Starting phenix.real_space_refine on Tue Mar 26 00:05:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wsg_21892/03_2024/6wsg_21892_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wsg_21892/03_2024/6wsg_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_21892/03_2024/6wsg_21892.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wsg_21892/03_2024/6wsg_21892.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wsg_21892/03_2024/6wsg_21892_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wsg_21892/03_2024/6wsg_21892_trim_updated.pdb" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 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 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. 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 21.56, per 1000 atoms: 0.41 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: 41.59 Conformation dependent library (CDL) restraints added in 5.6 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: 7.91 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: 20.42 Time building geometry restraints manager: 43.04 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: 21539 18.00 - 36.00: 2154 36.00 - 53.99: 526 53.99 - 71.99: 119 71.99 - 89.99: 26 Dihedral angle restraints: 24364 sinusoidal: 13755 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 24361 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 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: 3.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.730 Extract box with map and model: 15.630 Check model and map are aligned: 0.730 Set scattering table: 0.440 Process input model: 159.490 Find NCS groups from input model: 2.670 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 186.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 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 : 13.604 89.988 9986 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 % Allowed : 1.51 % Favored : 98.46 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS L 122 PHE 0.022 0.002 PHE K 17 TYR 0.027 0.002 TYR C 77 ARG 0.006 0.001 ARG F 307 *********************** 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 : 4.071 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 REVERT: L 7 ILE cc_start: 0.8677 (tt) cc_final: 0.7848 (tt) REVERT: L 153 MET cc_start: 0.2287 (mmm) cc_final: 0.1832 (mmm) REVERT: I 39 MET cc_start: 0.3879 (ppp) cc_final: 0.2591 (ppp) REVERT: I 78 ASP cc_start: 0.7223 (m-30) cc_final: 0.6941 (m-30) REVERT: I 153 MET cc_start: 0.1175 (mmm) cc_final: 0.0539 (mmm) REVERT: H 42 LEU cc_start: 0.8790 (tp) cc_final: 0.8491 (tp) REVERT: N 8 GLU cc_start: 0.6801 (tt0) cc_final: 0.6158 (tt0) REVERT: N 87 VAL cc_start: 0.9306 (t) cc_final: 0.8880 (t) REVERT: N 153 MET cc_start: 0.1322 (mmm) cc_final: 0.0743 (mmm) outliers start: 1 outliers final: 0 residues processed: 454 average time/residue: 0.9883 time to fit residues: 670.7160 Evaluate side-chains 312 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 312 time to evaluate : 4.183 ------------------------------------------------------------------------------- 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: 0.0970 chunk 250 optimal weight: 20.0000 chunk 138 optimal weight: 0.5980 chunk 85 optimal weight: 0.8980 chunk 168 optimal weight: 0.9980 chunk 133 optimal weight: 0.2980 chunk 258 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 157 optimal weight: 0.6980 chunk 192 optimal weight: 0.9990 chunk 299 optimal weight: 2.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- 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 406 GLN D 95 HIS D 406 GLN F 81 GLN F 208 GLN L 41 ASN ** J 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 ASN I 116 ASN H 116 ASN N 41 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.1697 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= 0.179 Angle : 0.513 5.989 35504 Z= 0.268 Chirality : 0.040 0.149 4149 Planarity : 0.004 0.049 4570 Dihedral : 6.055 67.500 3662 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.61 % Allowed : 6.02 % Favored : 93.37 % 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: -0.16 (0.14), residues: 3274 helix: 0.55 (0.12), residues: 1620 sheet: -0.07 (0.22), residues: 465 loop : -0.91 (0.16), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 95 PHE 0.011 0.001 PHE H 101 TYR 0.011 0.001 TYR F 96 ARG 0.006 0.000 ARG C 351 *********************** 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 359 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 342 time to evaluate : 3.991 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 revert: symmetry clash REVERT: L 153 MET cc_start: 0.2240 (mmm) cc_final: 0.1743 (mmm) REVERT: I 39 MET cc_start: 0.4114 (ppp) cc_final: 0.3008 (ppp) REVERT: I 153 MET cc_start: 0.1158 (mmm) cc_final: 0.0441 (mmm) REVERT: H 47 MET cc_start: 0.8262 (mtt) cc_final: 0.8029 (mtt) REVERT: N 5 MET cc_start: 0.4965 (mmm) cc_final: 0.4681 (mmm) outliers start: 17 outliers final: 15 residues processed: 351 average time/residue: 0.9215 time to fit residues: 503.7943 Evaluate side-chains 326 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 311 time to evaluate : 3.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 356 ASP Chi-restraints excluded: chain E residue 106 ASN Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain J residue 108 LYS Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain I residue 77 TYR Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 113 CYS Chi-restraints excluded: chain N residue 86 ASP Chi-restraints excluded: chain S residue 274 ASN 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: 1.9990 chunk 204 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 300 optimal weight: 8.9990 chunk 324 optimal weight: 20.0000 chunk 267 optimal weight: 50.0000 chunk 297 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 240 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 406 GLN D 406 GLN ** K 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 116 ASN ** J 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 26280 Z= 0.270 Angle : 0.477 4.901 35504 Z= 0.248 Chirality : 0.040 0.151 4149 Planarity : 0.003 0.063 4570 Dihedral : 5.871 69.709 3662 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.36 % Allowed : 7.71 % Favored : 91.93 % 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: 0.15 (0.14), residues: 3274 helix: 0.81 (0.13), residues: 1631 sheet: 0.13 (0.23), residues: 463 loop : -0.81 (0.17), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 260 PHE 0.010 0.001 PHE N 101 TYR 0.012 0.001 TYR F 96 ARG 0.004 0.000 ARG C 178 *********************** 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 322 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 312 time to evaluate : 3.980 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: L 153 MET cc_start: 0.2231 (mmm) cc_final: 0.1773 (mmm) REVERT: K 153 MET cc_start: 0.1558 (mmm) cc_final: 0.1137 (mmm) REVERT: I 39 MET cc_start: 0.4152 (ppp) cc_final: 0.3022 (ppp) REVERT: I 153 MET cc_start: 0.1249 (mmm) cc_final: 0.0518 (mmm) REVERT: N 5 MET cc_start: 0.4740 (mmm) cc_final: 0.4519 (mmm) outliers start: 10 outliers final: 9 residues processed: 316 average time/residue: 0.9147 time to fit residues: 445.6683 Evaluate side-chains 315 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 306 time to evaluate : 3.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 16 SER Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain I residue 77 TYR Chi-restraints excluded: chain I residue 113 CYS Chi-restraints excluded: chain H residue 113 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 296 optimal weight: 3.9990 chunk 225 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 201 optimal weight: 2.9990 chunk 301 optimal weight: 7.9990 chunk 318 optimal weight: 0.8980 chunk 157 optimal weight: 0.6980 chunk 285 optimal weight: 40.0000 chunk 85 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 9 GLN ** J 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.2352 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= 0.223 Angle : 0.454 5.735 35504 Z= 0.234 Chirality : 0.040 0.147 4149 Planarity : 0.004 0.069 4570 Dihedral : 5.780 70.627 3662 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.54 % Allowed : 8.07 % Favored : 91.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.14), residues: 3274 helix: 1.04 (0.13), residues: 1635 sheet: 0.14 (0.22), residues: 505 loop : -0.62 (0.17), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS D 260 PHE 0.007 0.001 PHE I 82 TYR 0.016 0.001 TYR F 96 ARG 0.018 0.000 ARG C 178 *********************** 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 336 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 321 time to evaluate : 4.285 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: L 94 GLN cc_start: 0.7253 (pt0) cc_final: 0.7034 (pt0) REVERT: L 153 MET cc_start: 0.2150 (mmm) cc_final: 0.1688 (mmm) REVERT: I 39 MET cc_start: 0.4187 (ppp) cc_final: 0.3038 (ppp) REVERT: I 153 MET cc_start: 0.1323 (mmm) cc_final: 0.0578 (mmm) outliers start: 15 outliers final: 12 residues processed: 326 average time/residue: 0.9605 time to fit residues: 482.2676 Evaluate side-chains 316 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 304 time to evaluate : 4.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 16 SER Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain I residue 113 CYS Chi-restraints excluded: chain H residue 51 GLU Chi-restraints excluded: chain H residue 113 CYS Chi-restraints excluded: chain S residue 274 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 265 optimal weight: 40.0000 chunk 181 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 237 optimal weight: 2.9990 chunk 131 optimal weight: 0.6980 chunk 272 optimal weight: 6.9990 chunk 220 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 162 optimal weight: 0.8980 chunk 286 optimal weight: 40.0000 chunk 80 optimal weight: 1.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 116 ASN ** J 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 26280 Z= 0.252 Angle : 0.458 9.499 35504 Z= 0.235 Chirality : 0.040 0.148 4149 Planarity : 0.003 0.058 4570 Dihedral : 5.753 71.156 3662 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.65 % Allowed : 8.43 % Favored : 90.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.15), residues: 3274 helix: 1.12 (0.13), residues: 1647 sheet: 0.22 (0.22), residues: 505 loop : -0.52 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS D 260 PHE 0.007 0.001 PHE B 298 TYR 0.017 0.001 TYR F 96 ARG 0.005 0.000 ARG K 111 *********************** 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 329 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 311 time to evaluate : 3.905 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: L 94 GLN cc_start: 0.7269 (pt0) cc_final: 0.7006 (pt0) REVERT: L 153 MET cc_start: 0.2215 (mmm) cc_final: 0.1696 (mmm) REVERT: I 39 MET cc_start: 0.4176 (ppp) cc_final: 0.3036 (ppp) REVERT: I 153 MET cc_start: 0.1329 (mmm) cc_final: 0.0572 (mmm) REVERT: M 12 ARG cc_start: 0.7058 (mtp180) cc_final: 0.6812 (mtp180) outliers start: 18 outliers final: 14 residues processed: 319 average time/residue: 0.9746 time to fit residues: 484.1027 Evaluate side-chains 312 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 298 time to evaluate : 4.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 390 MET Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain L residue 16 SER Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 91 CYS Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain I residue 113 CYS Chi-restraints excluded: chain H residue 51 GLU Chi-restraints excluded: chain H residue 113 CYS Chi-restraints excluded: chain N residue 14 GLU Chi-restraints excluded: chain S residue 274 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 107 optimal weight: 0.7980 chunk 287 optimal weight: 50.0000 chunk 63 optimal weight: 1.9990 chunk 187 optimal weight: 1.9990 chunk 78 optimal weight: 0.0370 chunk 319 optimal weight: 30.0000 chunk 265 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 167 optimal weight: 0.9990 overall best weight: 0.7662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 41 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 26280 Z= 0.156 Angle : 0.428 6.301 35504 Z= 0.219 Chirality : 0.039 0.154 4149 Planarity : 0.003 0.061 4570 Dihedral : 5.546 70.871 3662 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.54 % Allowed : 8.86 % Favored : 90.61 % 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: 0.81 (0.15), residues: 3274 helix: 1.34 (0.13), residues: 1641 sheet: 0.18 (0.22), residues: 527 loop : -0.38 (0.18), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 68 PHE 0.012 0.001 PHE C 350 TYR 0.014 0.001 TYR F 96 ARG 0.006 0.000 ARG K 111 *********************** 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 322 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 307 time to evaluate : 4.081 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: L 94 GLN cc_start: 0.7245 (pt0) cc_final: 0.6997 (pt0) REVERT: L 153 MET cc_start: 0.2117 (mmm) cc_final: 0.1627 (mmm) REVERT: I 39 MET cc_start: 0.4150 (ppp) cc_final: 0.3023 (ppp) outliers start: 15 outliers final: 15 residues processed: 314 average time/residue: 0.9263 time to fit residues: 449.9002 Evaluate side-chains 313 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 298 time to evaluate : 3.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain L residue 16 SER Chi-restraints excluded: chain L residue 120 MET Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 91 CYS Chi-restraints excluded: chain J residue 108 LYS Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain I residue 113 CYS Chi-restraints excluded: chain H residue 51 GLU Chi-restraints excluded: chain H residue 113 CYS Chi-restraints excluded: chain M residue 5 MET Chi-restraints excluded: chain S residue 274 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 307 optimal weight: 10.0000 chunk 35 optimal weight: 0.7980 chunk 181 optimal weight: 3.9990 chunk 233 optimal weight: 3.9990 chunk 180 optimal weight: 1.9990 chunk 268 optimal weight: 50.0000 chunk 178 optimal weight: 0.5980 chunk 318 optimal weight: 0.7980 chunk 199 optimal weight: 3.9990 chunk 193 optimal weight: 5.9990 chunk 146 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 406 GLN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 81 GLN ** J 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 116 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 26280 Z= 0.225 Angle : 0.442 4.792 35504 Z= 0.227 Chirality : 0.039 0.146 4149 Planarity : 0.003 0.060 4570 Dihedral : 5.389 71.618 3662 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.61 % Allowed : 9.00 % Favored : 90.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.15), residues: 3274 helix: 1.39 (0.13), residues: 1648 sheet: 0.24 (0.22), residues: 499 loop : -0.38 (0.18), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 73 PHE 0.017 0.001 PHE L 101 TYR 0.015 0.001 TYR F 96 ARG 0.007 0.000 ARG K 111 *********************** 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 318 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 301 time to evaluate : 4.158 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: L 94 GLN cc_start: 0.7259 (pt0) cc_final: 0.7035 (pt0) REVERT: L 153 MET cc_start: 0.2124 (mmm) cc_final: 0.1607 (mmm) REVERT: I 39 MET cc_start: 0.4158 (ppp) cc_final: 0.3024 (ppp) outliers start: 17 outliers final: 16 residues processed: 309 average time/residue: 0.9302 time to fit residues: 446.7096 Evaluate side-chains 313 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 297 time to evaluate : 3.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain L residue 16 SER Chi-restraints excluded: chain L residue 120 MET Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 91 CYS Chi-restraints excluded: chain J residue 108 LYS Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain I residue 113 CYS Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain H residue 51 GLU Chi-restraints excluded: chain H residue 113 CYS Chi-restraints excluded: chain N residue 14 GLU Chi-restraints excluded: chain S residue 274 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 196 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 189 optimal weight: 6.9990 chunk 95 optimal weight: 0.5980 chunk 62 optimal weight: 0.1980 chunk 61 optimal weight: 0.8980 chunk 202 optimal weight: 0.5980 chunk 216 optimal weight: 1.9990 chunk 157 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 250 optimal weight: 10.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 116 ASN M 41 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 26280 Z= 0.146 Angle : 0.423 5.380 35504 Z= 0.216 Chirality : 0.039 0.144 4149 Planarity : 0.003 0.060 4570 Dihedral : 5.244 71.153 3662 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.61 % Allowed : 9.29 % Favored : 90.10 % 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: 1.49 (0.13), residues: 1648 sheet: 0.23 (0.21), residues: 527 loop : -0.29 (0.19), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 68 PHE 0.013 0.001 PHE L 101 TYR 0.015 0.001 TYR J 77 ARG 0.008 0.000 ARG K 111 *********************** 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 320 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 303 time to evaluate : 3.950 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: L 94 GLN cc_start: 0.7255 (pt0) cc_final: 0.7047 (pt0) REVERT: L 153 MET cc_start: 0.2044 (mmm) cc_final: 0.1540 (mmm) REVERT: I 39 MET cc_start: 0.4145 (ppp) cc_final: 0.2994 (ppp) REVERT: N 15 ARG cc_start: 0.7840 (ptp-170) cc_final: 0.7564 (ptt-90) outliers start: 17 outliers final: 13 residues processed: 310 average time/residue: 0.9618 time to fit residues: 464.1935 Evaluate side-chains 310 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 297 time to evaluate : 3.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain L residue 16 SER Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 91 CYS Chi-restraints excluded: chain J residue 108 LYS Chi-restraints excluded: chain I residue 113 CYS Chi-restraints excluded: chain H residue 51 GLU Chi-restraints excluded: chain H residue 113 CYS Chi-restraints excluded: chain M residue 5 MET Chi-restraints excluded: chain M residue 41 ASN Chi-restraints excluded: chain S residue 274 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 289 optimal weight: 9.9990 chunk 304 optimal weight: 40.0000 chunk 278 optimal weight: 0.0040 chunk 296 optimal weight: 0.6980 chunk 178 optimal weight: 0.0980 chunk 129 optimal weight: 1.9990 chunk 232 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 267 optimal weight: 50.0000 chunk 280 optimal weight: 0.8980 chunk 295 optimal weight: 5.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 81 GLN ** 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: 0.7236 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 26280 Z= 0.147 Angle : 0.574 59.197 35504 Z= 0.321 Chirality : 0.039 0.145 4149 Planarity : 0.003 0.057 4570 Dihedral : 5.236 71.156 3662 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.54 % Allowed : 9.39 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.15), residues: 3274 helix: 1.50 (0.13), residues: 1648 sheet: 0.23 (0.21), residues: 527 loop : -0.27 (0.19), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 73 PHE 0.012 0.001 PHE L 101 TYR 0.015 0.001 TYR F 96 ARG 0.006 0.000 ARG K 111 *********************** 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 311 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 296 time to evaluate : 3.976 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: L 94 GLN cc_start: 0.7250 (pt0) cc_final: 0.7047 (pt0) REVERT: L 153 MET cc_start: 0.2043 (mmm) cc_final: 0.1546 (mmm) REVERT: I 39 MET cc_start: 0.4136 (ppp) cc_final: 0.2993 (ppp) outliers start: 15 outliers final: 14 residues processed: 302 average time/residue: 0.9686 time to fit residues: 456.0701 Evaluate side-chains 310 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 296 time to evaluate : 3.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain L residue 16 SER Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 91 CYS Chi-restraints excluded: chain J residue 108 LYS Chi-restraints excluded: chain I residue 113 CYS Chi-restraints excluded: chain H residue 51 GLU Chi-restraints excluded: chain H residue 113 CYS Chi-restraints excluded: chain M residue 5 MET Chi-restraints excluded: chain S residue 274 ASN 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: 4.9990 chunk 191 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 chunk 217 optimal weight: 0.0170 chunk 328 optimal weight: 10.0000 chunk 302 optimal weight: 2.9990 chunk 261 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 202 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 overall best weight: 1.8024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7236 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 26280 Z= 0.147 Angle : 0.574 59.197 35504 Z= 0.321 Chirality : 0.039 0.145 4149 Planarity : 0.003 0.057 4570 Dihedral : 5.236 71.156 3662 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.50 % Allowed : 9.39 % Favored : 90.10 % 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: 1.01 (0.15), residues: 3274 helix: 1.50 (0.13), residues: 1648 sheet: 0.23 (0.21), residues: 527 loop : -0.27 (0.19), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 73 PHE 0.012 0.001 PHE L 101 TYR 0.015 0.001 TYR F 96 ARG 0.006 0.000 ARG K 111 ********************** 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 310 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 296 time to evaluate : 4.007 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: L 94 GLN cc_start: 0.7253 (pt0) cc_final: 0.7047 (pt0) REVERT: L 153 MET cc_start: 0.2046 (mmm) cc_final: 0.1546 (mmm) REVERT: I 39 MET cc_start: 0.4136 (ppp) cc_final: 0.2993 (ppp) outliers start: 14 outliers final: 14 residues processed: 302 average time/residue: 0.9117 time to fit residues: 426.8650 Evaluate side-chains 310 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 296 time to evaluate : 4.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain L residue 16 SER Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 91 CYS Chi-restraints excluded: chain J residue 108 LYS Chi-restraints excluded: chain I residue 113 CYS Chi-restraints excluded: chain H residue 51 GLU Chi-restraints excluded: chain H residue 113 CYS Chi-restraints excluded: chain M residue 5 MET Chi-restraints excluded: chain S residue 274 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 207 optimal weight: 3.9990 chunk 278 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 241 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 262 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 269 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.163187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.116288 restraints weight = 145472.113| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 4.05 r_work: 0.3128 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 26280 Z= 0.147 Angle : 0.574 59.197 35504 Z= 0.321 Chirality : 0.039 0.145 4149 Planarity : 0.003 0.057 4570 Dihedral : 5.236 71.156 3662 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.50 % Allowed : 9.39 % Favored : 90.10 % 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: 1.01 (0.15), residues: 3274 helix: 1.50 (0.13), residues: 1648 sheet: 0.23 (0.21), residues: 527 loop : -0.27 (0.19), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 73 PHE 0.012 0.001 PHE L 101 TYR 0.015 0.001 TYR F 96 ARG 0.006 0.000 ARG K 111 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11151.09 seconds wall clock time: 197 minutes 6.18 seconds (11826.18 seconds total)