Starting phenix.real_space_refine on Tue Feb 20 10:02:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d45_30570/02_2024/7d45_30570_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d45_30570/02_2024/7d45_30570.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d45_30570/02_2024/7d45_30570.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d45_30570/02_2024/7d45_30570.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d45_30570/02_2024/7d45_30570_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d45_30570/02_2024/7d45_30570_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 142 5.16 5 C 17407 2.51 5 N 4827 2.21 5 O 5152 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 3": "OD1" <-> "OD2" Residue "A GLU 8": "OE1" <-> "OE2" Residue "A ARG 28": "NH1" <-> "NH2" Residue "A ASP 60": "OD1" <-> "OD2" Residue "A ARG 74": "NH1" <-> "NH2" Residue "A PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 132": "NH1" <-> "NH2" Residue "A ARG 147": "NH1" <-> "NH2" Residue "A PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 248": "OD1" <-> "OD2" Residue "A TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 16": "OE1" <-> "OE2" Residue "B ASP 37": "OD1" <-> "OD2" Residue "B GLU 54": "OE1" <-> "OE2" Residue "B ARG 74": "NH1" <-> "NH2" Residue "B GLU 82": "OE1" <-> "OE2" Residue "B GLU 95": "OE1" <-> "OE2" Residue "B ARG 132": "NH1" <-> "NH2" Residue "B ARG 136": "NH1" <-> "NH2" Residue "B PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 274": "OD1" <-> "OD2" Residue "B PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 298": "OD1" <-> "OD2" Residue "B GLU 299": "OE1" <-> "OE2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C GLU 59": "OE1" <-> "OE2" Residue "C ARG 90": "NH1" <-> "NH2" Residue "C GLU 135": "OE1" <-> "OE2" Residue "C GLU 202": "OE1" <-> "OE2" Residue "C ASP 219": "OD1" <-> "OD2" Residue "C PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 304": "OE1" <-> "OE2" Residue "C ARG 338": "NH1" <-> "NH2" Residue "D GLU 33": "OE1" <-> "OE2" Residue "D ARG 43": "NH1" <-> "NH2" Residue "D ARG 63": "NH1" <-> "NH2" Residue "D GLU 92": "OE1" <-> "OE2" Residue "D GLU 139": "OE1" <-> "OE2" Residue "D PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 219": "OD1" <-> "OD2" Residue "D PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 301": "OD1" <-> "OD2" Residue "E PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 44": "OE1" <-> "OE2" Residue "E ASP 81": "OD1" <-> "OD2" Residue "E ASP 111": "OD1" <-> "OD2" Residue "E ASP 125": "OD1" <-> "OD2" Residue "E ARG 133": "NH1" <-> "NH2" Residue "E ARG 155": "NH1" <-> "NH2" Residue "E ARG 166": "NH1" <-> "NH2" Residue "E ARG 192": "NH1" <-> "NH2" Residue "E ARG 194": "NH1" <-> "NH2" Residue "E ASP 213": "OD1" <-> "OD2" Residue "E PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 269": "OE1" <-> "OE2" Residue "E ARG 286": "NH1" <-> "NH2" Residue "E GLU 291": "OE1" <-> "OE2" Residue "F ASP 80": "OD1" <-> "OD2" Residue "F ASP 81": "OD1" <-> "OD2" Residue "F ASP 100": "OD1" <-> "OD2" Residue "F ASP 111": "OD1" <-> "OD2" Residue "F TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 125": "OD1" <-> "OD2" Residue "F ARG 133": "NH1" <-> "NH2" Residue "F GLU 178": "OE1" <-> "OE2" Residue "F ARG 192": "NH1" <-> "NH2" Residue "F TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 286": "NH1" <-> "NH2" Residue "F ASP 288": "OD1" <-> "OD2" Residue "F GLU 291": "OE1" <-> "OE2" Residue "G ASP 239": "OD1" <-> "OD2" Residue "G TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 344": "NH1" <-> "NH2" Residue "G PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 362": "OD1" <-> "OD2" Residue "G TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 417": "NH1" <-> "NH2" Residue "G GLU 445": "OE1" <-> "OE2" Residue "G ARG 446": "NH1" <-> "NH2" Residue "G ASP 458": "OD1" <-> "OD2" Residue "G GLU 469": "OE1" <-> "OE2" Residue "G GLU 495": "OE1" <-> "OE2" Residue "G ASP 498": "OD1" <-> "OD2" Residue "G ARG 517": "NH1" <-> "NH2" Residue "H TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 344": "NH1" <-> "NH2" Residue "H ASP 362": "OD1" <-> "OD2" Residue "H TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 417": "NH1" <-> "NH2" Residue "H ARG 446": "NH1" <-> "NH2" Residue "H PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 456": "OE1" <-> "OE2" Residue "H ASP 458": "OD1" <-> "OD2" Residue "H ASP 490": "OD1" <-> "OD2" Residue "H ARG 517": "NH1" <-> "NH2" Residue "I PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 65": "NH1" <-> "NH2" Residue "I TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 81": "OE1" <-> "OE2" Residue "I TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 154": "OD1" <-> "OD2" Residue "I ASP 199": "OD1" <-> "OD2" Residue "I PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 269": "NH1" <-> "NH2" Residue "I GLU 295": "OE1" <-> "OE2" Residue "I ARG 299": "NH1" <-> "NH2" Residue "I TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 455": "OD1" <-> "OD2" Residue "I GLU 458": "OE1" <-> "OE2" Residue "J ARG 65": "NH1" <-> "NH2" Residue "J TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 133": "OD1" <-> "OD2" Residue "J ARG 195": "NH1" <-> "NH2" Residue "J ARG 211": "NH1" <-> "NH2" Residue "J PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 265": "OD1" <-> "OD2" Residue "J ARG 269": "NH1" <-> "NH2" Residue "J GLU 281": "OE1" <-> "OE2" Residue "J ARG 299": "NH1" <-> "NH2" Residue "J TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 316": "NH1" <-> "NH2" Residue "J GLU 357": "OE1" <-> "OE2" Residue "J PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 421": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 27529 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2265 Classifications: {'peptide': 293} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 283} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2256 Classifications: {'peptide': 291} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 281} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 2476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2476 Classifications: {'peptide': 317} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 302} Chain breaks: 1 Chain: "D" Number of atoms: 2515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2515 Classifications: {'peptide': 324} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 309} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "E" Number of atoms: 2445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2445 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 11, 'TRANS': 334} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 258 Unresolved non-hydrogen angles: 323 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 4, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 99 Chain: "F" Number of atoms: 2465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2465 Classifications: {'peptide': 350} Incomplete info: {'truncation_to_alanine': 95} Link IDs: {'PTRANS': 12, 'TRANS': 337} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 266 Unresolved non-hydrogen angles: 333 Unresolved non-hydrogen dihedrals: 203 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 4, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 99 Chain: "G" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2750 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 334} Chain: "H" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2750 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 334} Chain: "I" Number of atoms: 3355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3355 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 3363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3363 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 409} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "K" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 889 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 158} Link IDs: {'PTRANS': 4, 'TRANS': 171} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 585 Unresolved non-hydrogen angles: 743 Unresolved non-hydrogen dihedrals: 481 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 12, 'TYR:plan': 9, 'ASN:plan1': 9, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 6, 'GLU:plan': 18, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 340 Time building chain proxies: 14.05, per 1000 atoms: 0.51 Number of scatterers: 27529 At special positions: 0 Unit cell: (164.64, 167.58, 163.17, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 142 16.00 P 1 15.00 O 5152 8.00 N 4827 7.00 C 17407 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.06 Conformation dependent library (CDL) restraints added in 5.5 seconds 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6938 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 120 helices and 36 sheets defined 34.9% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.48 Creating SS restraints... Processing helix chain 'A' and resid 5 through 16 Processing helix chain 'A' and resid 22 through 35 Processing helix chain 'A' and resid 43 through 57 removed outlier: 3.646A pdb=" N ALA A 47 " --> pdb=" O GLN A 43 " (cutoff:3.500A) WARNING: missing atoms! Processing helix chain 'A' and resid 63 through 75 Processing helix chain 'A' and resid 88 through 115 removed outlier: 4.670A pdb=" N ARG A 108 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ASN A 109 " --> pdb=" O SER A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 144 removed outlier: 3.871A pdb=" N ALA A 144 " --> pdb=" O ALA A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 171 removed outlier: 4.826A pdb=" N LEU A 171 " --> pdb=" O ALA A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 189 removed outlier: 4.006A pdb=" N GLY A 184 " --> pdb=" O ALA A 181 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ILE A 186 " --> pdb=" O VAL A 183 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N MET A 187 " --> pdb=" O GLY A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 221 removed outlier: 4.011A pdb=" N ASN A 213 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN A 214 " --> pdb=" O GLY A 211 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA A 219 " --> pdb=" O ALA A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 251 No H-bonds generated for 'chain 'A' and resid 248 through 251' Processing helix chain 'A' and resid 295 through 303 Processing helix chain 'B' and resid 3 through 16 Processing helix chain 'B' and resid 22 through 35 Processing helix chain 'B' and resid 46 through 59 removed outlier: 3.728A pdb=" N SER B 51 " --> pdb=" O ALA B 47 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY B 58 " --> pdb=" O GLU B 54 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N VAL B 59 " --> pdb=" O THR B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 76 Processing helix chain 'B' and resid 87 through 115 removed outlier: 3.926A pdb=" N LYS B 91 " --> pdb=" O SER B 87 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ARG B 108 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N ASN B 109 " --> pdb=" O SER B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 143 Processing helix chain 'B' and resid 161 through 171 removed outlier: 4.021A pdb=" N LEU B 171 " --> pdb=" O ALA B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 188 removed outlier: 4.864A pdb=" N GLU B 188 " --> pdb=" O GLY B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 221 removed outlier: 3.983A pdb=" N ASN B 213 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLN B 214 " --> pdb=" O GLY B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 245 No H-bonds generated for 'chain 'B' and resid 243 through 245' Processing helix chain 'B' and resid 293 through 303 removed outlier: 3.503A pdb=" N LYS B 302 " --> pdb=" O GLU B 299 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 303 " --> pdb=" O LEU B 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 23 Processing helix chain 'C' and resid 31 through 48 Processing helix chain 'C' and resid 54 through 71 Processing helix chain 'C' and resid 77 through 95 Processing helix chain 'C' and resid 129 through 158 removed outlier: 3.845A pdb=" N GLY C 146 " --> pdb=" O VAL C 142 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR C 147 " --> pdb=" O GLU C 143 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N MET C 148 " --> pdb=" O LEU C 144 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N GLU C 149 " --> pdb=" O GLU C 145 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU C 156 " --> pdb=" O ALA C 152 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N GLU C 157 " --> pdb=" O ALA C 153 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N HIS C 158 " --> pdb=" O GLN C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 182 removed outlier: 3.668A pdb=" N ALA C 181 " --> pdb=" O PHE C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 210 removed outlier: 4.351A pdb=" N ALA C 210 " --> pdb=" O ASN C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 225 removed outlier: 4.559A pdb=" N PHE C 223 " --> pdb=" O ALA C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 261 removed outlier: 3.885A pdb=" N HIS C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 303 No H-bonds generated for 'chain 'C' and resid 301 through 303' Processing helix chain 'C' and resid 334 through 343 Processing helix chain 'C' and resid 347 through 349 No H-bonds generated for 'chain 'C' and resid 347 through 349' Processing helix chain 'D' and resid 9 through 24 Processing helix chain 'D' and resid 31 through 46 Processing helix chain 'D' and resid 55 through 71 removed outlier: 4.076A pdb=" N ARG D 67 " --> pdb=" O ARG D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 96 Processing helix chain 'D' and resid 128 through 145 Processing helix chain 'D' and resid 147 through 155 Processing helix chain 'D' and resid 172 through 183 removed outlier: 4.563A pdb=" N ARG D 183 " --> pdb=" O LYS D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 210 removed outlier: 3.796A pdb=" N ALA D 210 " --> pdb=" O ASN D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 221 No H-bonds generated for 'chain 'D' and resid 219 through 221' Processing helix chain 'D' and resid 251 through 260 Processing helix chain 'D' and resid 291 through 293 No H-bonds generated for 'chain 'D' and resid 291 through 293' Processing helix chain 'D' and resid 297 through 299 No H-bonds generated for 'chain 'D' and resid 297 through 299' Processing helix chain 'D' and resid 301 through 303 No H-bonds generated for 'chain 'D' and resid 301 through 303' Processing helix chain 'D' and resid 333 through 343 removed outlier: 4.749A pdb=" N TYR D 337 " --> pdb=" O SER D 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 44 Proline residue: E 39 - end of helix Processing helix chain 'E' and resid 63 through 66 No H-bonds generated for 'chain 'E' and resid 63 through 66' Processing helix chain 'E' and resid 86 through 96 Proline residue: E 95 - end of helix Processing helix chain 'E' and resid 115 through 123 Processing helix chain 'E' and resid 184 through 189 Processing helix chain 'E' and resid 209 through 217 Processing helix chain 'E' and resid 229 through 237 removed outlier: 4.927A pdb=" N PHE E 237 " --> pdb=" O VAL E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 294 removed outlier: 4.330A pdb=" N TRP E 290 " --> pdb=" O ARG E 286 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU E 293 " --> pdb=" O ARG E 289 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER E 294 " --> pdb=" O TRP E 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 45 Proline residue: F 39 - end of helix removed outlier: 4.053A pdb=" N ARG F 45 " --> pdb=" O LEU F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 96 Proline residue: F 95 - end of helix Processing helix chain 'F' and resid 114 through 124 Processing helix chain 'F' and resid 184 through 189 Processing helix chain 'F' and resid 209 through 217 Processing helix chain 'F' and resid 224 through 227 No H-bonds generated for 'chain 'F' and resid 224 through 227' Processing helix chain 'F' and resid 229 through 235 Processing helix chain 'F' and resid 278 through 291 removed outlier: 4.130A pdb=" N ASN F 283 " --> pdb=" O ASP F 279 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N TRP F 290 " --> pdb=" O ARG F 286 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 180 No H-bonds generated for 'chain 'G' and resid 178 through 180' Processing helix chain 'G' and resid 192 through 195 Processing helix chain 'G' and resid 205 through 215 Processing helix chain 'G' and resid 222 through 238 Processing helix chain 'G' and resid 248 through 266 removed outlier: 4.414A pdb=" N VAL G 253 " --> pdb=" O SER G 249 " (cutoff:3.500A) Proline residue: G 258 - end of helix Processing helix chain 'G' and resid 271 through 285 Processing helix chain 'G' and resid 293 through 311 Processing helix chain 'G' and resid 314 through 325 removed outlier: 4.112A pdb=" N GLN G 325 " --> pdb=" O ARG G 321 " (cutoff:3.500A) Processing helix chain 'G' and resid 340 through 350 Processing helix chain 'G' and resid 370 through 379 removed outlier: 4.344A pdb=" N ALA G 379 " --> pdb=" O SER G 375 " (cutoff:3.500A) Processing helix chain 'G' and resid 388 through 394 removed outlier: 4.415A pdb=" N SER G 392 " --> pdb=" O PRO G 389 " (cutoff:3.500A) Processing helix chain 'G' and resid 420 through 430 Processing helix chain 'G' and resid 460 through 463 Processing helix chain 'G' and resid 510 through 516 Proline residue: G 513 - end of helix removed outlier: 3.801A pdb=" N LEU G 516 " --> pdb=" O PRO G 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 510 through 516' Processing helix chain 'H' and resid 178 through 180 No H-bonds generated for 'chain 'H' and resid 178 through 180' Processing helix chain 'H' and resid 192 through 195 Processing helix chain 'H' and resid 205 through 215 Processing helix chain 'H' and resid 222 through 238 Processing helix chain 'H' and resid 248 through 266 removed outlier: 4.638A pdb=" N VAL H 253 " --> pdb=" O SER H 249 " (cutoff:3.500A) Proline residue: H 258 - end of helix Processing helix chain 'H' and resid 271 through 286 removed outlier: 3.636A pdb=" N SER H 286 " --> pdb=" O LYS H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 293 through 311 Processing helix chain 'H' and resid 314 through 323 Processing helix chain 'H' and resid 341 through 351 Processing helix chain 'H' and resid 369 through 377 Processing helix chain 'H' and resid 388 through 396 removed outlier: 5.169A pdb=" N SER H 392 " --> pdb=" O PRO H 389 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N LEU H 395 " --> pdb=" O SER H 392 " (cutoff:3.500A) Proline residue: H 396 - end of helix Processing helix chain 'H' and resid 420 through 429 Processing helix chain 'H' and resid 460 through 462 No H-bonds generated for 'chain 'H' and resid 460 through 462' Processing helix chain 'H' and resid 509 through 511 No H-bonds generated for 'chain 'H' and resid 509 through 511' Processing helix chain 'I' and resid 65 through 67 No H-bonds generated for 'chain 'I' and resid 65 through 67' Processing helix chain 'I' and resid 75 through 86 removed outlier: 3.514A pdb=" N THR I 86 " --> pdb=" O PHE I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 99 through 107 Processing helix chain 'I' and resid 132 through 141 Processing helix chain 'I' and resid 162 through 175 Processing helix chain 'I' and resid 197 through 199 No H-bonds generated for 'chain 'I' and resid 197 through 199' Processing helix chain 'I' and resid 228 through 231 Processing helix chain 'I' and resid 254 through 262 removed outlier: 3.761A pdb=" N THR I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 278 Processing helix chain 'I' and resid 303 through 314 Processing helix chain 'I' and resid 339 through 341 No H-bonds generated for 'chain 'I' and resid 339 through 341' Processing helix chain 'J' and resid 59 through 61 No H-bonds generated for 'chain 'J' and resid 59 through 61' Processing helix chain 'J' and resid 65 through 67 No H-bonds generated for 'chain 'J' and resid 65 through 67' Processing helix chain 'J' and resid 75 through 85 Processing helix chain 'J' and resid 99 through 107 Processing helix chain 'J' and resid 131 through 141 Processing helix chain 'J' and resid 162 through 175 removed outlier: 3.712A pdb=" N GLU J 175 " --> pdb=" O ARG J 171 " (cutoff:3.500A) Processing helix chain 'J' and resid 229 through 234 Processing helix chain 'J' and resid 254 through 262 Processing helix chain 'J' and resid 269 through 276 Processing helix chain 'J' and resid 303 through 313 Processing helix chain 'J' and resid 339 through 341 No H-bonds generated for 'chain 'J' and resid 339 through 341' Processing helix chain 'K' and resid 53 through 55 No H-bonds generated for 'chain 'K' and resid 53 through 55' Processing helix chain 'K' and resid 60 through 64 Processing helix chain 'K' and resid 91 through 117 Processing helix chain 'K' and resid 123 through 138 Processing helix chain 'K' and resid 147 through 156 removed outlier: 5.393A pdb=" N VAL K 156 " --> pdb=" O PHE K 152 " (cutoff:3.500A) Processing helix chain 'K' and resid 170 through 179 Processing sheet with id= A, first strand: chain 'A' and resid 289 through 291 removed outlier: 4.150A pdb=" N LEU A 283 " --> pdb=" O PHE A 226 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU A 192 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N SER A 149 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N THR A 127 " --> pdb=" O SER A 149 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N TYR A 151 " --> pdb=" O THR A 127 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 206 through 208 Processing sheet with id= C, first strand: chain 'B' and resid 124 through 127 removed outlier: 6.061A pdb=" N SER B 149 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N THR B 127 " --> pdb=" O SER B 149 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N TYR B 151 " --> pdb=" O THR B 127 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 192 through 195 removed outlier: 7.448A pdb=" N VAL B 195 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR B 227 " --> pdb=" O VAL B 195 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 284 through 286 Processing sheet with id= F, first strand: chain 'C' and resid 164 through 168 removed outlier: 6.557A pdb=" N HIS C 188 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N THR C 167 " --> pdb=" O HIS C 188 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE C 190 " --> pdb=" O THR C 167 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 232 through 234 removed outlier: 3.561A pdb=" N THR C 322 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N VAL C 267 " --> pdb=" O THR C 322 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N PHE C 324 " --> pdb=" O VAL C 267 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 246 through 248 Processing sheet with id= I, first strand: chain 'D' and resid 189 through 193 Processing sheet with id= J, first strand: chain 'D' and resid 231 through 234 removed outlier: 7.422A pdb=" N ILE D 234 " --> pdb=" O PRO D 264 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ILE D 266 " --> pdb=" O ILE D 234 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'D' and resid 245 through 248 Processing sheet with id= L, first strand: chain 'D' and resid 324 through 326 Processing sheet with id= M, first strand: chain 'E' and resid 205 through 207 removed outlier: 7.239A pdb=" N TYR E 264 " --> pdb=" O MET E 130 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N MET E 132 " --> pdb=" O TYR E 264 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N PHE E 266 " --> pdb=" O MET E 132 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 193 through 196 removed outlier: 6.051A pdb=" N ASP E 161 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LEU E 167 " --> pdb=" O ASP E 161 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 362 through 364 removed outlier: 6.852A pdb=" N CYS E 379 " --> pdb=" O GLN E 363 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'F' and resid 3 through 8 removed outlier: 7.172A pdb=" N ASP F 100 " --> pdb=" O GLN F 4 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N VAL F 6 " --> pdb=" O ASP F 100 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N LEU F 102 " --> pdb=" O VAL F 6 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N MET F 8 " --> pdb=" O LEU F 102 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU F 104 " --> pdb=" O MET F 8 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 52 through 55 removed outlier: 7.037A pdb=" N VAL F 76 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N THR F 55 " --> pdb=" O VAL F 76 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ILE F 78 " --> pdb=" O THR F 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'F' and resid 194 through 196 removed outlier: 3.556A pdb=" N PHE F 157 " --> pdb=" O ALA F 171 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA F 171 " --> pdb=" O PHE F 157 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 352 through 354 Processing sheet with id= T, first strand: chain 'G' and resid 332 through 334 removed outlier: 6.287A pdb=" N ARG G 357 " --> pdb=" O ILE G 333 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'G' and resid 360 through 362 Processing sheet with id= V, first strand: chain 'G' and resid 414 through 416 Processing sheet with id= W, first strand: chain 'G' and resid 435 through 437 removed outlier: 5.586A pdb=" N LEU G 499 " --> pdb=" O VAL G 436 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'H' and resid 333 through 336 Processing sheet with id= Y, first strand: chain 'H' and resid 414 through 416 Processing sheet with id= Z, first strand: chain 'H' and resid 500 through 502 Processing sheet with id= AA, first strand: chain 'I' and resid 90 through 94 removed outlier: 6.167A pdb=" N LEU I 149 " --> pdb=" O VAL I 46 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N VAL I 48 " --> pdb=" O LEU I 149 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N VAL I 151 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'I' and resid 155 through 157 Processing sheet with id= AC, first strand: chain 'I' and resid 288 through 292 removed outlier: 3.572A pdb=" N GLU I 187 " --> pdb=" O THR I 292 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'I' and resid 238 through 241 removed outlier: 5.728A pdb=" N ASP I 206 " --> pdb=" O VAL I 212 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL I 212 " --> pdb=" O ASP I 206 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'I' and resid 373 through 375 Processing sheet with id= AF, first strand: chain 'J' and resid 155 through 157 Processing sheet with id= AG, first strand: chain 'J' and resid 238 through 241 removed outlier: 5.328A pdb=" N ASP J 206 " --> pdb=" O VAL J 212 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N VAL J 212 " --> pdb=" O ASP J 206 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'J' and resid 373 through 375 Processing sheet with id= AI, first strand: chain 'K' and resid 18 through 21 removed outlier: 6.907A pdb=" N ASP K 83 " --> pdb=" O ILE K 73 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N VAL K 75 " --> pdb=" O TYR K 81 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N TYR K 81 " --> pdb=" O VAL K 75 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'K' and resid 41 through 46 removed outlier: 3.906A pdb=" N SER K 25 " --> pdb=" O TYR K 32 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N SER K 34 " --> pdb=" O VAL K 23 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N VAL K 23 " --> pdb=" O SER K 34 " (cutoff:3.500A) 901 hydrogen bonds defined for protein. 2472 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: 8.18 Time building geometry restraints manager: 11.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9217 1.34 - 1.46: 4840 1.46 - 1.58: 13726 1.58 - 1.70: 4 1.70 - 1.82: 216 Bond restraints: 28003 Sorted by residual: bond pdb=" CA ALA G 349 " pdb=" C ALA G 349 " ideal model delta sigma weight residual 1.522 1.467 0.055 1.31e-02 5.83e+03 1.74e+01 bond pdb=" CA LEU C 96 " pdb=" C LEU C 96 " ideal model delta sigma weight residual 1.523 1.475 0.048 1.48e-02 4.57e+03 1.03e+01 bond pdb=" CA ARG J 121 " pdb=" CB ARG J 121 " ideal model delta sigma weight residual 1.524 1.483 0.041 1.33e-02 5.65e+03 9.40e+00 bond pdb=" CA ALA D 258 " pdb=" C ALA D 258 " ideal model delta sigma weight residual 1.523 1.485 0.039 1.34e-02 5.57e+03 8.30e+00 bond pdb=" C SER C 275 " pdb=" N PRO C 276 " ideal model delta sigma weight residual 1.331 1.309 0.022 7.90e-03 1.60e+04 7.97e+00 ... (remaining 27998 not shown) Histogram of bond angle deviations from ideal: 97.61 - 105.22: 497 105.22 - 112.82: 15668 112.82 - 120.43: 11352 120.43 - 128.04: 10303 128.04 - 135.65: 205 Bond angle restraints: 38025 Sorted by residual: angle pdb=" C THR G 241 " pdb=" N THR G 242 " pdb=" CA THR G 242 " ideal model delta sigma weight residual 122.67 104.49 18.18 2.19e+00 2.09e-01 6.89e+01 angle pdb=" N VAL J 178 " pdb=" CA VAL J 178 " pdb=" C VAL J 178 " ideal model delta sigma weight residual 113.53 106.31 7.22 9.80e-01 1.04e+00 5.42e+01 angle pdb=" N PRO F 24 " pdb=" CA PRO F 24 " pdb=" CB PRO F 24 " ideal model delta sigma weight residual 103.25 110.96 -7.71 1.05e+00 9.07e-01 5.39e+01 angle pdb=" N PRO F 26 " pdb=" CA PRO F 26 " pdb=" CB PRO F 26 " ideal model delta sigma weight residual 103.25 110.15 -6.90 1.05e+00 9.07e-01 4.32e+01 angle pdb=" N PRO J 40 " pdb=" CA PRO J 40 " pdb=" CB PRO J 40 " ideal model delta sigma weight residual 103.00 110.21 -7.21 1.10e+00 8.26e-01 4.29e+01 ... (remaining 38020 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 14980 17.69 - 35.39: 1650 35.39 - 53.08: 318 53.08 - 70.77: 37 70.77 - 88.47: 19 Dihedral angle restraints: 17004 sinusoidal: 6339 harmonic: 10665 Sorted by residual: dihedral pdb=" CA ALA B 197 " pdb=" C ALA B 197 " pdb=" N GLU B 198 " pdb=" CA GLU B 198 " ideal model delta harmonic sigma weight residual -180.00 -144.57 -35.43 0 5.00e+00 4.00e-02 5.02e+01 dihedral pdb=" CA LYS B 209 " pdb=" C LYS B 209 " pdb=" N ILE B 210 " pdb=" CA ILE B 210 " ideal model delta harmonic sigma weight residual -180.00 -151.37 -28.63 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA HIS D 125 " pdb=" C HIS D 125 " pdb=" N TYR D 126 " pdb=" CA TYR D 126 " ideal model delta harmonic sigma weight residual -180.00 -153.01 -26.99 0 5.00e+00 4.00e-02 2.91e+01 ... (remaining 17001 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 3240 0.054 - 0.109: 1063 0.109 - 0.163: 185 0.163 - 0.217: 6 0.217 - 0.271: 3 Chirality restraints: 4497 Sorted by residual: chirality pdb=" CA PRO F 24 " pdb=" N PRO F 24 " pdb=" C PRO F 24 " pdb=" CB PRO F 24 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA PRO J 40 " pdb=" N PRO J 40 " pdb=" C PRO J 40 " pdb=" CB PRO J 40 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA PRO F 26 " pdb=" N PRO F 26 " pdb=" C PRO F 26 " pdb=" CB PRO F 26 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 4494 not shown) Planarity restraints: 4909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU G 395 " -0.042 5.00e-02 4.00e+02 6.31e-02 6.37e+00 pdb=" N PRO G 396 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO G 396 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO G 396 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU H 395 " 0.041 5.00e-02 4.00e+02 6.19e-02 6.12e+00 pdb=" N PRO H 396 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO H 396 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO H 396 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG H 364 " 0.035 5.00e-02 4.00e+02 5.20e-02 4.33e+00 pdb=" N PRO H 365 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO H 365 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO H 365 " 0.024 5.00e-02 4.00e+02 ... (remaining 4906 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 631 2.65 - 3.21: 28296 3.21 - 3.77: 42112 3.77 - 4.34: 57075 4.34 - 4.90: 94056 Nonbonded interactions: 222170 Sorted by model distance: nonbonded pdb=" OG1 THR D 76 " pdb=" OG1 THR D 238 " model vdw 2.082 2.440 nonbonded pdb=" O PRO E 95 " pdb=" NZ LYS E 98 " model vdw 2.084 2.520 nonbonded pdb=" OH TYR F 94 " pdb=" OD1 ASP F 213 " model vdw 2.089 2.440 nonbonded pdb=" OD2 ASP J 62 " pdb=" OG SER J 433 " model vdw 2.096 2.440 nonbonded pdb=" O LYS E 235 " pdb=" OG SER E 238 " model vdw 2.124 2.440 ... (remaining 222165 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 1 through 253 or resid 268 through 305)) selection = (chain 'B' and (resid 1 through 90 or (resid 91 and (name N or name CA or name C \ or name O or name CB )) or resid 92 through 305)) } ncs_group { reference = (chain 'C' and (resid 8 through 343 or (resid 344 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name C \ E2 or name CZ )) or resid 345 through 351)) selection = (chain 'D' and (resid 8 through 98 or resid 126 through 351)) } ncs_group { reference = chain 'E' selection = (chain 'F' and (resid 1 through 11 or resid 25 through 444)) } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = (chain 'I' and (resid 41 through 170 or (resid 171 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name NE or name CZ )) or resid \ 172 through 467)) selection = (chain 'J' and resid 41 through 467) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 7.030 Check model and map are aligned: 0.430 Set scattering table: 0.280 Process input model: 72.080 Find NCS groups from input model: 1.810 Set up NCS constraints: 0.140 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 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 : 0.009 0.064 28003 Z= 0.577 Angle : 0.919 18.183 38025 Z= 0.525 Chirality : 0.052 0.271 4497 Planarity : 0.005 0.063 4909 Dihedral : 15.228 88.467 10066 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 19.92 Ramachandran Plot: Outliers : 0.22 % Allowed : 16.65 % Favored : 83.13 % Rotamer: Outliers : 0.35 % Allowed : 11.64 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.81 (0.12), residues: 3610 helix: -1.98 (0.12), residues: 1258 sheet: -4.19 (0.19), residues: 442 loop : -3.92 (0.12), residues: 1910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 51 HIS 0.011 0.001 HIS G 479 PHE 0.030 0.003 PHE D 177 TYR 0.030 0.003 TYR J 343 ARG 0.009 0.001 ARG H 417 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 426 time to evaluate : 3.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.8212 (tpp) cc_final: 0.7637 (tpt) REVERT: A 210 ILE cc_start: 0.7998 (pt) cc_final: 0.7664 (pt) REVERT: B 14 MET cc_start: 0.7097 (mmm) cc_final: 0.6531 (tpp) REVERT: B 187 MET cc_start: 0.8917 (tpp) cc_final: 0.8655 (tpt) REVERT: B 244 GLN cc_start: 0.8504 (tp40) cc_final: 0.8284 (tp-100) REVERT: D 139 GLU cc_start: 0.7881 (tm-30) cc_final: 0.7483 (tm-30) REVERT: D 163 GLU cc_start: 0.6572 (mt-10) cc_final: 0.6333 (mt-10) REVERT: D 184 LYS cc_start: 0.8406 (mmmt) cc_final: 0.7646 (tptt) REVERT: D 203 MET cc_start: 0.8325 (ttt) cc_final: 0.8032 (ttt) REVERT: E 84 MET cc_start: 0.6048 (ttt) cc_final: 0.5842 (ttt) REVERT: E 92 TYR cc_start: 0.7804 (t80) cc_final: 0.7552 (t80) REVERT: E 289 ARG cc_start: 0.6929 (tmt170) cc_final: 0.6134 (tpt170) REVERT: F 125 ASP cc_start: 0.7693 (t0) cc_final: 0.7443 (t0) REVERT: G 195 PHE cc_start: 0.6841 (m-80) cc_final: 0.6155 (m-80) REVERT: G 386 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8100 (pp) REVERT: H 207 MET cc_start: 0.8056 (mmt) cc_final: 0.7782 (mmt) REVERT: H 489 TYR cc_start: 0.8130 (m-80) cc_final: 0.7475 (m-80) REVERT: I 78 TYR cc_start: 0.8747 (m-80) cc_final: 0.8481 (m-80) REVERT: I 97 TRP cc_start: 0.8319 (t60) cc_final: 0.7800 (t-100) REVERT: I 186 LYS cc_start: 0.8364 (tttp) cc_final: 0.7930 (tptt) REVERT: I 246 ASP cc_start: 0.8737 (t0) cc_final: 0.8407 (t0) REVERT: J 285 ASN cc_start: 0.7027 (m-40) cc_final: 0.6783 (m-40) REVERT: J 305 MET cc_start: 0.8277 (ttt) cc_final: 0.8042 (ttm) REVERT: J 441 ILE cc_start: 0.7268 (OUTLIER) cc_final: 0.6607 (mt) outliers start: 10 outliers final: 6 residues processed: 432 average time/residue: 0.4108 time to fit residues: 275.9600 Evaluate side-chains 325 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 317 time to evaluate : 3.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 398 VAL Chi-restraints excluded: chain I residue 328 THR Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 441 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 304 optimal weight: 0.7980 chunk 273 optimal weight: 0.9990 chunk 151 optimal weight: 20.0000 chunk 93 optimal weight: 1.9990 chunk 184 optimal weight: 10.0000 chunk 146 optimal weight: 10.0000 chunk 282 optimal weight: 0.2980 chunk 109 optimal weight: 0.5980 chunk 172 optimal weight: 0.9990 chunk 210 optimal weight: 0.5980 chunk 327 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN A 48 ASN A 214 GLN A 244 GLN B 13 GLN B 116 HIS ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 ASN C 138 ASN C 158 HIS C 230 ASN D 44 GLN ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 252 HIS D 277 GLN D 280 ASN D 331 ASN E 41 ASN E 190 HIS E 283 ASN F 115 HIS G 265 GLN H 265 GLN ** H 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 347 GLN H 422 GLN ** I 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 214 HIS J 105 HIS J 160 ASN J 248 HIS J 288 HIS J 359 ASN J 376 ASN J 440 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28003 Z= 0.217 Angle : 0.629 10.978 38025 Z= 0.320 Chirality : 0.045 0.162 4497 Planarity : 0.005 0.075 4909 Dihedral : 5.533 33.766 3934 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.01 % Favored : 91.88 % Rotamer: Outliers : 2.46 % Allowed : 17.83 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.48 % 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: -3.43 (0.13), residues: 3610 helix: -0.60 (0.14), residues: 1272 sheet: -3.68 (0.20), residues: 471 loop : -3.20 (0.13), residues: 1867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 282 HIS 0.006 0.001 HIS F 115 PHE 0.023 0.002 PHE E 67 TYR 0.017 0.002 TYR E 205 ARG 0.005 0.000 ARG C 14 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 393 time to evaluate : 3.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 187 MET cc_start: 0.8783 (tpp) cc_final: 0.8449 (tpt) REVERT: C 32 GLU cc_start: 0.8030 (tt0) cc_final: 0.7680 (tt0) REVERT: C 44 GLN cc_start: 0.7884 (tt0) cc_final: 0.7605 (mt0) REVERT: C 68 MET cc_start: 0.7370 (mtt) cc_final: 0.7001 (mtm) REVERT: C 184 LYS cc_start: 0.7699 (mmtm) cc_final: 0.7456 (mttp) REVERT: D 184 LYS cc_start: 0.8259 (mmmt) cc_final: 0.7646 (tptt) REVERT: D 325 ILE cc_start: 0.9127 (mm) cc_final: 0.8906 (mt) REVERT: E 92 TYR cc_start: 0.7788 (t80) cc_final: 0.7285 (t80) REVERT: E 176 LEU cc_start: 0.6851 (OUTLIER) cc_final: 0.6351 (pp) REVERT: E 289 ARG cc_start: 0.6465 (tmt170) cc_final: 0.5919 (tpt170) REVERT: F 172 ASN cc_start: 0.7292 (m-40) cc_final: 0.6976 (m-40) REVERT: G 195 PHE cc_start: 0.6924 (m-80) cc_final: 0.6286 (m-80) REVERT: G 386 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.8037 (pp) REVERT: H 489 TYR cc_start: 0.7961 (m-80) cc_final: 0.7524 (m-80) REVERT: J 94 PHE cc_start: 0.8323 (m-10) cc_final: 0.7797 (m-10) REVERT: J 368 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8599 (mt) REVERT: J 441 ILE cc_start: 0.6987 (OUTLIER) cc_final: 0.6665 (mm) outliers start: 70 outliers final: 40 residues processed: 442 average time/residue: 0.3446 time to fit residues: 252.6908 Evaluate side-chains 365 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 321 time to evaluate : 3.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain B residue 116 HIS Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain C residue 340 MET Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 205 TYR Chi-restraints excluded: chain F residue 64 CYS Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 398 VAL Chi-restraints excluded: chain G residue 436 VAL Chi-restraints excluded: chain H residue 518 VAL Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 128 TYR Chi-restraints excluded: chain I residue 291 VAL Chi-restraints excluded: chain I residue 328 THR Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 304 HIS Chi-restraints excluded: chain J residue 328 THR Chi-restraints excluded: chain J residue 348 VAL Chi-restraints excluded: chain J residue 368 ILE Chi-restraints excluded: chain J residue 430 VAL Chi-restraints excluded: chain J residue 441 ILE Chi-restraints excluded: chain J residue 449 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 182 optimal weight: 20.0000 chunk 101 optimal weight: 1.9990 chunk 272 optimal weight: 2.9990 chunk 223 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 328 optimal weight: 2.9990 chunk 354 optimal weight: 6.9990 chunk 292 optimal weight: 3.9990 chunk 325 optimal weight: 0.2980 chunk 111 optimal weight: 0.9990 chunk 263 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 HIS B 213 ASN ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 236 GLN ** H 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 286 GLN ** I 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 28003 Z= 0.312 Angle : 0.654 9.982 38025 Z= 0.330 Chirality : 0.046 0.172 4497 Planarity : 0.004 0.066 4909 Dihedral : 5.509 37.362 3934 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.02 % Favored : 88.86 % Rotamer: Outliers : 3.80 % Allowed : 19.97 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.48 % 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: -3.01 (0.13), residues: 3610 helix: -0.23 (0.15), residues: 1270 sheet: -3.44 (0.22), residues: 407 loop : -3.02 (0.13), residues: 1933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 282 HIS 0.011 0.001 HIS B 116 PHE 0.029 0.002 PHE E 67 TYR 0.018 0.002 TYR G 489 ARG 0.005 0.000 ARG I 339 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 338 time to evaluate : 3.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.8092 (mmm) cc_final: 0.7551 (tpt) REVERT: B 14 MET cc_start: 0.6786 (tpp) cc_final: 0.6223 (tpp) REVERT: B 187 MET cc_start: 0.8852 (tpp) cc_final: 0.8505 (tpt) REVERT: B 236 VAL cc_start: 0.8943 (OUTLIER) cc_final: 0.8735 (m) REVERT: C 32 GLU cc_start: 0.8099 (tt0) cc_final: 0.7651 (tt0) REVERT: C 44 GLN cc_start: 0.7907 (tt0) cc_final: 0.7582 (mt0) REVERT: C 68 MET cc_start: 0.7498 (mtt) cc_final: 0.7258 (mtt) REVERT: D 184 LYS cc_start: 0.8308 (mmmt) cc_final: 0.7695 (tptt) REVERT: D 340 MET cc_start: 0.8067 (mmt) cc_final: 0.7619 (mmt) REVERT: E 92 TYR cc_start: 0.7913 (t80) cc_final: 0.7401 (t80) REVERT: E 176 LEU cc_start: 0.6728 (OUTLIER) cc_final: 0.6155 (pp) REVERT: E 278 TYR cc_start: 0.5077 (m-80) cc_final: 0.4724 (m-10) REVERT: E 289 ARG cc_start: 0.6748 (tmt170) cc_final: 0.6039 (tpt170) REVERT: F 172 ASN cc_start: 0.7607 (t0) cc_final: 0.7192 (m-40) REVERT: F 215 LEU cc_start: 0.8327 (tp) cc_final: 0.8095 (mp) REVERT: G 195 PHE cc_start: 0.6922 (m-80) cc_final: 0.6287 (m-80) REVERT: G 386 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8221 (pp) REVERT: I 106 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8624 (tt) REVERT: J 94 PHE cc_start: 0.8312 (m-10) cc_final: 0.7800 (m-10) REVERT: J 368 ILE cc_start: 0.8910 (OUTLIER) cc_final: 0.8504 (mt) REVERT: J 441 ILE cc_start: 0.6967 (OUTLIER) cc_final: 0.6559 (mm) outliers start: 108 outliers final: 75 residues processed: 416 average time/residue: 0.3394 time to fit residues: 239.9339 Evaluate side-chains 394 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 313 time to evaluate : 3.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 340 MET Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 251 THR Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 205 TYR Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 64 CYS Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 398 VAL Chi-restraints excluded: chain G residue 435 LEU Chi-restraints excluded: chain G residue 436 VAL Chi-restraints excluded: chain G residue 490 ASP Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain H residue 212 LEU Chi-restraints excluded: chain H residue 485 LEU Chi-restraints excluded: chain H residue 514 VAL Chi-restraints excluded: chain H residue 518 VAL Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 128 TYR Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 286 GLN Chi-restraints excluded: chain I residue 291 VAL Chi-restraints excluded: chain I residue 328 THR Chi-restraints excluded: chain I residue 334 SER Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 377 SER Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 106 LEU Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 133 ASP Chi-restraints excluded: chain J residue 201 VAL Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 250 SER Chi-restraints excluded: chain J residue 313 VAL Chi-restraints excluded: chain J residue 348 VAL Chi-restraints excluded: chain J residue 350 LEU Chi-restraints excluded: chain J residue 368 ILE Chi-restraints excluded: chain J residue 394 THR Chi-restraints excluded: chain J residue 430 VAL Chi-restraints excluded: chain J residue 441 ILE Chi-restraints excluded: chain J residue 449 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 324 optimal weight: 0.3980 chunk 246 optimal weight: 0.9990 chunk 170 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 156 optimal weight: 9.9990 chunk 220 optimal weight: 0.0670 chunk 329 optimal weight: 0.7980 chunk 348 optimal weight: 0.0470 chunk 172 optimal weight: 1.9990 chunk 312 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 236 GLN G 190 ASN G 213 GLN G 430 HIS ** H 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 452 HIS J 288 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28003 Z= 0.182 Angle : 0.585 10.828 38025 Z= 0.294 Chirality : 0.044 0.186 4497 Planarity : 0.004 0.062 4909 Dihedral : 5.099 36.117 3934 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.98 % Favored : 92.91 % Rotamer: Outliers : 3.38 % Allowed : 22.96 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.14), residues: 3610 helix: 0.20 (0.15), residues: 1276 sheet: -3.17 (0.23), residues: 421 loop : -2.70 (0.13), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 282 HIS 0.009 0.001 HIS D 97 PHE 0.022 0.001 PHE J 264 TYR 0.018 0.001 TYR A 130 ARG 0.004 0.000 ARG I 339 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 354 time to evaluate : 3.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 MET cc_start: 0.6884 (mmm) cc_final: 0.6426 (mtt) REVERT: B 187 MET cc_start: 0.8774 (tpp) cc_final: 0.8082 (tpt) REVERT: B 236 VAL cc_start: 0.8869 (OUTLIER) cc_final: 0.8644 (m) REVERT: C 32 GLU cc_start: 0.8006 (tt0) cc_final: 0.7600 (tt0) REVERT: C 44 GLN cc_start: 0.7844 (tt0) cc_final: 0.7485 (mt0) REVERT: D 184 LYS cc_start: 0.8001 (mmmt) cc_final: 0.7483 (tptt) REVERT: D 340 MET cc_start: 0.7881 (mmt) cc_final: 0.7471 (mmt) REVERT: E 1 MET cc_start: 0.6388 (tpp) cc_final: 0.5821 (tpp) REVERT: E 92 TYR cc_start: 0.7860 (t80) cc_final: 0.7619 (t80) REVERT: E 176 LEU cc_start: 0.6767 (OUTLIER) cc_final: 0.6289 (pp) REVERT: E 210 TYR cc_start: 0.8077 (p90) cc_final: 0.7108 (t80) REVERT: E 278 TYR cc_start: 0.5133 (m-80) cc_final: 0.4910 (m-10) REVERT: E 289 ARG cc_start: 0.6452 (tmt170) cc_final: 0.5953 (tpt170) REVERT: F 172 ASN cc_start: 0.7600 (t0) cc_final: 0.7117 (m-40) REVERT: G 167 VAL cc_start: 0.8601 (t) cc_final: 0.8218 (m) REVERT: G 195 PHE cc_start: 0.6814 (m-80) cc_final: 0.6202 (m-80) REVERT: G 386 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8116 (pp) REVERT: H 212 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8724 (mt) REVERT: H 260 MET cc_start: 0.8161 (OUTLIER) cc_final: 0.7796 (mmm) REVERT: I 106 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8627 (tt) REVERT: J 181 MET cc_start: 0.6988 (ttt) cc_final: 0.6785 (ttt) REVERT: J 368 ILE cc_start: 0.8851 (OUTLIER) cc_final: 0.8515 (mt) REVERT: J 441 ILE cc_start: 0.6917 (OUTLIER) cc_final: 0.6618 (mm) outliers start: 96 outliers final: 59 residues processed: 422 average time/residue: 0.3249 time to fit residues: 231.1669 Evaluate side-chains 381 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 314 time to evaluate : 3.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 340 MET Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 205 TYR Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 64 CYS Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain G residue 242 THR Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 398 VAL Chi-restraints excluded: chain G residue 416 SER Chi-restraints excluded: chain G residue 435 LEU Chi-restraints excluded: chain G residue 436 VAL Chi-restraints excluded: chain H residue 212 LEU Chi-restraints excluded: chain H residue 260 MET Chi-restraints excluded: chain H residue 485 LEU Chi-restraints excluded: chain H residue 517 ARG Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 128 TYR Chi-restraints excluded: chain I residue 291 VAL Chi-restraints excluded: chain I residue 328 THR Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 133 ASP Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 250 SER Chi-restraints excluded: chain J residue 270 ASP Chi-restraints excluded: chain J residue 348 VAL Chi-restraints excluded: chain J residue 349 SER Chi-restraints excluded: chain J residue 350 LEU Chi-restraints excluded: chain J residue 368 ILE Chi-restraints excluded: chain J residue 430 VAL Chi-restraints excluded: chain J residue 441 ILE Chi-restraints excluded: chain J residue 449 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 290 optimal weight: 1.9990 chunk 198 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 259 optimal weight: 0.9980 chunk 143 optimal weight: 0.9990 chunk 297 optimal weight: 4.9990 chunk 241 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 178 optimal weight: 0.4980 chunk 313 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 190 ASN H 274 HIS ** H 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 286 GLN ** I 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 28003 Z= 0.250 Angle : 0.607 9.941 38025 Z= 0.305 Chirality : 0.045 0.168 4497 Planarity : 0.004 0.062 4909 Dihedral : 5.085 37.276 3934 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.78 % Favored : 91.11 % Rotamer: Outliers : 4.25 % Allowed : 23.52 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.14), residues: 3610 helix: 0.29 (0.15), residues: 1285 sheet: -3.08 (0.23), residues: 429 loop : -2.62 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 282 HIS 0.008 0.001 HIS D 97 PHE 0.019 0.001 PHE D 177 TYR 0.019 0.002 TYR A 130 ARG 0.003 0.000 ARG C 183 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 319 time to evaluate : 3.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.6649 (mmt) cc_final: 0.6396 (mmt) REVERT: A 93 MET cc_start: 0.6871 (mmm) cc_final: 0.6185 (mtp) REVERT: B 236 VAL cc_start: 0.8898 (OUTLIER) cc_final: 0.8698 (m) REVERT: C 32 GLU cc_start: 0.8014 (tt0) cc_final: 0.7718 (tt0) REVERT: C 44 GLN cc_start: 0.7840 (tt0) cc_final: 0.7468 (mt0) REVERT: D 125 HIS cc_start: 0.6001 (OUTLIER) cc_final: 0.2764 (p90) REVERT: D 184 LYS cc_start: 0.8075 (mmmt) cc_final: 0.7586 (tptt) REVERT: D 298 THR cc_start: 0.8604 (m) cc_final: 0.8330 (m) REVERT: E 1 MET cc_start: 0.6350 (tpp) cc_final: 0.5739 (tpp) REVERT: E 92 TYR cc_start: 0.8071 (t80) cc_final: 0.7734 (t80) REVERT: E 176 LEU cc_start: 0.6838 (OUTLIER) cc_final: 0.6285 (pp) REVERT: E 210 TYR cc_start: 0.8090 (p90) cc_final: 0.7131 (t80) REVERT: E 278 TYR cc_start: 0.5248 (m-80) cc_final: 0.4948 (m-10) REVERT: E 289 ARG cc_start: 0.6507 (tmt170) cc_final: 0.5968 (tpt170) REVERT: F 172 ASN cc_start: 0.7630 (t0) cc_final: 0.7142 (m-40) REVERT: G 190 ASN cc_start: 0.7204 (OUTLIER) cc_final: 0.6996 (p0) REVERT: G 195 PHE cc_start: 0.6832 (m-80) cc_final: 0.6223 (m-80) REVERT: G 386 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8096 (pp) REVERT: H 212 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8781 (mt) REVERT: H 260 MET cc_start: 0.8226 (OUTLIER) cc_final: 0.7828 (mmm) REVERT: I 106 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8571 (tt) REVERT: J 183 MET cc_start: 0.8081 (mpp) cc_final: 0.7830 (mtt) REVERT: J 368 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8435 (mt) REVERT: J 441 ILE cc_start: 0.6915 (OUTLIER) cc_final: 0.6585 (mm) outliers start: 121 outliers final: 81 residues processed: 399 average time/residue: 0.3249 time to fit residues: 222.2218 Evaluate side-chains 396 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 305 time to evaluate : 3.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 89 CYS Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 340 MET Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 125 HIS Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 347 ASP Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 205 TYR Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 64 CYS Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain G residue 190 ASN Chi-restraints excluded: chain G residue 242 THR Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 398 VAL Chi-restraints excluded: chain G residue 435 LEU Chi-restraints excluded: chain G residue 436 VAL Chi-restraints excluded: chain H residue 212 LEU Chi-restraints excluded: chain H residue 260 MET Chi-restraints excluded: chain H residue 437 CYS Chi-restraints excluded: chain H residue 485 LEU Chi-restraints excluded: chain H residue 517 ARG Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 128 TYR Chi-restraints excluded: chain I residue 286 GLN Chi-restraints excluded: chain I residue 291 VAL Chi-restraints excluded: chain I residue 303 LEU Chi-restraints excluded: chain I residue 328 THR Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 377 SER Chi-restraints excluded: chain I residue 431 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 133 ASP Chi-restraints excluded: chain J residue 180 VAL Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 250 SER Chi-restraints excluded: chain J residue 303 LEU Chi-restraints excluded: chain J residue 348 VAL Chi-restraints excluded: chain J residue 350 LEU Chi-restraints excluded: chain J residue 368 ILE Chi-restraints excluded: chain J residue 394 THR Chi-restraints excluded: chain J residue 430 VAL Chi-restraints excluded: chain J residue 431 LEU Chi-restraints excluded: chain J residue 441 ILE Chi-restraints excluded: chain J residue 449 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 117 optimal weight: 0.9990 chunk 314 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 204 optimal weight: 2.9990 chunk 86 optimal weight: 0.0370 chunk 349 optimal weight: 10.0000 chunk 289 optimal weight: 8.9990 chunk 161 optimal weight: 0.0980 chunk 29 optimal weight: 5.9990 chunk 115 optimal weight: 0.0000 chunk 183 optimal weight: 20.0000 overall best weight: 0.3664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 190 ASN H 275 ASN ** I 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28003 Z= 0.172 Angle : 0.573 9.991 38025 Z= 0.286 Chirality : 0.044 0.211 4497 Planarity : 0.004 0.063 4909 Dihedral : 4.843 36.024 3934 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.84 % Favored : 93.05 % Rotamer: Outliers : 3.73 % Allowed : 24.02 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.14), residues: 3610 helix: 0.52 (0.15), residues: 1284 sheet: -2.85 (0.23), residues: 444 loop : -2.44 (0.14), residues: 1882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 282 HIS 0.007 0.001 HIS D 97 PHE 0.016 0.001 PHE D 177 TYR 0.019 0.001 TYR A 130 ARG 0.002 0.000 ARG I 339 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 345 time to evaluate : 3.571 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.6588 (mmt) cc_final: 0.6314 (mmt) REVERT: A 93 MET cc_start: 0.6840 (mmm) cc_final: 0.6201 (mtp) REVERT: B 236 VAL cc_start: 0.8846 (OUTLIER) cc_final: 0.8639 (m) REVERT: C 32 GLU cc_start: 0.7961 (tt0) cc_final: 0.7582 (tt0) REVERT: C 44 GLN cc_start: 0.7783 (tt0) cc_final: 0.7388 (mt0) REVERT: D 125 HIS cc_start: 0.5707 (OUTLIER) cc_final: 0.2583 (p90) REVERT: D 167 THR cc_start: 0.8850 (OUTLIER) cc_final: 0.8592 (p) REVERT: D 184 LYS cc_start: 0.7985 (mmmt) cc_final: 0.7547 (tptt) REVERT: D 298 THR cc_start: 0.8597 (m) cc_final: 0.8284 (m) REVERT: D 340 MET cc_start: 0.7957 (mmt) cc_final: 0.7666 (mmt) REVERT: E 1 MET cc_start: 0.6363 (tpp) cc_final: 0.5778 (tpp) REVERT: E 92 TYR cc_start: 0.8020 (t80) cc_final: 0.7736 (t80) REVERT: E 210 TYR cc_start: 0.8094 (p90) cc_final: 0.7025 (t80) REVERT: E 289 ARG cc_start: 0.6464 (tmt170) cc_final: 0.5956 (tpt170) REVERT: F 172 ASN cc_start: 0.7679 (t0) cc_final: 0.7257 (m-40) REVERT: G 265 GLN cc_start: 0.8468 (mm-40) cc_final: 0.8171 (mm-40) REVERT: H 212 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8729 (mt) REVERT: H 260 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.7758 (mmm) REVERT: I 106 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8571 (tt) REVERT: J 183 MET cc_start: 0.8136 (mpp) cc_final: 0.7822 (mtt) REVERT: J 368 ILE cc_start: 0.8811 (OUTLIER) cc_final: 0.8414 (mt) REVERT: J 441 ILE cc_start: 0.6801 (mt) cc_final: 0.6519 (mm) outliers start: 106 outliers final: 66 residues processed: 415 average time/residue: 0.3325 time to fit residues: 234.0477 Evaluate side-chains 395 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 322 time to evaluate : 3.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 89 CYS Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 125 HIS Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 347 ASP Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 205 TYR Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain G residue 242 THR Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 435 LEU Chi-restraints excluded: chain G residue 436 VAL Chi-restraints excluded: chain G residue 450 ASP Chi-restraints excluded: chain G residue 461 ASP Chi-restraints excluded: chain H residue 212 LEU Chi-restraints excluded: chain H residue 260 MET Chi-restraints excluded: chain H residue 437 CYS Chi-restraints excluded: chain H residue 485 LEU Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 128 TYR Chi-restraints excluded: chain I residue 291 VAL Chi-restraints excluded: chain I residue 303 LEU Chi-restraints excluded: chain I residue 328 THR Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 431 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 133 ASP Chi-restraints excluded: chain J residue 180 VAL Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 250 SER Chi-restraints excluded: chain J residue 270 ASP Chi-restraints excluded: chain J residue 348 VAL Chi-restraints excluded: chain J residue 350 LEU Chi-restraints excluded: chain J residue 368 ILE Chi-restraints excluded: chain J residue 394 THR Chi-restraints excluded: chain J residue 430 VAL Chi-restraints excluded: chain J residue 431 LEU Chi-restraints excluded: chain J residue 449 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 336 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 199 optimal weight: 0.8980 chunk 255 optimal weight: 0.2980 chunk 197 optimal weight: 8.9990 chunk 294 optimal weight: 0.0070 chunk 195 optimal weight: 3.9990 chunk 347 optimal weight: 0.0970 chunk 217 optimal weight: 0.9990 chunk 212 optimal weight: 0.3980 chunk 160 optimal weight: 0.5980 overall best weight: 0.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 28003 Z= 0.161 Angle : 0.570 9.711 38025 Z= 0.283 Chirality : 0.043 0.157 4497 Planarity : 0.004 0.064 4909 Dihedral : 4.567 35.216 3929 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.73 % Favored : 93.16 % Rotamer: Outliers : 3.52 % Allowed : 24.65 % Favored : 71.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.48 % 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: -1.85 (0.14), residues: 3610 helix: 0.70 (0.15), residues: 1286 sheet: -2.74 (0.23), residues: 466 loop : -2.29 (0.14), residues: 1858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 366 HIS 0.005 0.001 HIS D 97 PHE 0.023 0.001 PHE F 237 TYR 0.021 0.001 TYR A 130 ARG 0.005 0.000 ARG J 136 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 348 time to evaluate : 3.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.6480 (mmt) cc_final: 0.6220 (mmt) REVERT: A 93 MET cc_start: 0.6913 (mmm) cc_final: 0.6259 (mtp) REVERT: A 208 ASN cc_start: 0.7628 (t0) cc_final: 0.7389 (t0) REVERT: C 44 GLN cc_start: 0.7692 (tt0) cc_final: 0.7265 (mt0) REVERT: D 125 HIS cc_start: 0.5637 (OUTLIER) cc_final: 0.2594 (p90) REVERT: D 167 THR cc_start: 0.8813 (OUTLIER) cc_final: 0.8541 (p) REVERT: D 184 LYS cc_start: 0.7963 (mmmt) cc_final: 0.7527 (tptt) REVERT: E 1 MET cc_start: 0.6404 (tpp) cc_final: 0.5692 (tpp) REVERT: E 92 TYR cc_start: 0.7984 (t80) cc_final: 0.7716 (t80) REVERT: E 176 LEU cc_start: 0.6872 (OUTLIER) cc_final: 0.6425 (pp) REVERT: E 210 TYR cc_start: 0.8078 (p90) cc_final: 0.6936 (t80) REVERT: E 289 ARG cc_start: 0.6457 (tmt170) cc_final: 0.6091 (tpt170) REVERT: F 172 ASN cc_start: 0.7677 (t0) cc_final: 0.7239 (m-40) REVERT: G 190 ASN cc_start: 0.6976 (p0) cc_final: 0.6760 (p0) REVERT: G 252 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7753 (tp) REVERT: H 212 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8712 (mt) REVERT: H 260 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7749 (mmm) REVERT: H 415 MET cc_start: 0.7469 (ttt) cc_final: 0.7159 (ttt) REVERT: I 106 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8559 (tt) REVERT: I 355 ILE cc_start: 0.8910 (mm) cc_final: 0.8469 (mp) REVERT: J 183 MET cc_start: 0.8177 (mpp) cc_final: 0.7807 (mtt) REVERT: J 368 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8354 (mt) REVERT: J 441 ILE cc_start: 0.6736 (OUTLIER) cc_final: 0.6480 (mm) outliers start: 100 outliers final: 64 residues processed: 418 average time/residue: 0.3267 time to fit residues: 234.0068 Evaluate side-chains 389 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 316 time to evaluate : 3.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 89 CYS Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 125 HIS Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 347 ASP Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 205 TYR Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain G residue 242 THR Chi-restraints excluded: chain G residue 252 LEU Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 435 LEU Chi-restraints excluded: chain G residue 436 VAL Chi-restraints excluded: chain G residue 450 ASP Chi-restraints excluded: chain H residue 212 LEU Chi-restraints excluded: chain H residue 260 MET Chi-restraints excluded: chain H residue 485 LEU Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 128 TYR Chi-restraints excluded: chain I residue 202 VAL Chi-restraints excluded: chain I residue 291 VAL Chi-restraints excluded: chain I residue 303 LEU Chi-restraints excluded: chain I residue 328 THR Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 431 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 180 VAL Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 270 ASP Chi-restraints excluded: chain J residue 348 VAL Chi-restraints excluded: chain J residue 349 SER Chi-restraints excluded: chain J residue 350 LEU Chi-restraints excluded: chain J residue 368 ILE Chi-restraints excluded: chain J residue 394 THR Chi-restraints excluded: chain J residue 430 VAL Chi-restraints excluded: chain J residue 431 LEU Chi-restraints excluded: chain J residue 441 ILE Chi-restraints excluded: chain J residue 449 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 215 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 207 optimal weight: 0.9980 chunk 104 optimal weight: 0.2980 chunk 68 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 221 optimal weight: 2.9990 chunk 237 optimal weight: 2.9990 chunk 172 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 273 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 274 HIS ** I 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 28003 Z= 0.226 Angle : 0.593 9.250 38025 Z= 0.295 Chirality : 0.044 0.243 4497 Planarity : 0.004 0.062 4909 Dihedral : 4.631 36.360 3928 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.09 % Favored : 91.80 % Rotamer: Outliers : 3.34 % Allowed : 25.14 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.48 % 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: -1.85 (0.14), residues: 3610 helix: 0.69 (0.15), residues: 1293 sheet: -2.88 (0.23), residues: 450 loop : -2.26 (0.14), residues: 1867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 366 HIS 0.005 0.001 HIS B 128 PHE 0.022 0.002 PHE E 266 TYR 0.021 0.001 TYR A 130 ARG 0.005 0.000 ARG J 136 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 319 time to evaluate : 3.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.6505 (mmt) cc_final: 0.6261 (mmt) REVERT: A 93 MET cc_start: 0.6862 (mmm) cc_final: 0.6273 (mtp) REVERT: C 44 GLN cc_start: 0.7748 (tt0) cc_final: 0.7390 (mt0) REVERT: D 85 VAL cc_start: 0.8745 (OUTLIER) cc_final: 0.8428 (t) REVERT: D 125 HIS cc_start: 0.5678 (OUTLIER) cc_final: 0.2580 (p90) REVERT: D 167 THR cc_start: 0.8849 (OUTLIER) cc_final: 0.8619 (p) REVERT: D 184 LYS cc_start: 0.8052 (mmmt) cc_final: 0.7600 (tptt) REVERT: D 298 THR cc_start: 0.8635 (m) cc_final: 0.8334 (m) REVERT: E 1 MET cc_start: 0.6277 (tpp) cc_final: 0.5626 (tpp) REVERT: E 92 TYR cc_start: 0.8063 (t80) cc_final: 0.7736 (t80) REVERT: E 176 LEU cc_start: 0.6852 (OUTLIER) cc_final: 0.6403 (pp) REVERT: E 210 TYR cc_start: 0.8091 (p90) cc_final: 0.6973 (t80) REVERT: E 289 ARG cc_start: 0.6497 (tmt170) cc_final: 0.5922 (tpt170) REVERT: F 172 ASN cc_start: 0.7712 (t0) cc_final: 0.7295 (m-40) REVERT: G 252 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7874 (tp) REVERT: G 499 LEU cc_start: 0.8594 (mt) cc_final: 0.8316 (mt) REVERT: H 212 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8761 (mt) REVERT: H 415 MET cc_start: 0.7640 (ttt) cc_final: 0.7342 (ttt) REVERT: H 459 ASP cc_start: 0.7385 (t70) cc_final: 0.7150 (t0) REVERT: I 106 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8542 (tt) REVERT: J 90 GLU cc_start: 0.7587 (mp0) cc_final: 0.7374 (mp0) REVERT: J 183 MET cc_start: 0.8188 (mpp) cc_final: 0.7815 (mtt) REVERT: J 368 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8208 (mp) REVERT: J 441 ILE cc_start: 0.6849 (OUTLIER) cc_final: 0.6532 (mm) outliers start: 95 outliers final: 76 residues processed: 388 average time/residue: 0.3283 time to fit residues: 217.3983 Evaluate side-chains 396 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 311 time to evaluate : 3.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 125 HIS Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 347 ASP Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 205 TYR Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain G residue 242 THR Chi-restraints excluded: chain G residue 252 LEU Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 398 VAL Chi-restraints excluded: chain G residue 435 LEU Chi-restraints excluded: chain G residue 436 VAL Chi-restraints excluded: chain G residue 450 ASP Chi-restraints excluded: chain H residue 212 LEU Chi-restraints excluded: chain H residue 517 ARG Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 128 TYR Chi-restraints excluded: chain I residue 202 VAL Chi-restraints excluded: chain I residue 291 VAL Chi-restraints excluded: chain I residue 303 LEU Chi-restraints excluded: chain I residue 328 THR Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 377 SER Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 431 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 106 LEU Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 180 VAL Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 250 SER Chi-restraints excluded: chain J residue 270 ASP Chi-restraints excluded: chain J residue 303 LEU Chi-restraints excluded: chain J residue 348 VAL Chi-restraints excluded: chain J residue 350 LEU Chi-restraints excluded: chain J residue 368 ILE Chi-restraints excluded: chain J residue 394 THR Chi-restraints excluded: chain J residue 430 VAL Chi-restraints excluded: chain J residue 431 LEU Chi-restraints excluded: chain J residue 441 ILE Chi-restraints excluded: chain J residue 449 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 316 optimal weight: 3.9990 chunk 333 optimal weight: 4.9990 chunk 304 optimal weight: 0.8980 chunk 324 optimal weight: 0.7980 chunk 195 optimal weight: 3.9990 chunk 141 optimal weight: 6.9990 chunk 254 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 292 optimal weight: 4.9990 chunk 306 optimal weight: 0.8980 chunk 323 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 28003 Z= 0.252 Angle : 0.610 9.511 38025 Z= 0.303 Chirality : 0.045 0.258 4497 Planarity : 0.004 0.061 4909 Dihedral : 4.733 37.134 3928 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.31 % Favored : 91.58 % Rotamer: Outliers : 3.48 % Allowed : 25.35 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.48 % 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: -1.83 (0.14), residues: 3610 helix: 0.68 (0.15), residues: 1296 sheet: -2.86 (0.23), residues: 442 loop : -2.24 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 366 HIS 0.004 0.001 HIS G 479 PHE 0.023 0.002 PHE E 266 TYR 0.021 0.002 TYR A 130 ARG 0.004 0.000 ARG J 136 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 320 time to evaluate : 3.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.6510 (mmt) cc_final: 0.6255 (mmt) REVERT: A 93 MET cc_start: 0.6859 (mmm) cc_final: 0.6295 (mtp) REVERT: A 208 ASN cc_start: 0.7910 (t0) cc_final: 0.7653 (t0) REVERT: C 44 GLN cc_start: 0.7891 (tt0) cc_final: 0.7419 (mt0) REVERT: D 85 VAL cc_start: 0.8771 (OUTLIER) cc_final: 0.8462 (t) REVERT: D 125 HIS cc_start: 0.5626 (OUTLIER) cc_final: 0.4947 (p90) REVERT: D 167 THR cc_start: 0.8865 (OUTLIER) cc_final: 0.8634 (p) REVERT: D 184 LYS cc_start: 0.8133 (mmmt) cc_final: 0.7665 (tptt) REVERT: D 298 THR cc_start: 0.8646 (m) cc_final: 0.8333 (m) REVERT: E 1 MET cc_start: 0.6641 (tpp) cc_final: 0.5950 (tpp) REVERT: E 92 TYR cc_start: 0.8053 (t80) cc_final: 0.7768 (t80) REVERT: E 176 LEU cc_start: 0.6903 (OUTLIER) cc_final: 0.6463 (pp) REVERT: E 210 TYR cc_start: 0.8090 (p90) cc_final: 0.6990 (t80) REVERT: E 289 ARG cc_start: 0.6512 (tmt170) cc_final: 0.5942 (tpt170) REVERT: F 172 ASN cc_start: 0.7689 (t0) cc_final: 0.7221 (m-40) REVERT: G 252 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7893 (tp) REVERT: G 499 LEU cc_start: 0.8611 (mt) cc_final: 0.8341 (mt) REVERT: H 212 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8771 (mt) REVERT: H 459 ASP cc_start: 0.7353 (t70) cc_final: 0.7075 (t0) REVERT: I 106 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8530 (tt) REVERT: J 368 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.8267 (mp) REVERT: J 441 ILE cc_start: 0.6905 (OUTLIER) cc_final: 0.6589 (mm) outliers start: 99 outliers final: 82 residues processed: 390 average time/residue: 0.3310 time to fit residues: 221.3943 Evaluate side-chains 407 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 316 time to evaluate : 3.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 125 HIS Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 347 ASP Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 205 TYR Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 64 CYS Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain G residue 242 THR Chi-restraints excluded: chain G residue 252 LEU Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 398 VAL Chi-restraints excluded: chain G residue 435 LEU Chi-restraints excluded: chain G residue 436 VAL Chi-restraints excluded: chain G residue 450 ASP Chi-restraints excluded: chain G residue 461 ASP Chi-restraints excluded: chain H residue 212 LEU Chi-restraints excluded: chain H residue 517 ARG Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 128 TYR Chi-restraints excluded: chain I residue 202 VAL Chi-restraints excluded: chain I residue 291 VAL Chi-restraints excluded: chain I residue 303 LEU Chi-restraints excluded: chain I residue 328 THR Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 377 SER Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 431 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 106 LEU Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 180 VAL Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 250 SER Chi-restraints excluded: chain J residue 303 LEU Chi-restraints excluded: chain J residue 348 VAL Chi-restraints excluded: chain J residue 350 LEU Chi-restraints excluded: chain J residue 368 ILE Chi-restraints excluded: chain J residue 394 THR Chi-restraints excluded: chain J residue 430 VAL Chi-restraints excluded: chain J residue 431 LEU Chi-restraints excluded: chain J residue 441 ILE Chi-restraints excluded: chain J residue 449 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 212 optimal weight: 0.0870 chunk 342 optimal weight: 5.9990 chunk 209 optimal weight: 0.5980 chunk 162 optimal weight: 8.9990 chunk 238 optimal weight: 0.8980 chunk 359 optimal weight: 20.0000 chunk 331 optimal weight: 1.9990 chunk 286 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 221 optimal weight: 1.9990 chunk 175 optimal weight: 0.8980 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 286 GLN ** I 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 28003 Z= 0.248 Angle : 0.607 9.949 38025 Z= 0.302 Chirality : 0.045 0.271 4497 Planarity : 0.004 0.061 4909 Dihedral : 4.745 37.067 3928 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.50 % Favored : 91.39 % Rotamer: Outliers : 3.52 % Allowed : 25.39 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.48 % 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: -1.77 (0.14), residues: 3610 helix: 0.67 (0.15), residues: 1306 sheet: -2.82 (0.23), residues: 465 loop : -2.16 (0.14), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 282 HIS 0.004 0.001 HIS F 115 PHE 0.031 0.002 PHE E 237 TYR 0.020 0.002 TYR A 130 ARG 0.004 0.000 ARG J 136 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 321 time to evaluate : 3.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.6501 (mmt) cc_final: 0.6244 (mmt) REVERT: A 93 MET cc_start: 0.6853 (mmm) cc_final: 0.6311 (mtp) REVERT: B 243 GLN cc_start: 0.7595 (mm-40) cc_final: 0.7369 (mm-40) REVERT: C 44 GLN cc_start: 0.7888 (tt0) cc_final: 0.7418 (mt0) REVERT: D 85 VAL cc_start: 0.8770 (OUTLIER) cc_final: 0.8459 (t) REVERT: D 125 HIS cc_start: 0.5661 (OUTLIER) cc_final: 0.5235 (p90) REVERT: D 167 THR cc_start: 0.8856 (OUTLIER) cc_final: 0.8645 (p) REVERT: D 184 LYS cc_start: 0.8135 (mmmt) cc_final: 0.7676 (tptt) REVERT: D 298 THR cc_start: 0.8653 (m) cc_final: 0.8329 (m) REVERT: E 1 MET cc_start: 0.6719 (tpp) cc_final: 0.6052 (tpp) REVERT: E 92 TYR cc_start: 0.8072 (t80) cc_final: 0.7782 (t80) REVERT: E 176 LEU cc_start: 0.6809 (OUTLIER) cc_final: 0.6379 (pp) REVERT: E 210 TYR cc_start: 0.8070 (p90) cc_final: 0.6990 (t80) REVERT: E 289 ARG cc_start: 0.6508 (tmt170) cc_final: 0.5948 (tpt170) REVERT: F 172 ASN cc_start: 0.7701 (t0) cc_final: 0.7248 (m-40) REVERT: G 252 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7904 (tp) REVERT: G 499 LEU cc_start: 0.8563 (mt) cc_final: 0.8250 (mt) REVERT: H 459 ASP cc_start: 0.7341 (t70) cc_final: 0.7077 (t0) REVERT: I 106 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8506 (tt) REVERT: J 368 ILE cc_start: 0.8838 (OUTLIER) cc_final: 0.8405 (mt) REVERT: J 441 ILE cc_start: 0.6947 (OUTLIER) cc_final: 0.6638 (mm) outliers start: 100 outliers final: 84 residues processed: 394 average time/residue: 0.3195 time to fit residues: 215.5500 Evaluate side-chains 408 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 316 time to evaluate : 3.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 89 CYS Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 125 HIS Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 347 ASP Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 205 TYR Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 64 CYS Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain G residue 242 THR Chi-restraints excluded: chain G residue 252 LEU Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 398 VAL Chi-restraints excluded: chain G residue 435 LEU Chi-restraints excluded: chain G residue 436 VAL Chi-restraints excluded: chain G residue 461 ASP Chi-restraints excluded: chain H residue 212 LEU Chi-restraints excluded: chain H residue 517 ARG Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 128 TYR Chi-restraints excluded: chain I residue 202 VAL Chi-restraints excluded: chain I residue 286 GLN Chi-restraints excluded: chain I residue 291 VAL Chi-restraints excluded: chain I residue 303 LEU Chi-restraints excluded: chain I residue 328 THR Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 377 SER Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 431 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 106 LEU Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 180 VAL Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 250 SER Chi-restraints excluded: chain J residue 303 LEU Chi-restraints excluded: chain J residue 348 VAL Chi-restraints excluded: chain J residue 350 LEU Chi-restraints excluded: chain J residue 368 ILE Chi-restraints excluded: chain J residue 394 THR Chi-restraints excluded: chain J residue 430 VAL Chi-restraints excluded: chain J residue 431 LEU Chi-restraints excluded: chain J residue 441 ILE Chi-restraints excluded: chain J residue 449 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 227 optimal weight: 0.0770 chunk 305 optimal weight: 0.5980 chunk 87 optimal weight: 0.0000 chunk 264 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 79 optimal weight: 0.5980 chunk 286 optimal weight: 0.0770 chunk 120 optimal weight: 0.0870 chunk 294 optimal weight: 0.4980 chunk 36 optimal weight: 0.0010 chunk 52 optimal weight: 0.4980 overall best weight: 0.0484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 248 HIS ** 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 = 0.3888 r_free = 0.3888 target = 0.145772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.128646 restraints weight = 40449.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.128076 restraints weight = 51822.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.129198 restraints weight = 42396.102| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 28003 Z= 0.156 Angle : 0.588 14.185 38025 Z= 0.290 Chirality : 0.043 0.205 4497 Planarity : 0.004 0.060 4909 Dihedral : 4.425 32.919 3928 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.46 % Favored : 94.43 % Rotamer: Outliers : 2.43 % Allowed : 26.37 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.48 % 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: -1.50 (0.14), residues: 3610 helix: 0.85 (0.15), residues: 1311 sheet: -2.47 (0.23), residues: 495 loop : -2.01 (0.14), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 282 HIS 0.017 0.001 HIS I 288 PHE 0.023 0.001 PHE E 266 TYR 0.023 0.001 TYR A 130 ARG 0.004 0.000 ARG J 136 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5291.88 seconds wall clock time: 97 minutes 33.75 seconds (5853.75 seconds total)