Starting phenix.real_space_refine (version: dev) on Fri Dec 23 00:51:13 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wsg_21892/12_2022/6wsg_21892_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wsg_21892/12_2022/6wsg_21892.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wsg_21892/12_2022/6wsg_21892.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wsg_21892/12_2022/6wsg_21892.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wsg_21892/12_2022/6wsg_21892_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wsg_21892/12_2022/6wsg_21892_trim_updated.pdb" } resolution = 3.16 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= 1.000 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ASP 137": "OD1" <-> "OD2" Residue "A ASP 170": "OD1" <-> "OD2" Residue "A ASP 187": "OD1" <-> "OD2" Residue "A ARG 261": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 279": "OD1" <-> "OD2" Residue "A GLU 320": "OE1" <-> "OE2" Residue "A ARG 370": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 157": "OD1" <-> "OD2" Residue "B ASP 201": "OD1" <-> "OD2" Residue "B ARG 261": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 279": "OD1" <-> "OD2" Residue "B ASP 347": "OD1" <-> "OD2" Residue "B ASP 404": "OD1" <-> "OD2" Residue "C ASP 194": "OD1" <-> "OD2" Residue "C ARG 261": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 352": "OD1" <-> "OD2" Residue "C ARG 370": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 392": "OD1" <-> "OD2" Residue "D ASP 157": "OD1" <-> "OD2" Residue "D ASP 194": "OD1" <-> "OD2" Residue "D ARG 200": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 261": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 370": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 377": "OE1" <-> "OE2" Residue "D ASP 392": "OD1" <-> "OD2" Residue "E ARG 261": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ASP 352": "OD1" <-> "OD2" Residue "F ASP 103": "OD1" <-> "OD2" Residue "F GLU 109": "OE1" <-> "OE2" Residue "F GLU 150": "OE1" <-> "OE2" Residue "F GLU 159": "OE1" <-> "OE2" Residue "F GLU 185": "OE1" <-> "OE2" Residue "F ARG 200": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 261": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 347": "OD1" <-> "OD2" Residue "F GLU 353": "OE1" <-> "OE2" Residue "F ARG 370": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 399": "OD1" <-> "OD2" Residue "F ASP 404": "OD1" <-> "OD2" Residue "L ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L GLU 141": "OE1" <-> "OE2" Residue "L ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ASP 134": "OD1" <-> "OD2" Residue "K GLU 141": "OE1" <-> "OE2" Residue "K ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K GLU 162": "OE1" <-> "OE2" Residue "K ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J GLU 53": "OE1" <-> "OE2" Residue "J TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J GLU 141": "OE1" <-> "OE2" Residue "J ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J GLU 162": "OE1" <-> "OE2" Residue "J ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J GLU 169": "OE1" <-> "OE2" Residue "J ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I GLU 141": "OE1" <-> "OE2" Residue "I ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I GLU 162": "OE1" <-> "OE2" Residue "I GLU 165": "OE1" <-> "OE2" Residue "I ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I GLU 181": "OE1" <-> "OE2" Residue "H ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 14": "OE1" <-> "OE2" Residue "H ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 136": "OE1" <-> "OE2" Residue "H GLU 141": "OE1" <-> "OE2" Residue "H ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 165": "OE1" <-> "OE2" Residue "H ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ASP 171": "OD1" <-> "OD2" Residue "N ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N GLU 53": "OE1" <-> "OE2" Residue "N GLU 56": "OE1" <-> "OE2" Residue "N ASP 86": "OD1" <-> "OD2" Residue "N ASP 134": "OD1" <-> "OD2" Residue "N ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N GLU 165": "OE1" <-> "OE2" Residue "N ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ASP 171": "OD1" <-> "OD2" Residue "M GLU 8": "OE1" <-> "OE2" Residue "M ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M GLU 14": "OE1" <-> "OE2" Residue "M ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ASP 37": "OD1" <-> "OD2" Residue "M PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M GLU 136": "OE1" <-> "OE2" Residue "M ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M GLU 162": "OE1" <-> "OE2" Residue "M GLU 165": "OE1" <-> "OE2" Residue "M ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 52087 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 4718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 4718 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 9, 'TRANS': 291} Chain breaks: 4 Chain: "B" Number of atoms: 5175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 5175 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 12, 'TRANS': 321} Chain breaks: 3 Chain: "C" Number of atoms: 5243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5243 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 13, 'TRANS': 324} Chain breaks: 2 Chain: "D" Number of atoms: 5235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5235 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 13, 'TRANS': 324} Chain breaks: 2 Chain: "E" Number of atoms: 5224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 5224 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 13, 'TRANS': 327} Chain breaks: 2 Chain: "F" Number of atoms: 5131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 5131 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 12, 'TRANS': 318} Chain breaks: 3 Chain: "L" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "K" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "J" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 3002 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain: "I" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "H" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "N" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 3002 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain: "M" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 3002 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain: "S" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 125 Classifications: {'peptide': 10} Modifications used: {'COO': 1} Link IDs: {'TRANS': 9} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 20.41, per 1000 atoms: 0.39 Number of scatterers: 52087 At special positions: 0 Unit cell: (150.51, 133.98, 127.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 119 16.00 P 15 15.00 Mg 4 11.99 O 5037 8.00 N 4399 7.00 C 16358 6.00 H 26155 1.00 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: 38.79 Conformation dependent library (CDL) restraints added in 4.0 seconds 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6138 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 145 helices and 40 sheets defined 45.8% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.75 Creating SS restraints... Processing helix chain 'A' and resid 67 through 77 removed outlier: 3.650A pdb=" N ASP A 76 " --> pdb=" O ASN A 72 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR A 77 " --> pdb=" O HIS A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 99 Processing helix chain 'A' and resid 125 through 135 removed outlier: 3.727A pdb=" N ALA A 129 " --> pdb=" O LYS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 168 Processing helix chain 'A' and resid 173 through 178 removed outlier: 4.144A pdb=" N ARG A 178 " --> pdb=" O GLN A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 189 Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.543A pdb=" N LEU A 214 " --> pdb=" O ALA A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 262 removed outlier: 3.613A pdb=" N ARG A 261 " --> pdb=" O VAL A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 279 No H-bonds generated for 'chain 'A' and resid 277 through 279' Processing helix chain 'A' and resid 292 through 297 Processing helix chain 'A' and resid 302 through 307 removed outlier: 3.713A pdb=" N ARG A 307 " --> pdb=" O GLU A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 327 Processing helix chain 'A' and resid 333 through 342 Processing helix chain 'A' and resid 352 through 365 Processing helix chain 'A' and resid 373 through 385 removed outlier: 4.868A pdb=" N ASP A 382 " --> pdb=" O ALA A 378 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N THR A 383 " --> pdb=" O ALA A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 404 removed outlier: 3.525A pdb=" N ASP A 404 " --> pdb=" O GLU A 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 400 through 404' Processing helix chain 'B' and resid 67 through 75 Processing helix chain 'B' and resid 82 through 100 Processing helix chain 'B' and resid 125 through 135 removed outlier: 3.706A pdb=" N LEU B 135 " --> pdb=" O THR B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 169 Processing helix chain 'B' and resid 173 through 176 No H-bonds generated for 'chain 'B' and resid 173 through 176' Processing helix chain 'B' and resid 186 through 189 Processing helix chain 'B' and resid 205 through 216 removed outlier: 3.679A pdb=" N LYS B 213 " --> pdb=" O GLN B 209 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 262 Processing helix chain 'B' and resid 283 through 289 removed outlier: 3.528A pdb=" N ALA B 288 " --> pdb=" O GLY B 284 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLN B 289 " --> pdb=" O GLU B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 298 Processing helix chain 'B' and resid 302 through 307 Processing helix chain 'B' and resid 319 through 325 Processing helix chain 'B' and resid 333 through 344 removed outlier: 3.528A pdb=" N GLU B 344 " --> pdb=" O LEU B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 365 Processing helix chain 'B' and resid 371 through 386 removed outlier: 5.255A pdb=" N ASP B 382 " --> pdb=" O ALA B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 404 removed outlier: 3.688A pdb=" N ASP B 404 " --> pdb=" O GLU B 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 400 through 404' Processing helix chain 'C' and resid 67 through 75 Processing helix chain 'C' and resid 82 through 100 Processing helix chain 'C' and resid 125 through 135 removed outlier: 3.964A pdb=" N LEU C 135 " --> pdb=" O THR C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 168 Processing helix chain 'C' and resid 173 through 176 No H-bonds generated for 'chain 'C' and resid 173 through 176' Processing helix chain 'C' and resid 186 through 189 Processing helix chain 'C' and resid 205 through 216 removed outlier: 4.546A pdb=" N LYS C 213 " --> pdb=" O GLN C 209 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LEU C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 263 Processing helix chain 'C' and resid 283 through 289 removed outlier: 3.512A pdb=" N ALA C 288 " --> pdb=" O GLY C 284 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN C 289 " --> pdb=" O GLU C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 298 Processing helix chain 'C' and resid 302 through 307 Processing helix chain 'C' and resid 319 through 327 removed outlier: 3.876A pdb=" N LYS C 327 " --> pdb=" O ILE C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 344 Processing helix chain 'C' and resid 352 through 365 removed outlier: 3.603A pdb=" N ASP C 356 " --> pdb=" O ASP C 352 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA C 364 " --> pdb=" O LYS C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 387 removed outlier: 4.000A pdb=" N VAL C 376 " --> pdb=" O ARG C 373 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLU C 377 " --> pdb=" O SER C 374 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU C 381 " --> pdb=" O ALA C 378 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N ASP C 382 " --> pdb=" O ALA C 379 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU C 387 " --> pdb=" O MET C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 404 removed outlier: 3.734A pdb=" N ASP C 404 " --> pdb=" O GLU C 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 400 through 404' Processing helix chain 'D' and resid 67 through 75 Processing helix chain 'D' and resid 82 through 100 Processing helix chain 'D' and resid 125 through 135 removed outlier: 3.572A pdb=" N LEU D 135 " --> pdb=" O THR D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 168 Processing helix chain 'D' and resid 173 through 176 No H-bonds generated for 'chain 'D' and resid 173 through 176' Processing helix chain 'D' and resid 186 through 189 removed outlier: 3.730A pdb=" N ILE D 189 " --> pdb=" O ILE D 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 186 through 189' Processing helix chain 'D' and resid 205 through 216 removed outlier: 3.657A pdb=" N GLN D 209 " --> pdb=" O GLU D 205 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA D 210 " --> pdb=" O GLY D 206 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LYS D 213 " --> pdb=" O GLN D 209 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU D 214 " --> pdb=" O ALA D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 262 Processing helix chain 'D' and resid 283 through 289 removed outlier: 4.211A pdb=" N ALA D 288 " --> pdb=" O GLY D 284 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLN D 289 " --> pdb=" O GLU D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 298 Processing helix chain 'D' and resid 302 through 307 removed outlier: 3.572A pdb=" N ARG D 307 " --> pdb=" O GLU D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 327 Processing helix chain 'D' and resid 333 through 344 removed outlier: 3.914A pdb=" N GLU D 344 " --> pdb=" O LEU D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 365 Processing helix chain 'D' and resid 368 through 379 removed outlier: 3.579A pdb=" N LEU D 372 " --> pdb=" O ALA D 369 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL D 376 " --> pdb=" O ARG D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 386 Processing helix chain 'D' and resid 400 through 404 Processing helix chain 'E' and resid 67 through 75 Processing helix chain 'E' and resid 82 through 101 Processing helix chain 'E' and resid 125 through 135 Processing helix chain 'E' and resid 158 through 168 Processing helix chain 'E' and resid 173 through 176 No H-bonds generated for 'chain 'E' and resid 173 through 176' Processing helix chain 'E' and resid 186 through 188 No H-bonds generated for 'chain 'E' and resid 186 through 188' Processing helix chain 'E' and resid 205 through 216 removed outlier: 4.597A pdb=" N LYS E 213 " --> pdb=" O GLN E 209 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU E 214 " --> pdb=" O ALA E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 262 Processing helix chain 'E' and resid 284 through 289 removed outlier: 3.754A pdb=" N ALA E 288 " --> pdb=" O GLY E 284 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLN E 289 " --> pdb=" O GLU E 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 284 through 289' Processing helix chain 'E' and resid 292 through 298 Processing helix chain 'E' and resid 302 through 306 Processing helix chain 'E' and resid 319 through 327 removed outlier: 3.707A pdb=" N LYS E 327 " --> pdb=" O ILE E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 344 removed outlier: 4.359A pdb=" N GLU E 344 " --> pdb=" O LEU E 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 352 through 365 Processing helix chain 'E' and resid 371 through 386 removed outlier: 5.464A pdb=" N ASP E 382 " --> pdb=" O ALA E 378 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N THR E 383 " --> pdb=" O ALA E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 404 removed outlier: 3.579A pdb=" N ASP E 404 " --> pdb=" O GLU E 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 400 through 404' Processing helix chain 'F' and resid 67 through 77 removed outlier: 3.603A pdb=" N TYR F 77 " --> pdb=" O HIS F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 101 Processing helix chain 'F' and resid 125 through 135 Processing helix chain 'F' and resid 158 through 168 Processing helix chain 'F' and resid 173 through 177 Processing helix chain 'F' and resid 205 through 216 removed outlier: 4.527A pdb=" N LYS F 213 " --> pdb=" O GLN F 209 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU F 214 " --> pdb=" O ALA F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 262 Processing helix chain 'F' and resid 284 through 289 removed outlier: 4.063A pdb=" N GLN F 289 " --> pdb=" O GLU F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 298 Processing helix chain 'F' and resid 302 through 307 Processing helix chain 'F' and resid 319 through 327 removed outlier: 3.505A pdb=" N LEU F 326 " --> pdb=" O LEU F 322 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS F 327 " --> pdb=" O ILE F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 344 removed outlier: 3.721A pdb=" N GLU F 344 " --> pdb=" O LEU F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 364 Processing helix chain 'F' and resid 372 through 387 removed outlier: 5.197A pdb=" N ASP F 382 " --> pdb=" O ALA F 378 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N THR F 383 " --> pdb=" O ALA F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 403 No H-bonds generated for 'chain 'F' and resid 400 through 403' Processing helix chain 'L' and resid 19 through 26 removed outlier: 3.572A pdb=" N GLU L 26 " --> pdb=" O ARG L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 53 Processing helix chain 'L' and resid 70 through 82 Processing helix chain 'L' and resid 97 through 104 Processing helix chain 'L' and resid 132 through 157 Processing helix chain 'L' and resid 161 through 168 Processing helix chain 'L' and resid 176 through 182 Processing helix chain 'K' and resid 19 through 26 removed outlier: 3.653A pdb=" N LEU K 23 " --> pdb=" O ILE K 19 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU K 26 " --> pdb=" O ARG K 22 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 53 Processing helix chain 'K' and resid 70 through 82 removed outlier: 3.520A pdb=" N ILE K 76 " --> pdb=" O ALA K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 97 through 104 Processing helix chain 'K' and resid 132 through 157 Processing helix chain 'K' and resid 161 through 168 Processing helix chain 'K' and resid 176 through 182 Processing helix chain 'J' and resid 19 through 26 removed outlier: 3.660A pdb=" N LEU J 23 " --> pdb=" O ILE J 19 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU J 26 " --> pdb=" O ARG J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 53 Processing helix chain 'J' and resid 70 through 82 Processing helix chain 'J' and resid 97 through 104 Processing helix chain 'J' and resid 132 through 157 Processing helix chain 'J' and resid 161 through 168 Processing helix chain 'J' and resid 176 through 182 Processing helix chain 'I' and resid 21 through 26 removed outlier: 3.620A pdb=" N GLU I 26 " --> pdb=" O ARG I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 53 Processing helix chain 'I' and resid 70 through 82 Processing helix chain 'I' and resid 97 through 104 Processing helix chain 'I' and resid 132 through 157 Processing helix chain 'I' and resid 161 through 168 Processing helix chain 'I' and resid 176 through 182 Processing helix chain 'H' and resid 19 through 26 removed outlier: 3.860A pdb=" N LEU H 23 " --> pdb=" O ILE H 19 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU H 26 " --> pdb=" O ARG H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 53 Processing helix chain 'H' and resid 70 through 82 removed outlier: 3.573A pdb=" N SER H 75 " --> pdb=" O THR H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 104 Processing helix chain 'H' and resid 132 through 157 Processing helix chain 'H' and resid 161 through 168 Processing helix chain 'H' and resid 176 through 182 Processing helix chain 'N' and resid 19 through 26 removed outlier: 3.772A pdb=" N LEU N 23 " --> pdb=" O ILE N 19 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU N 24 " --> pdb=" O TYR N 20 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU N 26 " --> pdb=" O ARG N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 53 Processing helix chain 'N' and resid 70 through 82 Processing helix chain 'N' and resid 97 through 104 Processing helix chain 'N' and resid 132 through 157 Processing helix chain 'N' and resid 161 through 168 Processing helix chain 'N' and resid 176 through 182 Processing helix chain 'M' and resid 19 through 26 removed outlier: 3.524A pdb=" N LEU M 23 " --> pdb=" O ILE M 19 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU M 24 " --> pdb=" O TYR M 20 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU M 26 " --> pdb=" O ARG M 22 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 53 Processing helix chain 'M' and resid 70 through 82 removed outlier: 3.573A pdb=" N SER M 75 " --> pdb=" O THR M 71 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE M 76 " --> pdb=" O ALA M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 104 Processing helix chain 'M' and resid 132 through 157 Processing helix chain 'M' and resid 161 through 168 Processing helix chain 'M' and resid 176 through 182 removed outlier: 3.501A pdb=" N VAL M 180 " --> pdb=" O ALA M 176 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU M 181 " --> pdb=" O PRO M 177 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 115 through 118 removed outlier: 6.722A pdb=" N VAL A 310 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ILE A 118 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ALA A 312 " --> pdb=" O ILE A 118 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 140 through 143 removed outlier: 6.443A pdb=" N ILE A 180 " --> pdb=" O THR A 141 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ALA A 143 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N TYR A 182 " --> pdb=" O ALA A 143 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU A 244 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N ILE A 183 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE A 246 " --> pdb=" O ILE A 183 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 347 through 350 removed outlier: 3.573A pdb=" N ILE A 398 " --> pdb=" O GLU A 349 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS A 395 " --> pdb=" O ILE A 412 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 312 through 314 removed outlier: 3.965A pdb=" N GLY B 119 " --> pdb=" O GLY B 249 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 220 through 222 Processing sheet with id= F, first strand: chain 'B' and resid 347 through 350 removed outlier: 6.646A pdb=" N ILE B 412 " --> pdb=" O GLU B 394 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N VAL B 396 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LEU B 410 " --> pdb=" O VAL B 396 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 310 through 314 removed outlier: 3.879A pdb=" N GLY C 119 " --> pdb=" O GLY C 249 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 219 through 222 Processing sheet with id= I, first strand: chain 'C' and resid 347 through 350 removed outlier: 6.871A pdb=" N ILE C 412 " --> pdb=" O GLU C 394 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N VAL C 396 " --> pdb=" O LEU C 410 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LEU C 410 " --> pdb=" O VAL C 396 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 310 through 314 removed outlier: 3.809A pdb=" N GLY D 119 " --> pdb=" O GLY D 249 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 219 through 222 Processing sheet with id= L, first strand: chain 'D' and resid 347 through 350 removed outlier: 7.102A pdb=" N ILE D 412 " --> pdb=" O GLU D 394 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 310 through 313 Processing sheet with id= N, first strand: chain 'E' and resid 219 through 223 Processing sheet with id= O, first strand: chain 'E' and resid 347 through 350 removed outlier: 6.801A pdb=" N ILE E 412 " --> pdb=" O GLU E 394 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL E 396 " --> pdb=" O LEU E 410 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU E 410 " --> pdb=" O VAL E 396 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 310 through 314 Processing sheet with id= Q, first strand: chain 'F' and resid 219 through 222 Processing sheet with id= R, first strand: chain 'F' and resid 347 through 350 removed outlier: 3.645A pdb=" N ILE F 398 " --> pdb=" O GLU F 349 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS F 395 " --> pdb=" O ILE F 412 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'L' and resid 5 through 10 removed outlier: 3.832A pdb=" N GLY L 13 " --> pdb=" O THR L 10 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'L' and resid 28 through 32 removed outlier: 6.443A pdb=" N TYR L 60 " --> pdb=" O ILE L 29 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N LEU L 31 " --> pdb=" O TYR L 60 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N TYR L 62 " --> pdb=" O LEU L 31 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'L' and resid 112 through 114 removed outlier: 6.711A pdb=" N SER L 187 " --> pdb=" O CYS L 113 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'L' and resid 118 through 121 Processing sheet with id= W, first strand: chain 'K' and resid 5 through 9 Processing sheet with id= X, first strand: chain 'K' and resid 28 through 32 removed outlier: 6.406A pdb=" N TYR K 60 " --> pdb=" O ILE K 29 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N LEU K 31 " --> pdb=" O TYR K 60 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N TYR K 62 " --> pdb=" O LEU K 31 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N SER K 187 " --> pdb=" O CYS K 113 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'K' and resid 118 through 121 Processing sheet with id= Z, first strand: chain 'J' and resid 5 through 9 Processing sheet with id= AA, first strand: chain 'J' and resid 28 through 32 removed outlier: 6.414A pdb=" N TYR J 60 " --> pdb=" O ILE J 29 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N LEU J 31 " --> pdb=" O TYR J 60 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N TYR J 62 " --> pdb=" O LEU J 31 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'J' and resid 118 through 121 Processing sheet with id= AC, first strand: chain 'I' and resid 5 through 8 Processing sheet with id= AD, first strand: chain 'I' and resid 28 through 32 removed outlier: 6.414A pdb=" N TYR I 60 " --> pdb=" O ILE I 29 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU I 31 " --> pdb=" O TYR I 60 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N TYR I 62 " --> pdb=" O LEU I 31 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N SER I 187 " --> pdb=" O CYS I 113 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'I' and resid 118 through 121 Processing sheet with id= AF, first strand: chain 'H' and resid 5 through 9 Processing sheet with id= AG, first strand: chain 'H' and resid 28 through 32 removed outlier: 6.370A pdb=" N TYR H 60 " --> pdb=" O ILE H 29 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N LEU H 31 " --> pdb=" O TYR H 60 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N TYR H 62 " --> pdb=" O LEU H 31 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N SER H 187 " --> pdb=" O CYS H 113 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'H' and resid 119 through 121 Processing sheet with id= AI, first strand: chain 'N' and resid 5 through 8 Processing sheet with id= AJ, first strand: chain 'N' and resid 28 through 32 removed outlier: 6.593A pdb=" N TYR N 60 " --> pdb=" O ILE N 29 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N LEU N 31 " --> pdb=" O TYR N 60 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N TYR N 62 " --> pdb=" O LEU N 31 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N SER N 187 " --> pdb=" O CYS N 113 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'N' and resid 118 through 121 Processing sheet with id= AL, first strand: chain 'M' and resid 5 through 9 Processing sheet with id= AM, first strand: chain 'M' and resid 28 through 32 removed outlier: 6.570A pdb=" N TYR M 60 " --> pdb=" O ILE M 29 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N LEU M 31 " --> pdb=" O TYR M 60 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N TYR M 62 " --> pdb=" O LEU M 31 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS M 91 " --> pdb=" O PHE M 112 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'M' and resid 118 through 121 1107 hydrogen bonds defined for protein. 3015 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: 16.77 Time building geometry restraints manager: 40.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.05: 26135 1.05 - 1.27: 4548 1.27 - 1.50: 11308 1.50 - 1.72: 10231 1.72 - 1.95: 213 Bond restraints: 52435 Sorted by residual: bond pdb=" N LYS B 192 " pdb=" CA LYS B 192 " ideal model delta sigma weight residual 1.452 1.487 -0.036 1.30e-02 5.92e+03 7.54e+00 bond pdb=" N ASP C 399 " pdb=" CA ASP C 399 " ideal model delta sigma weight residual 1.453 1.488 -0.036 1.31e-02 5.83e+03 7.40e+00 bond pdb=" N ILE C 398 " pdb=" H ILE C 398 " ideal model delta sigma weight residual 0.860 0.913 -0.053 2.00e-02 2.50e+03 7.07e+00 bond pdb=" N LYS B 192 " pdb=" H LYS B 192 " ideal model delta sigma weight residual 0.860 0.911 -0.051 2.00e-02 2.50e+03 6.62e+00 bond pdb=" CG1 ILE D 79 " pdb=" CD1 ILE D 79 " ideal model delta sigma weight residual 1.513 1.413 0.100 3.90e-02 6.57e+02 6.59e+00 ... (remaining 52430 not shown) Histogram of bond angle deviations from ideal: 96.45 - 103.62: 342 103.62 - 110.79: 56681 110.79 - 117.96: 16003 117.96 - 125.14: 21287 125.14 - 132.31: 850 Bond angle restraints: 95163 Sorted by residual: angle pdb=" CA GLU C 400 " pdb=" C GLU C 400 " pdb=" O GLU C 400 " ideal model delta sigma weight residual 120.55 116.89 3.66 1.06e+00 8.90e-01 1.19e+01 angle pdb=" N GLY C 80 " pdb=" CA GLY C 80 " pdb=" C GLY C 80 " ideal model delta sigma weight residual 114.92 119.33 -4.41 1.30e+00 5.92e-01 1.15e+01 angle pdb=" CA SER C 401 " pdb=" C SER C 401 " pdb=" O SER C 401 " ideal model delta sigma weight residual 120.55 117.02 3.53 1.06e+00 8.90e-01 1.11e+01 angle pdb=" N GLU F 328 " pdb=" CA GLU F 328 " pdb=" C GLU F 328 " ideal model delta sigma weight residual 109.81 117.16 -7.35 2.21e+00 2.05e-01 1.11e+01 angle pdb=" N GLY F 80 " pdb=" CA GLY F 80 " pdb=" C GLY F 80 " ideal model delta sigma weight residual 115.27 119.81 -4.54 1.41e+00 5.03e-01 1.04e+01 ... (remaining 95158 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 18452 18.00 - 36.00: 1883 36.00 - 53.99: 246 53.99 - 71.99: 52 71.99 - 89.99: 26 Dihedral angle restraints: 20659 sinusoidal: 10050 harmonic: 10609 Sorted by residual: dihedral pdb=" CB GLU S 273 " pdb=" CG GLU S 273 " pdb=" CD GLU S 273 " pdb=" OE1 GLU S 273 " ideal model delta sinusoidal sigma weight residual 0.00 89.99 -89.99 1 3.00e+01 1.11e-03 1.07e+01 dihedral pdb=" CA ASP F 170 " pdb=" CB ASP F 170 " pdb=" CG ASP F 170 " pdb=" OD1 ASP F 170 " ideal model delta sinusoidal sigma weight residual -30.00 -85.18 55.18 1 2.00e+01 2.50e-03 1.03e+01 dihedral pdb=" CG ARG C 98 " pdb=" CD ARG C 98 " pdb=" NE ARG C 98 " pdb=" CZ ARG C 98 " ideal model delta sinusoidal sigma weight residual 180.00 136.24 43.76 2 1.50e+01 4.44e-03 1.02e+01 ... (remaining 20656 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2720 0.047 - 0.095: 1090 0.095 - 0.142: 296 0.142 - 0.190: 39 0.190 - 0.237: 4 Chirality restraints: 4149 Sorted by residual: chirality pdb=" CA ILE C 398 " pdb=" N ILE C 398 " pdb=" C ILE C 398 " pdb=" CB ILE C 398 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA PRO D 329 " pdb=" N PRO D 329 " pdb=" C PRO D 329 " pdb=" CB PRO D 329 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CB ILE C 268 " pdb=" CA ILE C 268 " pdb=" CG1 ILE C 268 " pdb=" CG2 ILE C 268 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.86e-01 ... (remaining 4146 not shown) Planarity restraints: 7739 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN I 150 " -0.026 2.00e-02 2.50e+03 4.30e-01 2.77e+03 pdb=" CG ASN I 150 " 0.002 2.00e-02 2.50e+03 pdb=" OD1 ASN I 150 " 0.026 2.00e-02 2.50e+03 pdb=" ND2 ASN I 150 " -0.000 2.00e-02 2.50e+03 pdb="HD21 ASN I 150 " -0.745 2.00e-02 2.50e+03 pdb="HD22 ASN I 150 " 0.743 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN L 116 " 0.055 2.00e-02 2.50e+03 5.80e-02 5.05e+01 pdb=" CG ASN L 116 " -0.006 2.00e-02 2.50e+03 pdb=" OD1 ASN L 116 " -0.050 2.00e-02 2.50e+03 pdb=" ND2 ASN L 116 " -0.002 2.00e-02 2.50e+03 pdb="HD21 ASN L 116 " -0.084 2.00e-02 2.50e+03 pdb="HD22 ASN L 116 " 0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU C 400 " -0.014 2.00e-02 2.50e+03 2.48e-02 6.16e+00 pdb=" N SER C 401 " 0.043 2.00e-02 2.50e+03 pdb=" CA SER C 401 " -0.011 2.00e-02 2.50e+03 pdb=" H SER C 401 " -0.018 2.00e-02 2.50e+03 ... (remaining 7736 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.01: 330 2.01 - 2.66: 77653 2.66 - 3.30: 152414 3.30 - 3.95: 198429 3.95 - 4.60: 321600 Nonbonded interactions: 750426 Sorted by model distance: nonbonded pdb=" HG1 THR J 10 " pdb=" O GLY J 13 " model vdw 1.360 1.850 nonbonded pdb=" O LEU D 214 " pdb=" HG1 THR D 240 " model vdw 1.366 1.850 nonbonded pdb=" O LEU C 326 " pdb=" HG1 THR C 334 " model vdw 1.387 1.850 nonbonded pdb=" O LEU F 326 " pdb=" HG1 THR F 334 " model vdw 1.396 1.850 nonbonded pdb=" HH TYR A 93 " pdb=" OE2 GLU F 344 " model vdw 1.412 1.850 ... (remaining 750421 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 65 through 264 or (resid 265 and (name N or name CA or nam \ e C or name O )) or (resid 266 and (name N or name CA or name C or name O or nam \ e CB or name OG )) or resid 267 through 276 or (resid 281 and (name N or name CA \ or name C or name O or name CB )) or (resid 282 and (name N or name CA or name \ C or name O or name CB or name OG )) or resid 283 through 413)) selection = (chain 'B' and (resid 65 through 100 or resid 108 through 147 or (resid 157 and \ (name N or name CA or name C or name O or name CB or name CG or name OD1 or name \ OD2 or name HA or name HB2 or name HB3)) or resid 158 through 191 or (resid 206 \ and (name N or name CA or name C or name O or name HA2 or name HA3)) or resid 2 \ 07 through 219 or resid 238 through 264 or (resid 265 and (name N or name CA or \ name C or name O )) or (resid 266 and (name N or name CA or name C or name O or \ name CB or name OG )) or resid 267 through 276 or (resid 281 and (name N or name \ CA or name C or name O or name CB )) or (resid 282 and (name N or name CA or na \ me C or name O or name CB or name OG )) or resid 283 through 413)) selection = (chain 'C' and (resid 65 through 100 or resid 108 through 147 or (resid 157 and \ (name N or name CA or name C or name O or name CB or name CG or name OD1 or name \ OD2 or name HA or name HB2 or name HB3)) or resid 158 through 191 or (resid 206 \ and (name N or name CA or name C or name O or name HA2 or name HA3)) or resid 2 \ 07 through 219 or resid 238 through 264 or (resid 265 and (name N or name CA or \ name C or name O )) or (resid 266 and (name N or name CA or name C or name O or \ name CB or name OG )) or resid 267 through 276 or (resid 281 and (name N or name \ CA or name C or name O or name CB )) or (resid 282 and (name N or name CA or na \ me C or name O or name CB or name OG )) or resid 283 through 413)) selection = (chain 'D' and (resid 65 through 100 or resid 108 through 147 or (resid 157 and \ (name N or name CA or name C or name O or name CB or name CG or name OD1 or name \ OD2 or name HA or name HB2 or name HB3)) or resid 158 through 191 or (resid 206 \ and (name N or name CA or name C or name O or name HA2 or name HA3)) or resid 2 \ 07 through 219 or resid 238 through 264 or (resid 265 and (name N or name CA or \ name C or name O )) or (resid 266 and (name N or name CA or name C or name O or \ name CB or name OG )) or resid 267 through 276 or (resid 281 and (name N or name \ CA or name C or name O or name CB )) or (resid 282 and (name N or name CA or na \ me C or name O or name CB or name OG )) or resid 283 through 413)) selection = (chain 'E' and (resid 65 through 100 or resid 108 through 147 or (resid 157 and \ (name N or name CA or name C or name O or name CB or name CG or name OD1 or name \ OD2 or name HA or name HB2 or name HB3)) or resid 158 through 191 or (resid 206 \ and (name N or name CA or name C or name O or name HA2 or name HA3)) or resid 2 \ 07 through 219 or resid 238 through 276 or resid 281 through 413)) selection = (chain 'F' and (resid 65 through 100 or resid 108 through 147 or (resid 157 and \ (name N or name CA or name C or name O or name CB or name CG or name OD1 or name \ OD2 or name HA or name HB2 or name HB3)) or resid 158 through 191 or (resid 206 \ and (name N or name CA or name C or name O or name HA2 or name HA3)) or resid 2 \ 07 through 219 or resid 238 through 264 or (resid 265 and (name N or name CA or \ name C or name O )) or (resid 266 and (name N or name CA or name C or name O or \ name CB or name OG )) or resid 267 through 276 or (resid 281 and (name N or name \ CA or name C or name O or name CB )) or (resid 282 and (name N or name CA or na \ me C or name O or name CB or name OG )) or resid 283 through 413)) } ncs_group { reference = (chain 'H' and resid 2 through 192) selection = (chain 'I' and resid 2 through 192) selection = chain 'J' selection = (chain 'K' and resid 2 through 192) selection = (chain 'L' and resid 2 through 192) selection = chain 'M' selection = chain 'N' } 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: 7 Type Number sf(0) Gaussians P 15 5.49 5 Mg 4 5.21 5 S 119 5.16 5 C 16358 2.51 5 N 4399 2.21 5 O 5037 1.98 5 H 26155 0.53 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: 4.430 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: 0.600 Extract box with map and model: 16.650 Check model and map are aligned: 0.730 Convert atoms to be neutral: 0.400 Process input model: 139.190 Find NCS groups from input model: 2.150 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 166.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 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 0.100 26280 Z= 0.722 Angle : 0.831 8.025 35504 Z= 0.448 Chirality : 0.053 0.237 4149 Planarity : 0.005 0.064 4570 Dihedral : 13.350 89.988 9931 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer Outliers : 0.04 % 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: -1.08 (0.13), residues: 3274 helix: -0.36 (0.12), residues: 1612 sheet: -0.46 (0.23), residues: 433 loop : -1.12 (0.16), residues: 1229 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 453 time to evaluate : 3.821 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 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 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 454 average time/residue: 0.8814 time to fit residues: 608.0898 Evaluate side-chains 312 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 312 time to evaluate : 3.999 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.8377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 278 optimal weight: 6.9990 chunk 250 optimal weight: 9.9990 chunk 138 optimal weight: 0.6980 chunk 85 optimal weight: 0.5980 chunk 168 optimal weight: 0.8980 chunk 133 optimal weight: 0.2980 chunk 258 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 157 optimal weight: 0.6980 chunk 192 optimal weight: 0.6980 chunk 299 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 HIS B 167 GLN B 289 GLN C 167 GLN C 406 GLN D 95 HIS D 406 GLN F 81 GLN F 208 GLN I 41 ASN I 116 ASN ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 41 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 26280 Z= 0.191 Angle : 0.517 5.562 35504 Z= 0.272 Chirality : 0.040 0.149 4149 Planarity : 0.004 0.050 4570 Dihedral : 4.697 65.884 3607 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer Outliers : 0.57 % 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: -0.21 (0.14), residues: 3274 helix: 0.50 (0.12), residues: 1630 sheet: -0.06 (0.23), residues: 465 loop : -0.95 (0.17), residues: 1179 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 337 time to evaluate : 3.180 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 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 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 14 residues processed: 346 average time/residue: 0.7761 time to fit residues: 417.6442 Evaluate side-chains 326 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 312 time to evaluate : 3.260 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.5365 time to fit residues: 17.0346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 166 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 249 optimal weight: 50.0000 chunk 204 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 300 optimal weight: 4.9990 chunk 324 optimal weight: 9.9990 chunk 267 optimal weight: 50.0000 chunk 297 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 240 optimal weight: 0.7980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 9 GLN J 116 ASN ** J 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 150 ASN S 274 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 26280 Z= 0.325 Angle : 0.517 7.000 35504 Z= 0.265 Chirality : 0.041 0.162 4149 Planarity : 0.003 0.050 4570 Dihedral : 4.832 68.687 3607 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer Outliers : 0.36 % 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 (0.14), residues: 3274 helix: 0.75 (0.13), residues: 1637 sheet: 0.08 (0.22), residues: 504 loop : -0.81 (0.17), residues: 1133 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 320 time to evaluate : 3.921 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 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 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: 10 outliers final: 7 residues processed: 322 average time/residue: 0.7729 time to fit residues: 383.9156 Evaluate side-chains 311 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 304 time to evaluate : 3.825 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.4647 time to fit residues: 9.9470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 296 optimal weight: 2.9990 chunk 225 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 chunk 201 optimal weight: 2.9990 chunk 301 optimal weight: 8.9990 chunk 318 optimal weight: 0.4980 chunk 157 optimal weight: 1.9990 chunk 285 optimal weight: 50.0000 chunk 85 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 167 GLN J 116 ASN ** J 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 41 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 26280 Z= 0.218 Angle : 0.459 6.859 35504 Z= 0.235 Chirality : 0.040 0.146 4149 Planarity : 0.003 0.057 4570 Dihedral : 4.834 68.513 3607 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer Outliers : 0.22 % 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: 0.43 (0.15), residues: 3274 helix: 1.02 (0.13), residues: 1635 sheet: 0.12 (0.22), residues: 535 loop : -0.62 (0.18), residues: 1104 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 321 time to evaluate : 3.987 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 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 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: 6 outliers final: 4 residues processed: 321 average time/residue: 0.8573 time to fit residues: 431.6956 Evaluate side-chains 306 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 302 time to evaluate : 3.155 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.5150 time to fit residues: 8.0211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 265 optimal weight: 0.0970 chunk 181 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 237 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 272 optimal weight: 6.9990 chunk 220 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 162 optimal weight: 0.9990 chunk 286 optimal weight: 50.0000 chunk 80 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 41 ASN ** J 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 GLN M 41 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 26280 Z= 0.222 Angle : 0.452 5.701 35504 Z= 0.231 Chirality : 0.039 0.154 4149 Planarity : 0.003 0.057 4570 Dihedral : 4.802 68.480 3607 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.15), residues: 3274 helix: 1.21 (0.13), residues: 1631 sheet: 0.14 (0.22), residues: 536 loop : -0.53 (0.18), residues: 1107 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 313 time to evaluate : 3.350 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 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 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 revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 316 average time/residue: 0.7488 time to fit residues: 367.5428 Evaluate side-chains 304 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 300 time to evaluate : 3.166 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.4726 time to fit residues: 7.5073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 107 optimal weight: 1.9990 chunk 287 optimal weight: 50.0000 chunk 63 optimal weight: 1.9990 chunk 187 optimal weight: 1.9990 chunk 78 optimal weight: 0.2980 chunk 319 optimal weight: 40.0000 chunk 265 optimal weight: 20.0000 chunk 147 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 167 optimal weight: 0.9980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 41 ASN M 41 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 26280 Z= 0.219 Angle : 0.447 6.161 35504 Z= 0.228 Chirality : 0.039 0.146 4149 Planarity : 0.003 0.062 4570 Dihedral : 4.802 68.420 3607 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer Outliers : 0.25 % 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: 0.76 (0.15), residues: 3274 helix: 1.34 (0.13), residues: 1636 sheet: 0.17 (0.22), residues: 536 loop : -0.47 (0.18), residues: 1102 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 304 time to evaluate : 3.170 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 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 307 average time/residue: 0.8100 time to fit residues: 388.4637 Evaluate side-chains 302 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 297 time to evaluate : 3.135 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.4651 time to fit residues: 8.4977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 307 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 233 optimal weight: 4.9990 chunk 180 optimal weight: 0.7980 chunk 268 optimal weight: 50.0000 chunk 178 optimal weight: 0.9990 chunk 318 optimal weight: 0.1980 chunk 199 optimal weight: 3.9990 chunk 193 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 116 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 26280 Z= 0.213 Angle : 0.449 9.803 35504 Z= 0.228 Chirality : 0.039 0.145 4149 Planarity : 0.003 0.062 4570 Dihedral : 4.808 68.208 3607 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer Outliers : 0.14 % 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: 0.83 (0.15), residues: 3274 helix: 1.37 (0.13), residues: 1644 sheet: 0.21 (0.22), residues: 532 loop : -0.40 (0.19), residues: 1098 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 297 time to evaluate : 3.177 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 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 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: 4 outliers final: 3 residues processed: 297 average time/residue: 0.7674 time to fit residues: 352.5221 Evaluate side-chains 293 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 290 time to evaluate : 3.086 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.4673 time to fit residues: 6.6058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 196 optimal weight: 0.5980 chunk 127 optimal weight: 2.9990 chunk 189 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 62 optimal weight: 0.1980 chunk 61 optimal weight: 1.9990 chunk 202 optimal weight: 0.5980 chunk 216 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 250 optimal weight: 30.0000 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 41 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 26280 Z= 0.168 Angle : 0.433 6.606 35504 Z= 0.220 Chirality : 0.039 0.143 4149 Planarity : 0.003 0.061 4570 Dihedral : 4.754 67.228 3607 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer Outliers : 0.14 % 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: 0.99 (0.15), residues: 3274 helix: 1.50 (0.13), residues: 1641 sheet: 0.28 (0.22), residues: 530 loop : -0.33 (0.19), residues: 1103 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 301 time to evaluate : 4.008 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 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 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: 4 outliers final: 2 residues processed: 303 average time/residue: 0.8001 time to fit residues: 379.3563 Evaluate side-chains 292 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 290 time to evaluate : 3.137 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4669 time to fit residues: 5.9881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 289 optimal weight: 6.9990 chunk 304 optimal weight: 20.0000 chunk 278 optimal weight: 0.6980 chunk 296 optimal weight: 2.9990 chunk 178 optimal weight: 0.3980 chunk 129 optimal weight: 1.9990 chunk 232 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 chunk 267 optimal weight: 20.0000 chunk 280 optimal weight: 0.9990 chunk 295 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 41 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 26280 Z= 0.190 Angle : 0.444 6.491 35504 Z= 0.225 Chirality : 0.039 0.143 4149 Planarity : 0.003 0.060 4570 Dihedral : 4.740 67.475 3607 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer Outliers : 0.11 % 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: 0.97 (0.15), residues: 3274 helix: 1.52 (0.13), residues: 1647 sheet: 0.12 (0.21), residues: 550 loop : -0.34 (0.19), residues: 1077 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 291 time to evaluate : 3.154 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 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 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: 3 outliers final: 3 residues processed: 292 average time/residue: 0.7780 time to fit residues: 354.1896 Evaluate side-chains 291 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 288 time to evaluate : 3.080 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.4491 time to fit residues: 6.5565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 194 optimal weight: 5.9990 chunk 313 optimal weight: 6.9990 chunk 191 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 chunk 217 optimal weight: 0.0060 chunk 328 optimal weight: 50.0000 chunk 302 optimal weight: 3.9990 chunk 261 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 202 optimal weight: 0.9980 chunk 160 optimal weight: 2.9990 overall best weight: 2.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 26280 Z= 0.360 Angle : 0.514 6.694 35504 Z= 0.263 Chirality : 0.041 0.176 4149 Planarity : 0.003 0.066 4570 Dihedral : 4.872 70.484 3607 Min Nonbonded Distance : 1.729 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer Outliers : 0.14 % 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: 0.76 (0.15), residues: 3274 helix: 1.36 (0.13), residues: 1647 sheet: 0.04 (0.22), residues: 550 loop : -0.46 (0.19), residues: 1077 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 280 time to evaluate : 3.151 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 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 281 average time/residue: 0.7643 time to fit residues: 334.4259 Evaluate side-chains 280 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 277 time to evaluate : 3.101 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.5372 time to fit residues: 6.8302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 207 optimal weight: 2.9990 chunk 278 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 chunk 241 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 72 optimal weight: 0.4980 chunk 262 optimal weight: 4.9990 chunk 109 optimal weight: 0.7980 chunk 269 optimal weight: 50.0000 chunk 33 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 406 GLN ** J 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 GLN ** M 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.163150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.113845 restraints weight = 143734.012| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 4.20 r_work: 0.3075 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 26280 Z= 0.164 Angle : 0.448 6.697 35504 Z= 0.228 Chirality : 0.039 0.141 4149 Planarity : 0.003 0.063 4570 Dihedral : 4.851 67.873 3607 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer Outliers : 0.04 % 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: 0.93 (0.15), residues: 3274 helix: 1.54 (0.13), residues: 1640 sheet: 0.03 (0.21), residues: 552 loop : -0.39 (0.19), residues: 1082 =============================================================================== Job complete usr+sys time: 9290.72 seconds wall clock time: 162 minutes 15.63 seconds (9735.63 seconds total)