N THR G 50 " pdb=" CA THR G 50 " ideal model delta harmonic sigma weight residual 180.00 45.09 134.91 0 5.00e+00 4.00e-02 7.28e+02 dihedral pdb=" CA LEU G 57 " pdb=" C LEU G 57 " pdb=" N ASP G 58 " pdb=" CA ASP G 58 " ideal model delta harmonic sigma weight residual 180.00 68.17 111.83 0 5.00e+00 4.00e-02 5.00e+02 dihedral pdb=" CA ASP G 58 " pdb=" C ASP G 58 " pdb=" N ARG G 59 " pdb=" CA ARG G 59 " ideal model delta harmonic sigma weight residual -180.00 -73.00 -107.00 0 5.00e+00 4.00e-02 4.58e+02 ... (remaining 17603 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2064 0.057 - 0.115: 1611 0.115 - 0.172: 671 0.172 - 0.230: 148 0.230 - 0.287: 9 Chirality restraints: 4503 Sorted by residual: chirality pdb=" C1' U 1 21 " pdb=" O4' U 1 21 " pdb=" C2' U 1 21 " pdb=" N1 U 1 21 " both_signs ideal model delta sigma weight residual False 2.47 2.18 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CA GLU I 85 " pdb=" N GLU I 85 " pdb=" C GLU I 85 " pdb=" CB GLU I 85 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA TYR I 140 " pdb=" N TYR I 140 " pdb=" C TYR I 140 " pdb=" CB TYR I 140 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 4500 not shown) Planarity restraints: 5002 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU D 127 " -0.064 2.00e-02 2.50e+03 1.20e-01 1.44e+02 pdb=" CD GLU D 127 " 0.208 2.00e-02 2.50e+03 pdb=" OE1 GLU D 127 " -0.069 2.00e-02 2.50e+03 pdb=" OE2 GLU D 127 " -0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER G 403 " 0.013 2.00e-02 2.50e+03 2.49e-02 6.21e+00 pdb=" C SER G 403 " -0.043 2.00e-02 2.50e+03 pdb=" O SER G 403 " 0.016 2.00e-02 2.50e+03 pdb=" N PRO G 404 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS I 7 " 0.012 2.00e-02 2.50e+03 2.25e-02 5.07e+00 pdb=" C LYS I 7 " -0.039 2.00e-02 2.50e+03 pdb=" O LYS I 7 " 0.014 2.00e-02 2.50e+03 pdb=" N PRO I 8 " 0.013 2.00e-02 2.50e+03 ... (remaining 4999 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.99: 34 1.99 - 2.71: 1053 2.71 - 3.44: 37508 3.44 - 4.17: 66348 4.17 - 4.90: 117979 Nonbonded interactions: 222922 Sorted by model distance: nonbonded pdb=" CG TYR H 5 " pdb=" CD1 ILE H 199 " model vdw 1.256 3.680 nonbonded pdb=" CE MET F 346 " pdb=" N1 U 1 35 " model vdw 1.271 3.540 nonbonded pdb=" CD1 ILE G 42 " pdb=" CB LEU G 56 " model vdw 1.282 3.860 nonbonded pdb=" O ASP G 48 " pdb=" ND2 ASN G 131 " model vdw 1.347 2.520 nonbonded pdb=" CE MET F 220 " pdb=" N7 G 1 41 " model vdw 1.376 3.540 ... (remaining 222917 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 43 or resid 70 through 230 or resid 243 through \ 349)) selection = (chain 'B' and (resid 2 through 43 or resid 70 through 230 or resid 243 through \ 349)) selection = (chain 'C' and (resid 2 through 43 or resid 70 through 230 or resid 243 through \ 349)) selection = (chain 'D' and (resid 2 through 43 or resid 70 through 230 or resid 243 through \ 349)) selection = (chain 'E' and (resid 2 through 43 or resid 70 through 230 or resid 243 through \ 349)) selection = chain 'F' } ncs_group { reference = (chain 'I' and (resid 1 through 232 or resid 236 through 351 or resid 361 throug \ h 393)) selection = (chain 'J' and (resid 1 through 162 or resid 195 through 351 or resid 361 throug \ h 393)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 59 5.49 5 S 142 5.16 5 C 18194 2.51 5 N 5003 2.21 5 O 5556 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.600 Check model and map are aligned: 0.470 Process input model: 75.270 Find NCS groups from input model: 1.730 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Set scattering table: 0.260 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 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 : 0.014 0.166 29814 Z= 0.897 Angle : 1.738 9.218 40742 Z= 1.228 Chirality : 0.085 0.287 4503 Planarity : 0.004 0.120 5002 Dihedral : 16.209 178.905 11034 Min Nonbonded Distance : 1.256 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 3.91 % Allowed : 14.76 % Favored : 81.32 % Rotamer Outliers : 2.17 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.80 % Twisted Proline : 6.06 % Twisted General : 2.55 % 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: -4.83 (0.11), residues: 3400 helix: -2.66 (0.14), residues: 880 sheet: -1.93 (0.21), residues: 477 loop : -4.02 (0.11), residues: 2043 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 3053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 643 time to evaluate : 4.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 25 residues processed: 694 average time/residue: 0.4654 time to fit residues: 489.0845 Evaluate side-chains 337 residues out of total 3053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 312 time to evaluate : 3.385 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 25 outliers final: 6 residues processed: 25 average time/residue: 0.2953 time to fit residues: 17.9019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 291 optimal weight: 4.9990 chunk 261 optimal weight: 5.9990 chunk 145 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 176 optimal weight: 0.7980 chunk 139 optimal weight: 1.9990 chunk 270 optimal weight: 7.9990 chunk 104 optimal weight: 6.9990 chunk 164 optimal weight: 4.9990 chunk 201 optimal weight: 7.9990 chunk 313 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN A 174 ASN A 218 ASN B 135 ASN B 183 ASN B 311 GLN B 312 GLN B 315 HIS C 104 ASN C 174 ASN C 311 GLN D 110 GLN D 174 ASN D 183 ASN E 241 GLN ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 311 GLN F 183 ASN F 218 ASN ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 GLN F 315 HIS ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 180 GLN G 196 ASN G 227 GLN G 384 ASN G 392 ASN G 444 GLN G 490 HIS ** G 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 588 HIS H 16 ASN H 88 ASN I 80 GLN ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 265 HIS J 46 HIS J 95 ASN ** J 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 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 : 0.003 0.064 29814 Z= 0.220 Angle : 0.833 11.663 40742 Z= 0.432 Chirality : 0.047 0.293 4503 Planarity : 0.005 0.089 5002 Dihedral : 13.101 176.100 4435 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 1.09 % Allowed : 13.71 % Favored : 85.21 % Rotamer Outliers : 2.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.83 % Twisted Proline : 5.45 % Twisted General : 1.75 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.88 (0.13), residues: 3400 helix: -1.39 (0.17), residues: 896 sheet: -1.05 (0.23), residues: 471 loop : -3.75 (0.11), residues: 2033 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 3053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 364 time to evaluate : 3.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 88 outliers final: 50 residues processed: 426 average time/residue: 0.4140 time to fit residues: 284.8469 Evaluate side-chains 317 residues out of total 3053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 267 time to evaluate : 3.560 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 1 residues processed: 50 average time/residue: 0.2738 time to fit residues: 30.3747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 174 optimal weight: 4.9990 chunk 97 optimal weight: 0.0980 chunk 260 optimal weight: 9.9990 chunk 213 optimal weight: 7.9990 chunk 86 optimal weight: 4.9990 chunk 313 optimal weight: 0.8980 chunk 339 optimal weight: 10.0000 chunk 279 optimal weight: 3.9990 chunk 311 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 chunk 251 optimal weight: 10.0000 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN A 311 GLN ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 349 HIS E 214 HIS E 241 GLN ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 GLN F 315 HIS ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 227 GLN ** G 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 518 HIS G 548 ASN ** G 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 HIS H 160 ASN H 188 ASN I 31 HIS ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 HIS J 47 ASN ** J 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 262 ASN J 381 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 29814 Z= 0.246 Angle : 0.786 14.888 40742 Z= 0.403 Chirality : 0.046 0.262 4503 Planarity : 0.005 0.065 5002 Dihedral : 12.628 177.178 4435 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.76 % Allowed : 15.44 % Favored : 83.79 % Rotamer Outliers : 2.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.83 % Twisted Proline : 4.85 % Twisted General : 1.38 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.61 (0.13), residues: 3400 helix: -1.03 (0.17), residues: 903 sheet: -1.13 (0.22), residues: 509 loop : -3.63 (0.12), residues: 1988 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 327 time to evaluate : 3.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 73 outliers final: 36 residues processed: 388 average time/residue: 0.4429 time to fit residues: 283.1704 Evaluate side-chains 312 residues out of total 3053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 276 time to evaluate : 3.076 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.3129 time to fit residues: 25.6673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 310 optimal weight: 10.0000 chunk 235 optimal weight: 10.0000 chunk 162 optimal weight: 0.8980 chunk 34 optimal weight: 9.9990 chunk 149 optimal weight: 0.9990 chunk 210 optimal weight: 20.0000 chunk 314 optimal weight: 9.9990 chunk 333 optimal weight: 0.8980 chunk 164 optimal weight: 10.0000 chunk 298 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN A 186 ASN ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 GLN C 104 ASN ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 GLN F 77 HIS F 218 ASN ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 315 HIS ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 618 ASN H 39 ASN H 72 GLN H 73 HIS H 88 ASN H 148 HIS H 160 ASN ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 296 HIS ** J 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.063 29814 Z= 0.315 Angle : 0.798 12.021 40742 Z= 0.410 Chirality : 0.047 0.250 4503 Planarity : 0.005 0.057 5002 Dihedral : 12.436 177.992 4435 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.85 % Allowed : 14.76 % Favored : 84.38 % Rotamer Outliers : 2.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.83 % Twisted Proline : 3.64 % Twisted General : 1.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.48 (0.13), residues: 3400 helix: -1.04 (0.17), residues: 933 sheet: -0.85 (0.22), residues: 497 loop : -3.57 (0.12), residues: 1970 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 299 time to evaluate : 3.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 71 outliers final: 40 residues processed: 350 average time/residue: 0.4089 time to fit residues: 232.9128 Evaluate side-chains 290 residues out of total 3053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 250 time to evaluate : 3.463 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.2611 time to fit residues: 24.9043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 277 optimal weight: 20.0000 chunk 189 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 248 optimal weight: 9.9990 chunk 137 optimal weight: 6.9990 chunk 284 optimal weight: 30.0000 chunk 230 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 170 optimal weight: 10.0000 chunk 299 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 HIS A 110 GLN ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 HIS ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 ASN ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 315 HIS ** G 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 ASN G 138 ASN ** G 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 ASN ** H 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 160 ASN ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 145 GLN I 154 ASN I 351 ASN ** J 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 225 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.088 29814 Z= 0.480 Angle : 0.889 12.952 40742 Z= 0.459 Chirality : 0.051 0.234 4503 Planarity : 0.006 0.058 5002 Dihedral : 12.705 179.589 4435 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.85 % Allowed : 17.06 % Favored : 82.09 % Rotamer Outliers : 2.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.83 % Twisted Proline : 2.42 % Twisted General : 1.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.13), residues: 3400 helix: -1.22 (0.17), residues: 946 sheet: -0.67 (0.23), residues: 488 loop : -3.55 (0.12), residues: 1966 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 272 time to evaluate : 3.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 82 outliers final: 42 residues processed: 339 average time/residue: 0.4049 time to fit residues: 224.6798 Evaluate side-chains 271 residues out of total 3053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 229 time to evaluate : 3.511 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 1 residues processed: 42 average time/residue: 0.2718 time to fit residues: 26.5438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 112 optimal weight: 1.9990 chunk 300 optimal weight: 10.0000 chunk 65 optimal weight: 0.0770 chunk 195 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 333 optimal weight: 9.9990 chunk 277 optimal weight: 30.0000 chunk 154 optimal weight: 0.0060 chunk 27 optimal weight: 7.9990 chunk 110 optimal weight: 7.9990 chunk 175 optimal weight: 4.9990 overall best weight: 1.1558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 315 HIS ** G 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 HIS ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 123 HIS ** I 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 381 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.4312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.075 29814 Z= 0.195 Angle : 0.758 15.201 40742 Z= 0.384 Chirality : 0.044 0.224 4503 Planarity : 0.005 0.062 5002 Dihedral : 12.219 176.761 4435 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.71 % Allowed : 13.82 % Favored : 85.47 % Rotamer Outliers : 1.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.86 % Twisted Proline : 1.82 % Twisted General : 0.98 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.23 (0.14), residues: 3400 helix: -0.88 (0.17), residues: 946 sheet: -0.80 (0.22), residues: 527 loop : -3.40 (0.12), residues: 1927 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 295 time to evaluate : 3.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 23 residues processed: 330 average time/residue: 0.4173 time to fit residues: 226.3020 Evaluate side-chains 270 residues out of total 3053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 247 time to evaluate : 3.633 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.2798 time to fit residues: 16.7454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 321 optimal weight: 0.0050 chunk 37 optimal weight: 5.9990 chunk 190 optimal weight: 4.9990 chunk 243 optimal weight: 10.0000 chunk 188 optimal weight: 6.9990 chunk 280 optimal weight: 20.0000 chunk 186 optimal weight: 4.9990 chunk 332 optimal weight: 20.0000 chunk 208 optimal weight: 0.8980 chunk 202 optimal weight: 9.9990 chunk 153 optimal weight: 0.9980 overall best weight: 2.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 588 HIS ** H 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 160 ASN ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 143 HIS ** I 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 381 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.4461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 29814 Z= 0.262 Angle : 0.778 13.980 40742 Z= 0.394 Chirality : 0.046 0.321 4503 Planarity : 0.005 0.069 5002 Dihedral : 12.006 178.116 4435 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.68 % Allowed : 15.53 % Favored : 83.79 % Rotamer Outliers : 1.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.86 % Twisted Proline : 2.42 % Twisted General : 0.98 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.14), residues: 3400 helix: -0.80 (0.17), residues: 943 sheet: -0.58 (0.22), residues: 520 loop : -3.39 (0.13), residues: 1937 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 3053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 266 time to evaluate : 3.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 19 residues processed: 291 average time/residue: 0.4167 time to fit residues: 200.0861 Evaluate side-chains 261 residues out of total 3053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 242 time to evaluate : 4.109 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2912 time to fit residues: 16.1067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 205 optimal weight: 0.7980 chunk 132 optimal weight: 5.9990 chunk 198 optimal weight: 0.0870 chunk 100 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 211 optimal weight: 40.0000 chunk 226 optimal weight: 5.9990 chunk 164 optimal weight: 6.9990 chunk 30 optimal weight: 0.0770 chunk 261 optimal weight: 0.0370 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN B 104 ASN ** C 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 GLN ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 588 HIS H 77 GLN ** H 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 237 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.4639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 29814 Z= 0.178 Angle : 0.733 13.736 40742 Z= 0.371 Chirality : 0.044 0.326 4503 Planarity : 0.005 0.062 5002 Dihedral : 11.792 176.165 4435 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.62 % Allowed : 14.29 % Favored : 85.09 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.86 % Twisted Proline : 2.42 % Twisted General : 0.89 % 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: -2.97 (0.14), residues: 3400 helix: -0.64 (0.17), residues: 950 sheet: -0.62 (0.23), residues: 529 loop : -3.26 (0.13), residues: 1921 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 294 time to evaluate : 3.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 6 residues processed: 305 average time/residue: 0.4138 time to fit residues: 206.0386 Evaluate side-chains 261 residues out of total 3053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 255 time to evaluate : 3.335 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2772 time to fit residues: 7.7521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 302 optimal weight: 1.9990 chunk 318 optimal weight: 0.2980 chunk 290 optimal weight: 8.9990 chunk 309 optimal weight: 5.9990 chunk 186 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 243 optimal weight: 7.9990 chunk 95 optimal weight: 8.9990 chunk 280 optimal weight: 0.2980 chunk 293 optimal weight: 9.9990 chunk 308 optimal weight: 0.6980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN ** C 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 315 HIS G 85 HIS ** G 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 272 HIS G 588 HIS ** H 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 160 ASN ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 HIS ** I 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 153 HIS ** J 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 262 ASN ** J 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.4756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 29814 Z= 0.208 Angle : 0.742 13.378 40742 Z= 0.377 Chirality : 0.045 0.343 4503 Planarity : 0.005 0.071 5002 Dihedral : 11.680 177.343 4435 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.59 % Allowed : 14.82 % Favored : 84.59 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.86 % Twisted Proline : 2.42 % Twisted General : 0.83 % 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: -2.86 (0.14), residues: 3400 helix: -0.54 (0.18), residues: 934 sheet: -0.41 (0.23), residues: 515 loop : -3.21 (0.13), residues: 1951 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 3053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 262 time to evaluate : 3.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 11 residues processed: 276 average time/residue: 0.3991 time to fit residues: 182.1771 Evaluate side-chains 263 residues out of total 3053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 252 time to evaluate : 3.308 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2788 time to fit residues: 10.0475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 203 optimal weight: 0.0050 chunk 327 optimal weight: 0.8980 chunk 199 optimal weight: 9.9990 chunk 155 optimal weight: 6.9990 chunk 227 optimal weight: 0.7980 chunk 343 optimal weight: 10.0000 chunk 316 optimal weight: 0.0170 chunk 273 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 chunk 211 optimal weight: 10.0000 chunk 167 optimal weight: 2.9990 overall best weight: 0.9434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN A 110 GLN A 242 ASN C 104 ASN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 299 HIS ** G 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 588 HIS ** H 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 160 ASN ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 293 ASN ** J 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 262 ASN J 381 GLN ** J 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.4888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 29814 Z= 0.182 Angle : 0.731 15.086 40742 Z= 0.369 Chirality : 0.044 0.304 4503 Planarity : 0.005 0.070 5002 Dihedral : 11.570 176.414 4435 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.53 % Allowed : 14.41 % Favored : 85.06 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.86 % Twisted Proline : 3.03 % Twisted General : 0.74 % 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: -2.78 (0.14), residues: 3400 helix: -0.43 (0.18), residues: 931 sheet: -0.52 (0.23), residues: 530 loop : -3.14 (0.13), residues: 1939 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 282 time to evaluate : 3.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 287 average time/residue: 0.4076 time to fit residues: 193.0821 Evaluate side-chains 256 residues out of total 3053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 253 time to evaluate : 3.379 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2630 time to fit residues: 6.1029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 217 optimal weight: 4.9990 chunk 291 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 252 optimal weight: 10.0000 chunk 40 optimal weight: 0.0370 chunk 76 optimal weight: 6.9990 chunk 274 optimal weight: 20.0000 chunk 114 optimal weight: 3.9990 chunk 281 optimal weight: 30.0000 chunk 34 optimal weight: 0.0770 chunk 50 optimal weight: 0.7980 overall best weight: 1.3820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 GLN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 315 HIS ** G 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 588 HIS ** H 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 160 ASN ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 293 ASN ** J 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.151659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.117574 restraints weight = 44326.482| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.65 r_work: 0.3107 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.4977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 29814 Z= 0.204 Angle : 0.742 14.764 40742 Z= 0.375 Chirality : 0.045 0.304 4503 Planarity : 0.005 0.068 5002 Dihedral : 11.503 177.286 4435 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.50 % Allowed : 15.03 % Favored : 84.47 % Rotamer Outliers : 0.46 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.86 % Twisted Proline : 3.03 % Twisted General : 0.68 % 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: -2.75 (0.14), residues: 3400 helix: -0.42 (0.18), residues: 942 sheet: -0.36 (0.23), residues: 508 loop : -3.14 (0.13), residues: 1950 =============================================================================== Job complete usr+sys time: 5876.90 seconds wall clock time: 108 minutes 54.54 seconds (6534.54 seconds total)